Opsin evolution: RBP3 (IRBP): Difference between revisions

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'''See also:''' [[Opsin_evolution|Curated Sequences]] | [[Opsin_evolution:_RPE65|RPE65]] | [[Opsin_evolution:_transducins|Transducins]] | [[USH2A_SNPs|Usher: USH2A]] | [[CDH23_SNPs|Usher: CDH23]] | [[LOXHD1_SNPs|LOXHD1]] | [[Opsin_evolution:_update_blog|Update Blog]]
== RPB3 (IRBP): introduction ==
== RPB3 (IRBP): introduction ==


Interphotoreceptor retinol-binding protein, poorly named by IGNC as RBP3 despite its complete lack of paralogs, is a 4 exon 1247 residue glycoprotein that shuttles retinoids between the photoreceptor cells and the retinal pigment epithelium. The protein's size results from four ancient internal tandem duplictions that became established prior to the intronation era (that is, the gene structure does not reflect the repeat structure; the repeats happened first, introns were inserted randomly later within the fourth repeat) though lamprey lacks the final intron. The repeats cluster best across species to the same-numbered repeat consistent with thus.
Interstitial retinol-binding protein, inexplicably named by RBP3 by [http://www.genenames.org/ HGNC] despite a lack of paralogs RBP1 or RBP2, likely confusion with ribosomal binding protein genes and widespread prior use of the protein name IRBP, is a 4 exon 1247 residue glycoprotein thought to shuttle retinoids interstitially between the photoreceptor cells and the retinal pigment epithelium. This role would only make sense for ciliary opsin systems that are unable to regenerate cis-retinal without an auxiliary pathway in an anatomically separate tissue (here RPE). Consequently -- since nearly all protein folds are extremely ancient -- RPB3 must have been co-opted from some other role.


Thus the origin of RBP3 seems to have preceded the origin of the RPE by an immense time span, suggesting an earlier non-visual function possibly related to beta-carotene metabolization. However the gene can really not be traced back earlier than amphioxus (where the match is strong but the genomic situation is quite confused). There is no significant match in cnidarians or protostomia. Xray crystallography establishes a curious fold relationship to crotonase/tail specific proteases in plants, suggesting recruitment of a pre-existing protein. It does not appear all four domains separately bind retinol.
The protein's size results from four ancient internal tandem duplications that became established prior to intronation (that is, the gene structure does not reflect the repeat structure; the repeats happened first, introns were inserted randomly later within the fourth repeat). Any given repeat module clusters markedly better to the same-numbered repeat in other species than to any of the internal repeats, establishing that repeats had arisen and diverged already prior to speciation rather than arising independently in descendent lineages (like RHO1 and RHO2 in lamprey).


The first three homology domains and part of the fourth are all encoded by the first large exon of 1090 amino acids. This exon has been much used in marsupial phylogeny (along with the first intron of transthyretin). Indeed the 96 marsupial species in 51 genera having determined IRBP sequences at GenBank include a Dec 2008 partial sequence for [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=158668312 Thylacinus cynocephalus], as well as for [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=47117971 Sarcophilus harrisii].
It was initially expected that IRBP as a self-contained homotetramer would load four molecules of trans-retinol to accomplish its passive shuttling efficiently. However experiments decisively show this to be false -- the subunits are quite inequivalent and only one molecule is transported. The structure of module 2 of frog was [determined in 2002 (PDB: 1J7X); it consists of two sub-domains and a cleft. The fold matches obscure proteases and hydrolases found in little-studied bacteria; this might represent convergent evolution as seen in TIM beta barrels rather than provide valid clues to ancestral function. A structural determination of the entire molecule is reportedly underway.


The closest matches to the thylacine IRBP are shown in the difference alignment of the first 60 residues below. These species all lie with the Dasyuromorphia. The indicated E-->K may be one of several phyloSNPs breaking this group into <font color="blue">blue</font> and <font color="green">green</font> subclades.  
Fragments of the protein have been sequenced from an immense number of species for phylogenetic purposes. That's because it evolves fast enough to provide a large number of seemingly informative sites and these can be obtained conveniently exploiting the large size of the first reading frame. While there is minimal risk of accidentally cross-matching different modules, the internal repeat structure implies that residues might not be evolving independently. While the modules might seem too diverged for cross-module gene conversion to still be operative, they retain patches of near identity.  


The numbat <font color="red">Myrmecobius</font> fits implausibly (its amino terminal sequence [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=124054062 EF028750] needs verification) -- its affinities seem to lie with the <font color="brown">Didelphimorphia</font>. Thylacinus is not basal within Dasyuromorphia relative to Myrmecobius using IRBP. However this may be a case of mis-comparison of genes.
Some very odd aspects of marsupial RBP3 are investigated below because of the implications in a gene so widely used in taxonomy. Teleost fish further raise the question of inhomogeneous recombination events arising from module mix-up. In fish, the ancestral four-module gene has [http://www.molvis.org/molvis/v12/a180/ given rise] to a two-module gene (M1 and M4) accompanied by an intronless upstream tandem fragment duplicate of M1-M3 without any indication of M4 in the residual 10 residues. Both genes are transcribed and apparently functional since the establishment event occurred prior to zebrafish and fugu divergence, though the upstream gene has been lost in many lineages including tetraodon, medaka, and stickleback but not cichlids.
   *          *                                    *
 
<font color="blue">STSKAPQHDSKFTNATQEELLALFQQIIKYQVLEGNVGYLRVDYIPGREMIEEVGEFLVN EU091365  0 Thylacinus cynocephalus
The upstream fragment suggests a truncated version of the first large exon. The lack of intron does not suggest retroprocessing in view of their lack in the parental gene and the locational adjacency but rather standard recombinational or flanking retroposon-driven tandem duplicating. The loss of M2 and M3 in the downstream gene but retention of standard introns again suggests recombinant loss, either as part of the initial tandem event or subsequent to it as a consequence of the new potential for exact misalignment. Note otherwise the four modules would have been quite diverged from each other prior to the emergence of rayfinned fish.
 
Conceivably whole genome or segmental duplication in fish set the stage for inhomogeneous recombination (as [http://www.molvis.org/molvis/v12/a180/nickerson-fig10.html modelled] by Nickerson), though simple local tandem duplication event mediated by retroposons during replication is another option. A great many tandem loci exist in genomes such as human for which wholesale duplication is inapplicable. This could possibly be resolved by sequencing basal teleost fish that diverged prior to the putative genome duplication to determine if the odd arrangement of genes was already established.
 
=== IRBP module alignment, conservation and structural aspects ===
The image below aligns the four module types from human to lamprey and amphioxus, with yellow showing exceptionally conserved residues and cyan moderately conserved. The number of species shown could be greatly expanded especially for module 1 but for clarity only a phylogenetically representative set is displayed. Module boundaries vary slightly according to the bioinformatics tool used to define the domain (eg crystallographic homology transfer, SuperFamily, Pfam, SwissProt, blastp of reference domains) but can be standardized by counting back a fixed number of residues N-terminally from the universally conserved tyrosine and forward from the C-terminal alanines because conserved residues must occupy near-identical positions within the tertiary structure.
 
It can be seen that M2 has two variable length insertional regions, no doubt relatively disordered loops. Amphioxus additionally has inserted residues in three regions that are suppressed in the figure -- observe that although its overall identity is low, identity is high in conserved residues. The modules each have distinctive class indels and characteristic residues that allow them to be readily distinguished from each other. These features were most likely established prior to lamprey divergence rather than later by convergence. Only two conserved patches are observed, GNvGLYRvD and RAivVGErT in human; other conserved residues are dispersed (at least within the linear structure).
 
[[Image:IRBPsstruc.png|left]]
 
The sole [http://tinyurl.com/cetu3a structural determination] to date, 1J7X_A the single module M2 of Xenopus laevis to 1.8 Å, describes two domains separated by a hydrophobic binding cleft (based on analogy to very similar protease and hydrolase folds). The smaller domain A is an an amino terminal three helix bundle that extends 8 residues past the M2 insertion region (to PGDSIQAEN in xenLae) . M2 was an unfortunate choice because it is most diverged and bares the least resemblance to early-diverging or ancestral sequence.
 
The observed fold similarities could not plausibly have arisen by chance. Crotonase has a binding site for hydrophobic chains of fatty acids and isomerizes them, with possible relevance in RBP3 to cis and trans retinoid stabilization and transport; however IRBP does not appear to be an enzyme or isomerase itself and RPE65 carries out the regenerative isomerization reaction.
 
M2 may have two distinct binding sites, one in the cleft between domains A and B and the other solely inside domain B. The assignment of conserved tryptophans to these sites and other conserved residues to the surface (suggesting a protein binding partner, possibly intra-module binding) has to be revisited in view of the much deeper phylogenetic array of sequences now available.
 
A peculiar feature of full four-module protein (after discounting a couple dozen residues for signal peptide and carboxy terminal wander) is the cheek-to-jowl adjacency of consecutive modules -- in human at most 3 amino acids separate the modules from each other.
 
This is far too short a bridge to allow many arrangement options for module-module quasi-homodimerization (or allosteric regulation of the binding subunit). Instead the modules must be arranged more as beads on a string. Linear donor-receptor docking in a M1-M2-M3-M4 arrangement risks endless polymerization unless the donor in M4 docks to the receptor in M1. However the bridge sequences are too short to permit closure into a tetrameric cycle.
 
Despite subunits quite diverged in sequence, a more likely arrangement is an anti-parallel dimer of M1-M2-M3-M4 to M4-M3-M2-M1 (as seen in [[Personal_genomics:_ACTN3#R577x_and_co-evolution_of_actinin_spectrin_repeats|actinin spectrin repeats]]). This arrangement allows each module to dimerize with the quasi dihedral symmetry, leaving no docking sites vacant. Because the binding patches are in paralogous modules, this explains why observed surface residue conservation in frog M2 carries over to the other modules.
 
If true, this implies co-evolution of amino acids in these binding patches on top of what already occurs internally to an individual module. All phylogenetic software assumes -- ridiculously -- independent evolution of sites. However like morphological characters, molecular characters can have dependencies that amount to couplings and coordination between individual reduced alphabets. Here the much studied M1 module has surface residues co-evolving with counterparts on M4.
 
IRBP has only a single site with glycosylation potential (in [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=V21ZK4W8012&log%24=protalign&blast_rank=1&list_uids=20150355 beta strand 8] of the hinge region of domain B at residues 204 and 515 which are paralogous under module alignment). Although the NxT motif occurs with excellent phylogenetic conservation depth (human to lamprey, also in fish fragmentary genes), only modules M1 and M2 exhibit it. Given the interstitial location and experimental support for glycoprotein nature, IRBP is very likely glycosylated. Bulky carbohydrate chains need to be out of the way of the putative dimerization patches.
 
[[Image:IRBPglycosyl.png]]
 
The situation with cysteines is not so clear. Here M1 has a cysteine at position 19 that is conserved back to lamprey (also in fish fragmentary genes) but A/T/S in other modules. A second conserved cysteine is found only in modules M2 and M3 at position 163 (human M1 numbering, residue is I). M4 has no conserved cysteines. A few other cysteines occur elsewhere but only sporadically in the comparative genomics sense. The cysteines at M2 and M3 could potentially form a disulfide in the antiparallel dimer model discussed above. Inter-modular disulfides are not feasible if modules are arranged linearly. No explanation is currently available for the conserved cysteine in M1.
 
An initial study of knockout mice disastrously used a strain carrying a [http://www.ncbi.nlm.nih.gov/pubmed/19074801 severe mutation] at L450 in [[Opsin_evolution:_RPE65|RPE65]], the enzyme catalyzing the rate-limiting isomerization step in the visual regeneration cycle. Lack of IRBP alone delays transfer of both bleached from photoreceptor cells and newly regenerated chromophore from RPE to photoreceptors.
 
A single known [http://www.ncbi.nlm.nih.gov/pubmed/19074801 disease mutation] D1080N causes a very rare recessive retinitis pigmentosa. This aspartate may disrupt an internal salt bridge according to the Xenopus M2 structure (and homology transfer to other modules]. It lies in M4 near the end of the second exon. This residue is conserved back to lamprey and amphioxus, indeed to crotonase and other weakly aligning homologs.
 
    *
AIILDLRYNLGGDREGVVHWASFFF RBP3_braFlo
A+I+D+R+N+GG    +    S+FF
AMIIDMRFNIGGPTSSIPILCSYFF RBP3_homSap
  +IID+R+N+GG ++SIPILCSYFF
ILIIDLRYNMGGYSTSIPILCSYFF RBP3_petMar
[[Image:IRBPconserved.png]]
 
<font color="blue">M1_homSap  LFQPSLVLDMAKVLLDNYCFPENLLGMQEAIQQAIKSHEILSISDPQTLASVLTAGVQSSLNDPRLVISYEPST-----------PEPPPQVPALTSLSEEELLAWLQRGLRHEVLEGNVGYLRVDSVPGQEVLSMMGEFLVAHVWGNLMGTSALVLDL
M1_bosTau  LFQPSLVLEMAQVLLDNYCFPENLMGMQGAIEQAIKSQEILSISDPQTLAHVLTAGVQSSLNDPRLVISYEPST-----------LEAPPRAPAVTNLTLEEIIAGLQDGLRHEILEGNVGYLRVDDIPGQEVMSKLRSFLVANVWRKLVNTSALVLDL
M1_monDom  IFQPSLVRDMAKILLDNYCFPENLMGMQEVIEQAIKSGEILDISDPQMLASVLTAGVQGALNDPRLVISFEPSI-----------PETPQHVPKLANVTQEELLILLQQMIKYQVLEGNVGYLRVDYIPGQEVVEKVGEFLVNNIWKKLMGTSSLVLDL
M1_macEug  IFQPSLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLASVLTAGVQGSLNDPRLVISYEPSP-----------AEAPQQSPKLTSLTQEELLTLLQQMIKYQVLDGNVGYLRVDYIPGQEVVEKVGEFLVNDIWKKLMGTSSLVLDL
M1_sacHar  IFQPTLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLANVLTAGVQGSLNDPRLVISYEPST-----------SEAPQHDPKFANATQEELLALFQKIIKYQVLEDNVGYLRVDYIPGRDMIEEVGEFLVNDIWKKVMETSSLVLDL
M1_ornAna  VSQPSMVLDVAKILLDNYCYPENLMGMQEAIEEAIQRGEILDIADPKRLASVLTAGVQGSLNDPRLVISYEPAP-----------VAVSQQPPEPASLPAEQPLERLRPAVGSEVLEGNVGYLRVDRLPGREEIERVGAVLGRDIWEKLLGTSALVLDL
M1_galGal  IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPSL-----------HAAPKQEAE-TYPTREQLLSLIEHVVIYDKLEGNVGYLRIDYIIGQEVVEKVGAFLVDKVWKTLINTSALVIDL
M1_taeGut  IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPLP-----------HSGPKQEAE-GSPTREQLLSLIEHVIMYDKLEGNVGYLRIDYIIGEEVVQKVGAFLVDKVWKTLIETSALVIDL
M1_anoCar  VLQSTLVLDMAKLLLDNYCLPENLVGMREAIEQAIKNGEVLDISDPKLLATVLTAGVQGALNDPRLVISYEPTA-----------PAAPKQRME-TSLTPEQLLSLIQHTVKYEVLDDNVGYLRIDYIMGQDIVQKIGSFLVEKVWKTLLGTSALILDL
M1_xenLae  LFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAVKGGEILHISDPDTLANVFTSGVQGYLNDPRLVVSYEPN-------------YSGPQTEQSLELTPEQLKFLINHSVKYDILPGNIGYLRIDFIIGQDVVQKVGPHLVNNIWKKLMPTSALILDL
M1_xenTro  VFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAMKSGEILHISDPETLANVFTSGVQGFLNDPRLVVSYEPN-------------YSGPRKEQSPEPTLEQLKFLLDHSVTYDLLPGNIGYLRIDFIIGQDVVQKVGPLLVNNIWKKLMPSSALILDL
M1_tetNig  AFPPSLIADMAKIVLDNYCSPEKLAGMKEAIKAAGTNTEVLNIPDGESLARVLSAGVQGTVSDPRLMVSFQPN-------------YVPAGPHKMPPLPPEHLVAVLQTSVKLDILEGNTGYLRIDHILGEEVADKVGPALIDLIWNKILPTSALIFDL
M1_takRub  AFPPSLITDMAKIVLDNYCSPEKLAGMKEAIEAAGTNTEVLNIPDGESLARVLSAGVQGTVSDSRLMVSYQPD-------------YVPAVPPKMPPLPPEHLVAVLQTSIKLDLLEGNTGYLRIDHIIGEDVAEKVGPSLIDLIWNKILPTSALIFDL
M1_gasAcu  GFAPNVIIDMAKIVIDNYCSPEKLAGMKEAIEAAGSNTEVLSIPDAETLANVLSAGVQTTVSDPRLMISYEPN-------------YVPVVPPKMPPLPPDQVIAVLQTSIKLDILEGNIGYLRIDHILGEDVAEKVGPLLLDLVWNKILPTSALIFDL
M1_oryLat  SFPPSLITDLAKIVMDNYCSPEKLSGMKEDIATAGANTDVLNIPDGEALAKVLTDGVQTTVSDPRLRVSYEPN-------------YVPVVP---PQLPPEQLIAVLQTSIKLDILEGNIGYLRIDSIIGEEVAEKVGPLLLELVWSKILPTSALIFDL
M1_danRer  NFSPTLIADMAKIFMDNYCSPEKLTGMEEAIDAASSNTEILSISDPTMLANVLTDGVKKTISDSRVKVTYEPD-------------LILAAPPAMPDIPLEHLAAMIKGTVKVEILEGNIGYLKIQHIIGEEMAQKVGPLLLEYIWDKILPTSAMILDF
M1_petMar  KFDTAVVLHLAKVLLDNYCIPENLVGMDEAIQRAVDNGELLGVSDPESAASALTEGIQAALNDPRIAVSYVA-----------------------PPHTFEELLATIPQKTSFAVLDGNVGYLRADEIISEATIKKLGPVIVQRIWNRLVDTDTFVLDL</font>
M1x_takRu  FYQHTLVLEMAKLLLENYCIPENLVGMQEAIQRAIKSREILQISDRKTLATVLTVGVQGALNDPRLSVSYEPS-------------FSPLPLQALSSLPVEQQLRLLRNSIKLDILDSDVGYLRIDRIIDEETLLKFGPLLRENVWDKAAQTSSLILDL
M1x_danRe  SFQSALVLDMAKILLDNYCFPENLIGMQEAIQQAINSGEILHISDRKTLASVLTAGVQGALNDPRLTVSYEPN-------------YTLITPPALHSLPTEQLIRLIRSTVKLEVMDNNIGYLRIDRIIGQETVVKLGRLLHNNIWKKVAHTSAMIFDL
<font color="red">M2_homSap  SALPGVVHCLQEVLKDYYTLVDRVPTLLQHLASM----DFSTVVSEEDLVTKLNAGLQAASEDPRLLVRAIGPTETPSWPAPDAAAEDSPGVAPELPEDEAIRQALVDSVFQVSVLPGNVGYLRFDSFADASVLGVLAPYVLRQVWEPLQDTEHLIMDL
M2_bosTau  RALPGVIQRLQEALREYYTLVDRVPALLSHLAAM----DLSSVVSEDDLVTKLNAGLQAVSEDPRLQVQVVRPKEASS--GPEEEAEEPPEAVPEVPEDEAVRRALVDSVFQVSVLPGNVGYLRFDSFADASVLEVLGPYILHQVWEPLQDTEHLIMDL
M2_monDom  RARPGAIQRLMEVLQNYYTLVDRVPALLHHLTAI----DYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATM-GSEASEEEDATPAANSLPEDESQRQALVDSVFQVSVLPGNVGYLRFDEFADSSVLGTLAPYVIRQVWEPLQDTNHLIMDL
M2_sacHar  RARPGAIQRLMEILQKYYTLVDRVPALLHHLTAI----DYSSVLTEEDLAAKLNAMLQAVSEDPRLLVRVLRPEEATV--EAEPGEESATPASVSLPESDAERQALIDSVFQVSVLPGNVGYLRFDEFADNSVLGTLAPYVLRQVWEPLQDTDHLIMDL
M2_macEug  RARPAAIQRLMEVLQNYYTLVDRVPALLHHLTAI----DYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATA--GAESREEAATAAPVPLPDGESQRQALVNSVFQVSVLPGNVGYLRFDEFADSSVLGALAPYVLQQVWEPLQDTDHLIMDL
M2_ornAna  GAVPGAVAHLADLLRDYYALVDRVPALLRHLAAL----DLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPEEAERGPPRKEEEQKEEEEEDQPSPGASILPGDGSSLFRVSVLPGNVGYLCFDEFPEASALERLGPLLGRRVWEPLEATDHLMVDL
M2_galGal  RAVPGTLSRLTDILKDYYSLVERVPVLLRHLTTS----DFSSVQSAEDLATKLNTEMQTLSEDPRLLVRTMMPGEA-----AAPPAEMPIAMAANLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYIVKKVWEPLQNTENLIMDL
M2_taeGut  RAVPGTISHLKNILKDYYSLVERVPALLRRLTTS----DFSSVQSSEDLATKLNTELQALSDDPRLMVRVMMPGEA-----ADSPAEKPVGMAADLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYLVHKVWEPLQNTENLIMDL
M2_anoCar  KAIPNSMSYLVDIIKNNYSMLEQVPVLLQHLSTF----DYSSVLSVKDLASKLNAELQTISEDPRLFLRVPASDEA-----VTSQTDEKVAMASDLPNNEQLMKALVMTVFKVSVLPGNVGYMRFDEFGDATVLVKLGPYLLQHVWEPLQATDYLIIDL
M2_xenTro  SSITHILLQLSEILVNNYAFSERIPTLLQHLPNL----DYSSVISEEDITAKLNYELQSLTEDPRLVLKSKTDSLV---------MPEDSTQVENLPDDEATLQALVNTVFKVSILPGNIGYLRFDEFADVSVLAKLGPYIVNTVWDPITVTENLIIDL
M2_xenLae  SSVTHVLHQLCDILANNYAFSERIPTLLQHLPNL----DYSTVISEEDIAAKLNYELQSLTEDPRLVLKSKTDTLV---------MPGDSIQAENIPEDEAMLQALVNTVFKVSILPGNIGYLRFDQFADVSVIAKLAPFIVNTVWEPITITENLIIDL
M2_petMar  GVARKAVEAAGELLLSSYTFVERASAIADHLSWS----EYGSVVSVEDLTSKLTQDLQSVAEDPRLVVSNREPEWV--------GAADPPGPPAPLPDDEQMLEAIVDSAFKVEVLEGNIGYLRFDEFGDASAVMKLRKQLVSKVWERIHPTDDVIIDL</font>
M2x_takRu  SRIPKVLQIVLDIIGRFYAFADRVQALLQQLESA----DLFSVVSEEDLAARLNHDLQTASEDPRLIIRHKRDNI------------PRAEEEPELHAANDHDGELVEG-FTVQVLPHNTGYLRLDRFVRCSEGDKLEEIVAEKVWGPLKDTQNLIIDL
M2x_danRe  KTIPKAVRRVSDIIKRYYSFKDKIPALLNQLAKA----DYFTVVSEEDLAGKLNHEMQSVFEDPRLLIKATQVLT------------DDASSE-DRSSSDDLTDPL----FKLEMISGNNGYLRFDRFPTPEVLLRLEDHIKKKIWQPVQETENLVIDL
<font color="green">M3_homSap  QSLGALVEGTGHLLEAHYARPEVVGQTSALLRAKLAQGAYRTAVDLESLASQLTADLQEVSGDHRLLVFHSPGELV---------VEEAP-PPPPAVPSPEELTYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVRLVWQQLVDTAALVIDL
M3_bosTau  RSLGELVEGTGRLLEAHYARPEVVGQMGALLRAKLAQGAYRTAVDLESLASQLTADLQEMSGDHRLLVFHSPGEMV---------AEEAP-PPPPVVPSPEELSYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVQLVWQKLVDTAALVVDL
M3_monDom  QRLGALVEGTGHLLEAHYALPEVVGQASALLKAKLEHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPV---------SEELT-PPQKGVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIAPQLVELVWEKLVHTEALVVDL
M3_macEug  QRLGALVEDAGHLLEAHYALPEVVGQASALLRARLVHGTYRTAVDFESLASQLTSDLQEVSGDHRVHVFHSPGELI---------PEELS-PPQNVVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIGPQLIELVWEKLVNTEALVVDL
M3_sacHar  QRLGALVEGTGHLVEAHYALPEVVGQASAFLRATLAHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPV---------PEESS-PPHKGVPSPEELTYLIEALFKTDVLP-QLGYLRFDMMAEVETVRAIGPQLVELVWEKLVNTEALVVDL
M3_taeGut  KNMGVLLEGTGQLLEDHYAIPEVAAKASAMLSTKRAQGGYRSAIDSETLASQLTSDLQEASGDHRLHVFHSHVEPT---------PEEQL-PNV--IPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLLQMVWNKLVDTDAMIIDM
M3_galGal  RKMGILLESTGQLLEAHYAIPEVAEKASVMLSTKRVQGGYRSAVDFETLASQLTSDLQEASGDHRLHVFHSHVEPT---------PEEQL-PNM--IPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLVQMVWNKLVDTDAMIIDM
M3_anoCar  KGMGSLIERVGQLLEAHYAIPEMARRVSSMLNSKLAQGGYRTAVDFETLASQLTNDLQETSGDHQLHVFHSHVEPS---------LEEQS-PFK--TLTPEELNFIIEALFKVDVLPGNVGYLRFDMMAEFESVKTIEPQILHMVWEKLVETSAMIVDM
M3_xenTro  PSVFALVEGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASQLTSEMQENSGDHRLHVFYSDTEPE---------ILEDQ-PPK--IPSAEELNYIIDALFKIEVLQGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDM
M3_xenLae  PSIFPLVKGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASLLTSEMQENSGDHRLHVFYSDTEPE---------ILEDQ-PPK--IPSPEELNYIIDALFKIEVLPGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDM
M3_petMar  AKMASLLELAGALVEGYYAMLSDGENATAEILLKYREGWYRSVVDYEALASQLTSDLHEIWGDHRLHAF-YSDLQI---------ERMDE-DKTPSVPSPEELSVLIDTVFKVDILANNVGYLRFDMMTDAEVLKHVGPQLVEKVWNKISSTRSLVIDV</font>
M3x_takRu  QGLRSLIGRTGELLEKHYAIQEVAQKVGEVLLSKWAEGLYRSVVDLESLASQLTADLQEASGDHRLHVFRCDVELE---------SLHGV-PK---IAAVEEAGFVIDALFKSELLPRNVGYLRFDTMADIEAAKGAAPRLVKSVWNKLVDTDSLIIDM
M3x_danRr  KNIQGLVQEAGDLLEKHYSVPEVAAKVSRLLQSKLTEGLYRSVVDYESLASQLTSDLQETSGDQRLHIFYCETEPE---------TLHDT-PK---IPSPEEAGFIVEALFKVDVMSGNIGYLRFDMMEDIKVLQAINPEFLKVVWNKLVNTDMLIIDV
<font color="brown">M4_petMar  ADAPSILRTVGKLVADGYSRAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHLKAVCVPEHAT---------DRMPG-IVPMQMPPTESFEDLIKFSFITDVLEGNIGYLRFDLFSDLEALEHVAHLLVEHVWKKICDTEILIIDL
M4_homSap  AKVPTVLQTAGKLVADNYASAELGAKMATKLSGL--QSRYSRVTSEVALAEILGADLQMLSGDPHLKAAHIPENAK---------DRIPGIVPMQ-IPSPEVFEELIKFSFHTNVLEDNIGYLRFDMFGDGELLTQVSRLLVEHIWKKIMHTDAMRIID
M4_bosTau  AKVPTVLQTAGKLVADNYASPELGVKMAAELSGL--QSRYARVTSEAALAELLQADLQVLSGDPHLKTAHIPEDAK---------DRIPGIVPMQ-IPSPEVFEDLIKFSFHTNVLEGNVGYLRFDMFGDCELLTQVSELLVEHVWKKIVHTDALIVDM
M4_monDom  AKVPTILQTAGKLVADNYASLEVGSRVASKLAKL--QTQYRQVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAK---------DRIPGIVPMQ-LPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDM
M4_macEug  SKVPTILQTAGKLVADNYASPEVGSRVAAKLARL--QTQYRQVTSEGELADMLGADLQTLSGDSHLKTAHIPEDSK---------DRIPGIVPMQ-LPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDM
M4_sacHar  AKVPTILQTAGKLVADNYASPEVGSRVAAKLASL--QIQYGKVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAK---------DRIPGIVPMQ-LPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLIQVSDLLVEHVWKKVMHTDGMIIDM
M4_ornAna  SKVPTVLRTAAKLVADNYAFRETGAGVAAQMGGL--QARCGRVTSEGALAEVLGAHLRALSGDPHLQMVYIPEDAK---------DRIPGVVPMQ-IPSAETFEDLIKFSFHTSVMEGNIGYLRFDMFGDCELLTQVSELMVEHVWKKIVHTDGLIIDM
M4_xenLae  TKIPTVIQTAAKLVADNYAFADTGANVASKFIALVDKIDYKMIKSEVELAEKINDDLQSLSKDFHLKAVYIPENSK---------DRIPGVVPMQ-IPSPELFEELIKFSFHTDVFEKNIGYIRFDMFADSDLLNQVSDLLVEHVWKKVVDQDALIIDM
M4_xenTro  TKIPSVIQTAGKLVADNYAFADTGADVASKLIALVDKINYKMIKSEVELAEKLNYDLQSLSKDVHLKAVYIPENSK---------DRIPGVVPMQ-IPSPEMFEDLIKFSFHTDVFEKNLGYIRFDMFADSDLLNQVSDLLVEHVWKKVVNQDALIIDM
M4_taeGut  AQVPQILQTVGKLVADNYAFVNTGTVIASNLTKNIHKDNYKRINTEEDLAGKVTAILQALSDDKHLKLLYIPEHAK---------DSIPGIMPKQ-IPPPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDSELLTQLSDLMIEHVWKKIFHTDALIIDL
M4_galGal  TQVPQIVQTVGKLVAENYAFVDIGTDIASNLTKSVNKENYKRINSEKELARKLTAILQALSDDEHLKILYIPEHAK---------DSIPGILPKQ-IPSPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDCELLTQVSDLLVEHVWKKIVHTDALIIDM
M4_anoCar  TKLPSVLNTIGKLVADNYAFADIGATVAAKFADYAKKGTYRKINSEIELSGKLAADLKALSGDRHLMISHIPERSK---------GRILGLVPMQQIPPPEILEDLIKFSLHTNVFENNIGYLRFDMFGDCELMSQVSELLVQHVWNKIVNTDALIIDM
M4_tetNig  AQIPAIIEGTAALVANNYAFEATGADVAKELRELQANGQYSSVVSKESLEAALSADLQRLSGDKSLKTT----------------PNTPVLPPMD--YTPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDL
M4_takRub  AQIPAIIEGAATLIAKNYAFEATGADVATKLRELLAKGQYNSVVSSESLEVALSADLQRLSGDKSLKAT----------------QNAPVLPPMD--YSPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDL
M4_gasAcu  NRVPAIIEGSATLIADNYAFEDIGAAVAEKLKGLLANGEYSKVVSKDSLEMKLSADLRTLSGDKSLKTT----------------SNVPALPPMN--YSPEMYIELIKVSFHTDVFEDNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDAMIVDL
M4_oryLat  LQVPAIIEESATLVANNYAFESTAADVAEKLKGHLANGDYNMVVSKESLEAKLSADLQSLSGDKSLTVS----------------SNTGAPPPME--YTPEMYIELIKISFHTDVFENNIGYLRFDMFGDFEEVKAIAQVIVEHVWNKVLHTDAMIIDL
M4_danRer  AEIPALAQAAATLIADNYAFPSIGEHVAEKLEAVVAGGEYNLISTKEDLEERLSEDLLKLSEDKCLKTT----------------SNIPALPPMN--PTPEMFIALIKSSFQTDVFENNIGYLRFDMFGDFEHVATIAQIIVEHVWNKVVDTDALIIDL</font>
<font color="blue">M1_homSap  RHCTGGQVS-GIPYIISYLHPGN-TILHVDTIYNRPSNTTTEIWTLPQVLGERYGADKDVVVLTSSQTRGVAEDIAHILKQMRRAIVVGERTGGGALDLRKLRIGES------DFFFTVPVSRSLGPLGGGSQTWEGSGVLPCVGTPAEQALEKALAIL
M1_bosTau  RHCTGGHVS-GIPYVISYLHPGS-TVSHVDTVYDRPSNTTTEIWTLPEALGEKYSADKDVVVLTSSRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRVGQS------DFFLTVPVSRSLGPLGEGSQTWEGSGVLPCVGTPAEQALEKALAVL
M1_monDom  QHSSGGEIS-GIPFVISYLHQGD-ILLHVDTVYDRPSNTTTEIWTLPQVLGERYGGEKDMVVLTSHRTVGVAEDIAYILKKLRRAIVVGEQTLGGALDLRKLRIGQS------DFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALGKALAIL
M1_macEug  QHSTEGEVS-GIPFVISYLHEGD-ILLHVDTVYDRPSNTTTEIWTLPQVLGERYSGEKDLVILTSHRTVGVAEDIAYILKKMRRAIVVGEQTLGGALDLRKLRIGQS------DFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALEKALAIL
M1_sacHar  QHSRGGEVS-GIPFVISYLHQGD-ILLHVDTIYDRPSNTTTEIWTLPQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKKMRRAIVVGEQTQGGSLDLRKLRIGQS------DFFITVPVARSLSPLGGGSQTWEGSGVVPCVGIPAEQALEKALAIL
M1_galGal  RYSTGGQIS-GIPFIISYLHEAD-KMLHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITLGEKTAGGSLDIQKLRIGPS------NFYMMVPVSRSVSPLSGGGQSWEVSGVMPCVASEAEQALKKSLDIL
M1_taeGut  RHSTGGQIS-GLPFIISYLHEQD-KILHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITVGEKTAGGSLDIQKLRIGPS------NFYMMVPVSRSVSPLSGGGQSWEVSGVMPCVATEAEQALQKSLDIL
M1_anoCar  RYTTGGDVS-GIPFIISYLYNGD-KVLHVDTVYNRPSNTTVEILTLPKVLGVRYSKDKDVILLISKYTTGVAENVAYILKHMHRTIIVGEKSAGGSLDTQKMQIGNS------QFYMTVPLSCSVSPLSGSGQSWEISGVTPCVVISAEQALDKALAIL
M1_ornAna  RHSTGGHVS-GIPFFISYFYPEG-PALHVDTVYDRPSNATRQLWTLPRVLGARYAADKDVVVLTSRLTAGVAEDVAYILQQMRRAIVVGERTAGGPLVFRKLRVGLS------DFFITVPVACSLGPLGGGGRSWEGSGVLPCVAVPADRALDEALDIL
M1_xenLae  RYSTQGEVS-GIPFVVSYL--CD-SEIHIDSIYNRPSNTTTDLWTLPELMGERYGKVKDVVVLTSKYTKGVAEDASYILKHMNRAIVVGEKTAGGSLDTQKIKIGQS------DFYITVPVSRSLSPLTG--QSWEVSGVSPCVVVNAKDALDKAQAIL
M1_xenTro  RYSTQGKVS-GIPFVVSYL--TD-PQIHIDSIYNRPSNTTTDLWTLSELMGERYGKDKDVVVLTSKYTEGIAEGAAYILKHMSRAIVVGEKTAGGSLDIQKIKIGQS------EFYITVPVSRSISPLTG--QSWEVAGVFPCVVVNANNALNKAQGIL
M1_tetNig  RYTSSGDIS-GIPYIVSYFTQAE-PVVHIDSVYDRPSNTTTKLLSLPNLLGQRYGVSKPLIVLTSKNTKGIAEDVAYCLKNLKRATIVGEKTAGGSLKLDTFKVGDT------DFYITVPTAKSINPITG--SSWEIRGVTPHVEVNAEDALATAIKIV
M1_takRub  RYTSSGEIS-GIPYIVSYFTQAE-PVVHIDSVYDRPSNTTTKLFSLSNLLGERYGITKPLIILTSKNTKGIAEDVAYCLKNLKRATIVGERTAGGSVKLDNFKVGST------DFYITVPTAKSINPVTG--SSWEITGVKPDVEVNAEDALATAIKIV
M1_gasAcu  RYTSSGDIS-GIPYIVSYFTEAG-TPIHIDSIYDRPSNTTTKLFSMSTLLGERYSTSKPLIILTSKNTKGIAEDVAYCLQNLKRATIVGEKTAGGSVKVDKIQVRDT------GFYVTVPTAKSVNPITG--STWEVTGVTPNVEVNAEDALATAIKIV
M1_oryLat  RYTSSGDIT-GIPYIISYLTDAK-SEIHIDTIYDRPLNTTTKLLSMQSTLGQTYGGTKPLLVLTSKNTKDIAEDVAYCLKNLKRATIVGEKTAGGSAKIKKFRVGDT------DFYVTLPTAKSINPITG--SSWEVTGVKPNVEVNAEEALATALKII
M1_danRer  RSTVTGELS-GIPYIVSYFTDPE-PLIHIDSVYDRTADLTIELWSMPTLLGKRYGTSKPLIILTSKDTLGIAEDVAYCLKNLKRATIVGENTAGGTVKMSKMKVGDT------DFYVTVPVAKSINPITG--KSWEINGVAPDVDVAAEDALDAAIAII
M1_petMar  RYNSHGDIT-GLPYLVSCFCEPR-PVVHLDTVYYRPTNESKEIWSLPDLQGARFAKHKDVFVLVSANTEGVAENVAYVLKHLHRATVIGEQTAGGSLEVERFRLGDS------RFFVTVPTARS-EPAD---RSW---GVFPCVSAPSERALDKALEIL</font>
M1x_takRu  RFSTAGGWS-GIPSIVSYFTEPH-SLVHIDTVYDRPSNTTTELWTMSSVRGKTFGGKKDMIVLIGRRTAGAAEAVAYTLKHLNRAIVVGERSAGGSLKVRKFRIAES------DFYITMPVARSVSPITG--KSWEVSGISPTVNVAAREALAKAQTFL
M1x_danRe  RFSTAGELS-GLPYIVSYFSDSD-PLLHIDTIYERPTNITRELWTLPTLLGERFGKRKDLIVLISKRTIGAAEGVAYILKHLKRAVIIGERSAGGSVRVDKLKIGDS------GFYITVPVARSVNPVTG--QSWEVSGVAPSVTVNPKESIAKAKSLI
<font color="red">M2_homSap  RHNPGGPSS-AVPLLLSYFQGPEAGPVHLFTTYDRRTNITQEHFSHMELPGPRYSTQRGVYLLTSHRTATAAEEFAFLMQSLGWATLVGEITAGNLLHTRTVPLLDTPEG---SLALTVPVLTFIDNHG---EAWLGGGVVPDAIVLAEEALDKAQEVL
M2_bosTau  RQNPGGPSS-AVPLLLSYFQSPDASPVRLFSTYDRRTNITREHFSQTELLGRPYGTQRGVYLLTSHRTATAAEELAFLMQSLGWATLVGEITAGSLLHTHTVSLLETPEG---GLALTVPVLTFIDNHG---ECWLGGGVVPDAIVLAEEALDRAQEVL
M2_monDom  RYNPGGPSS-AVPLLLSYFQDPAAGPIRLFTTYDRQTNQTQEHLSRAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNG---NLVLTVPILTFIDNNG---ECWLGGGVVPDAIVLAEEALDKAKEVL
M2_sacHar  RYNPGGPSS-AVPLLLSYFQDPSAGPVRLFATYDRQTNQTQEYRSRAELLGKPYGAERGVYLLTSYHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNG---SLVLTVPTLTFIDNHG---ECWLGGGVVPDAIVLAEEALDKAKEVL
M2_macEug  RYNPGGPSS-AVPLLLSYFQDPAAGPVRLFATYDRQTNQTREYRSQAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGNLMHTRTFSLLQPPDG---SLVLTVPILTFIDNHG---ECWLGGGVVPDAIVLAEEALDKAKEVI
M2_galGal  RYNPGGPSSSAVPMLISYFQDPTAGPVHLFTTYDRRTNHTQEHNSQAELLAQPYGAQRGIYVLTSRHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTCTFPLVQPEQGITRGLTITVPVITFIDNHG---ESWMGGGVVPDAIVLAEDALEKAEEVL
M2_taeGut  RYNLGGPSSSAVPVLLSYFQDPAAGPVHLFTTYDRRTNHTQEHNSQAELLGQSYGAKRGVYLLTSHHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTRTFPLLQPGPGITRGLTITVPVITFIDNHG---ESWMGGGVVPDAIVLAEDALEKAEEVL
M2_anoCar  RYNIGGPSSSAVPVLLSYFQDPSAGPVHFFTTYNRLTNQTQAYSSSAEMVGKPYGARRGVYLLTSHNTATAAEEFAYLMQTLGRATLVGEITAGSLSHTHTFCILELGGGC--GLLINVPVITLIDNHG---EYWLGGGVVPDSIVLADEALEKAREVL
M2_ornAna  RNNPGGPSS-AVPLLLSYFQDPAAGPIRLFTTYNRPADVTREYASRAGALEKPYGARRGVYLLTSHRTATAAEEFAYLMQALGRATLVGEITAGRLLHSRTFPLLRPPWE---GLVLTVPFLTLFDPHG---EGWLGGGVVPDAIVLAEEALEKAGEVL
M2_xenTro  RYNIGG-SSTSIPLLLSYFQEPE-NRIHLFTIYNRQQNSTNEVYSLPKVLGKPYGSKKGVYVLTSHETATAAEEFAYLMQSLSRATIIGEITSGNLMHSKAFPLDGTR------LSVTVPIMNFIDNNG---DYWLGGGVVPDAIVLADEALDKAKEII
M2_xenLae  RYNVGG-SSTAVPLLLSYFLDPE-TKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFDGTQ------LSVTVPIINFIDSNG---DYWLGGGVVPDAIVLADEALDKAKEII
M2_petMar  RYNLGG-SSTAIPIVLSYFQDVA--PVHFYTVYDRLRNVTAEFHTVSNLTSQLYGSKKGVYLLTSQHTATAAEEFTYLMQSLNRATIVGEITSGRLAHSLAFRLSDT------GLYMTVPIVNFIDNND---EYWLGGGVVPDAIVLAENALDAAKEII</font>
M2x_takRu  RHNTGG-SSTSVALLLSYLRDPL-PKRHFFTIYDSVQNTTTEYGSRPHIPGPSYGSERGVYVLTSHYTAGAAEEFAYLIQSLHFGTVVGEITSGTLMHSKTFQVEGT------DIFITVPFINFLDNNG---EYWLGGGVVPDAIVLAEEALEHVNRTA
M2x_danRe  RFNTGG-STEALPILLSYMFDTS-SSTYLFSIYDSIKNTTFDFHTLNNISGPSYGSTKGVYVLTSYYTAEAGEEFAYLMQSLHRGTVIGEITSGMLLHSKTFQIEQT------SLAITVPIINFIDVNG---ECWLGGGVVPDAIVLAEEALERAHEII
<font color="green">M3_homSap  RYNPGSYST-AIPLLCSYFFEAE-PRQHLYSVFDRATSKVTEVWTLPQVAGQRYGSHKDLYILMSHTSGSAAEAFAHTMQDLQRATVIGEPTAGGALSVGIYQVGSS------PLYASMPTQMAMSATTG--KAWDLAGVEPDITVPMSEALSIAQDIV
M3_bosTau  RYNPGSYST-AVPLLCSYFFEAE-PRRHLYSVFDRATSRVTEVWTLPHVTGQRYGSHKDLYVLVSHTSGSAAEAFAHTMQDLQRATIIGEPTAGGALSVGIYQVGSS------ALYASMPTQMAMSASTG--EAWDLAGVEPDITVPMSVALSTARDIV
M3_monDom  RYNPGGYST-AVPLLCSYFFEAE-PRRHLYTIFDRAASQLTEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFVHTMKDQHRATVIGEPTGGGALSVGIYQVENS------PLYASMPTQVAISPVTG--KAWDMAGVEPDVSVLSSEALMTTQGIV
M3_macEug  RYNPGSYST-SVPLLCSYFFEAE-PRKHLYTIFDRAASQATEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFAHAMKDLRRATVIGEPTAGGALSVGIYQVSNS------PLYASMPTQVAISPVTG--KAWDIAGVEPDVSVPAREALITTQGIV
M3_sacHar  RYNPGSYST-TVPLLCSYFFEAE-PRKHLYTVFDRATSQFTEVWTLPQVTGERYGSQKDLYILISHTSGSAAEAFAHIMKDLQRATVIGEPTAGGALSVGIYQVGDS------PLYVSMPTQVALSPVTG--KAWDMAGVEPDVSVLANEALITAQGIV
M3_taeGut  RYNTGGYST-AIPILCSYFFDPE-PRKHLYTVFDRSTSRSTEVWTLPQLAGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVVGEPTVGGSLSVGIYRVGNS------SLYASIPSQVVLSPVTG--KVWSVSGVEPHITIQASEAMAAAQHIA
M3_galGal  RYNTGGYST-AVPILCSYFFEPE-PRQHLYTVFDRSTSRSTEVWTLPKVTGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVIGEPTVGGSLSVGIYRVGNS------SLYRSIPSQVVLSPVTG--KVWSVSGAEPHITIQASEALAAAKHIA
M3_anoCar  RYNTGSYST-AVPMFCSYFFDAE-PQQHLYTIIDRSTSQSTEVWTSSQVSGKRYGSTKDLYILISHASGSAAEAFTRSLKDLHRATVIGEPTVGGSLSASIYNIGST------PLYASIPSQIVLSPVSG--KVWSLSGIQPHVTTQSNEALASAQNII
M3_xenTro  RYNTGGYST-AIPIFCSYFFDPE-PLQHLYTVYDRSTSSGTDIWTLPEVVGERYGSTKDIYILTSHMTGSAAEVFTRSMKELNRATIIGEPTSGVSLSVGMYKVGES------NLYVSIPNQVVISSVTG--KVWSVSGVEPHVIAQASEAMNVAHHII
M3_xenLae  RYNTGGYST-AIPIFCSYFFDPE-PLQHLYTVYDRSTSTGKDIWTLPEVFGERYGSTKDIYILTSHMTGSAAEVFTRSLKDLNRATLIGEPTSGVSLSVGMYKVGDS------NLYVTIPNQVVISSVTG--KVWSVSGVEPHVIIQANEAMNIAHRII
M3_petMar  RYNMGGYST-SIPILCSYFFDAS-PPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDS------RLYVFIPNQAGVSPSGG--RTWSVAGVEPHVQTKASEALQSALRMV</font>
M3x_takRu  RYNAGGSST-AVPLWCSYFVDGE-PLQHLYTVYDRTTKTRVEVMTLPEVSGQRYDPGKDVYILTSHMTGSAAEAFVRAMRDLNRVTIVGEPTAGGSLSSATYQIGES------VLYASIPNQVVTSAATG--KLWSISGVEPDVFAQARDALPVAQRII
M3x_danRr  RYNTGGYST-AIPLLCTYFFDAQ-PLTHIYTLFDRSTATVTKVTTLPDVLGQKYSSQKDVYILTSHITGSAAEAFTRTMKDLKRATVIGEPTIGGALSSGTYQIGNS------ILYASIPNQAVLNAVTG--KPWSISGVEPHIVAQASDALIVAQKII
<font color="brown">M4_petMar  RYNMGGYST-SIPILCSYFFDAS-PPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDS------RLYVFIPNQAGVSPSGG--RTWSVAGVEPHVQTKASEALQSALRMV
M4_homSap  MFNIGGPTS-SIPILCSYFFDEG-PPVLLDKIYSRPDDSVSELWTHAQVVGERYGSKKSMVILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDT------NLYLTIPTARSVGASDG--SSWEGVGVTPHVVVPAEEALARAKEML
M4_bosTau  RFNIGGPTS-SISALCSYFFDEG-PPILLDKIYNRPNNSVSELWTLSQLEGERYGSKKSMVILTSTLTAGAAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDT------DLYLTIPTARSVGAADG--SSWEGVGVVPDVAVPAEAALTRAQEML
M4_monDom  RFNIGGPTS-SISALCSYFFDEG-QEVLLDQIYNRPNDSISEIWTQSQVAGERYGSKKSVIILTSSMTAGAAEEFVYVMQRLGRALVIGEVTSGGCQPPQTYHVDDT------DLYITIPTARSVGSGDK--PSWEGVGVAPHVEVPADQALSKAKEMF
M4_macEug  RFNIGGPTS-SISALCSYFFDEG-QKVLLDRIYNRPNDSIVEIWTQPHVTGERYGSKKSVIILTSSTTAGAAEEFVYIMQGLGRALVIGEVTSGGCQPPQTYHVDDT------DLYITIPTAQSVGSGDR--PSWEGIGVTPHVEVPADQALSKAKEMF
M4_sacHar  RFNIGGPTS-SISAMCSYFFDEG-QGVLLDRIYNRPNDSISEIWTQPQVIGERYGSKKTVVILTSSMTAGAAEEFVYIMQRLGRALVIGEVTSGGCQPPQTYHVDDT------DLYITIPTTRSVVSGDK--SSWEGVGVVPHMEVPADQALSKAKEMF
M4_ornAna  R-NIGGPTS-SISALCSYFFDED-HPVLLDKIYNRPNDSISEIWTHSHIAGERYGSRKSVVILTSNMTAGAAEEFVSIMKRLGRALVVGEVTGGGCHPPQTYHVDDT------HLYITIPTSRSVGSEDG--SSWEGVGVTPHLVVPADVALSRAKDLF
M4_xenLae  RFNIGGPTS-SIPIFCSYFFDEG-TPVLLDKIYSRTSNAMTDIWTLPDLVGKTFGSKKPLIILTSSLTEGAAEEFVYIMKRLGRAYVVGEVTSGGCHPPQTYHVDDT------HLYLTIPTSRSASAEPG--ESWEGKGVLPDLEISSETALLKAKEIL
M4_xenTro  RFNIGGPTS-SIPTFCSYFFDEG-TPVLLDKIYSRTTNAITDVWTLPHLVGNAFGSKKPVIILTSSLTEGAAEEFVYIMKRLGRAYVIGEVTSGGCHPPQTYHVDDT------HLYLTIPTSRSASAKPG--ESWEGKGVLPDLEITSETALMKAKEIL
M4_taeGut  RYNIGGSTT-PIAILCSYFFDEG-HPVLLDRVYDRPSDSVKEIWTQPQLKGERYGSQKGLVILTSAVTAGAAEEFVYIMKRLSRALIIGEQTSGGCHSPQTYQVDET------NFYVVIPTSRSVTSADS--TSWEGKGVSPHIETPAETALIKAKEML
M4_galGal  RYNIGGYTN-SIPILCSYFFDEG-HQVLLDKVYDRPSDSVKEIWTQPQLRGERYGSQKGLIILTSAVTAGAAEEFVFIMKRLGRALIIGEQTSGGSHSPQTYQVDDT------NFYIIIPTARSVISAES--ASWEGKGVPPHMETPAVTALIKAKEVL
M4_anoCar  RYNVGGPAC-SVPLLCSYFFDEG-HPILLDKVYNRPNDTTSNIWTVSKLAGKRYGLNKGLIILTSSVTSGAAEEFAHIMKRLGRAFIIGQKTSGGCHPPQTFHVDGT------NLYITTPVSRSVFSVN---DSWEGVGVSPHLDVSTDVALIKAKEML
M4_tetNig  RNNVGGPTT-AIAGFCSYFFDAD-KQNRVGQAVRQASGTTTELLTLSELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQTFRVGET------DVFLLIPTVHSDTGA-G--PAWEGAGIAPHIPASAEAALGTARAIL
M4_takRub  RNNVGGPTT-AIAGFCSYFFDAD-KLIVLDKLHDRPSGTTTELLTLPELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQVFSVGEI------GIFLSIPTVHSDTAA-G--PAWEGTGITPHIPVSAEAALGTAKGIL
M4_gasAcu  RNNIGGPTT-AIAGFCSYFFDSD-KQIVLDRLYDRPSGTTTELRTLPELTGTRYGSKKSLVMLTSRATAGAAEEFVYIMKKLGRAMIVGETTAGTSHPPKTFRVGET------DIFLSIPTVHSDTAA-G--PAWEGAGVAPHIPVPADAALETAKGIF
M4_oryLat  RNNVGGPTT-AIAGFCSYFFDGD-KQILLDKLYDRSTGTTTDLLTLGELTGERYGSKKSLIILASRATAGAAEEFVYIMKRLGRAMIVGETTAGASHPPKVFQVGES------DIFLSIPTVHSDTSA-G--PGWEGAGVAPHIPVAAGAALETAKAIL
M4_danRer  RNNIGGHAS-SIAGFCSYFFDAD-KQIVLDHIYDRPSNTTRDLQTLEQLTGRRYGSKKSVVILTSGVTAGAAEEFVFIMKRLGRAMIIGETTHGGCQPPETFAVGES------DIFLSIPISHS-TAQ-G--PSWEGAGIAPHIPVPAGAALDTAKGML</font>
 
=== Evolutionary origin of RBP3 (IRBP) ===
 
Lamprey sequence was recovered by a French group in 2008 from unassembled genome project contigs but not explicitly provided in the [http://www.ncbi.nlm.nih.gov/pubmed/18499481 article] nor posted to GenBank. They reported four modules despite uncertainty in whether these all resided in the same gene. Below, a nearly full length gene (exon 3 and 4 are missing) has been independently recovered from the initial lamprey assembly and parsed into its modules using Superfamily HMM. It indeed has four modules classifying to the expected types and ordering, proving the modern version of the gene was fully established prior to the last common ancestor of mammals and lamprey. As the lamprey ancestor already had fully modern ciliary color vision (so need for retinol shuttling), the role of RBP3 (IRBP) in extant species may have already been established 500 myr ago. 
 
It cannot yet be verified that lamprey has the third intron, though otherwise intron positions and phases are identical to other vertebrates. While no full length chondrichthyes sequence is available, close study of the elephantshark contig containing exon 3 establishes that the final intron occurs with the same phase 0 and position seen in later-diverging tetrapods. While intron loss in lamprey is possible, the simpler explanation is intron gain in the stem for reasons provided below.
 
Callorhinchus milii contig AAVX01012059 establishes that exon 3 has standard flanking phase 1 introns on both sides:
VIASTSSLIVDLR<font color="blue">YNIGGPTSSIPILCSYFFDDDKTVLLDTVYSRPTDTISEMKAIPQVAGNGSTESSVHSYI</font>GERYGSKKSMVIL
+I  T+SL  D R<font color="blue">YNIGGPTSSIPILCSYFFDDDKTVLLDTVYSRPTDTISEMKAIPQVAGNGSTESSVHSYI</font> E    K  +I+
LIIETNSL-RDHR<font color="blue">YNIGGPTSSIPILCSYFFDDDKTVLLDTVYSRPTDTISEMKAIPQVAGNGSTESSVHSYI</font>CEDLHHCKYGLII
Previous efforts to trace the gene back to earlier deuterostomes (or metazoa) proved futile. That remains the case in March 2009 for tunicate (despite a third assembly and massive transcript set) and much-studied sea urchin, establishing that in all likelihood homologs have been lost. However it is possible but implausible that sequences have diverged to the point of unrecognizability. It is equally implausible that a complex fold matching known bacterial folds arose de novo in Cambrian deuterostomes. This creates the unresolved dilemma of ghost gene retention over an immense time frame in ancestral eyeless species yet loss in almost all extant clades.
 
With the advent of the second assembly of the cephalochordate Branchiostoma floridae (which has far fewer polymorphism-related assembly stutters than the first release), it is straightforward to recover a homolog in this species (after rubbishing an unmotivated fusion to the adjacent sulfotransferase in a JGI gene model). The smaller gene here consists of a single module that clusters best with M3 and M4. This suggests that the module number expansion -- like so many key events in vertebrate gene evolution -- took place between cephalochordate and agnathan divergences.
 
The shocking aspect of the Branchiostoma RBP3 (IRBP) gene is its 9 exons. These range in size from 30 to 66 amino acids, quite typical of the average vertebrate gene. Splice junctions are all standard GT-AG. The anomaly here is really in the immense size of the first exon of the vertebrate four-module gene which extends for 1018 residues in human. That can be placed in prospective using the UCSC [http://genome.cse.ucsc.edu/cgi-bin/hgTables Table Browser] to determine the overall size distribution of the 190,000-odd human coding exons. The average protein has 450 residues and 8-9 exons.
 
The second anomaly is that the placement and phasing of the Branchiostoma introns do not correspond at all (via blastp registration) to those of module 4, the only vertebrate module with internal exons (3 of them). A great majority of introns are immensely conserved -- from human to cnidarian -- so the notion of massive erasure followed by de novo intronation in either the Branchiostoma or vertebrate gene can be discarded. However some explanation of descent is required because the genes are strongly homologous (chance expectation e-30) though at best 31% identical and gappy in alignment.
 
The Branchiostoma gene can be assumed orthologous to vertebrate IRBP for lack of a better candidate, but nearby genes in the assembly (EARS2 DNAJC19 UGT2B4 CD79B) bear no obvious synteny to those flanking the human RBP3 gene (RBP3  ZNF488 GDF2 GDF10 ANXA8L1) and only broken chromosomal correspondence is seen in whole genome alignment to human (net track).
 
It follows that searches for earlier diverging species that still carry a homolog should probably be carried out with a single-domain protein as query. The amphioxus protein is the only one currently available and may be highly diverged from its ancestral form. In any event, it does not expose any cryptic homologs in tunicate or echinoderm, much less lophotrochozoa, arthropods or cnidaria known to have ciliary opsin systems.
 
Under the twin assumptions of orthology and approximately ancestral intronation pattern in Branchiostoma, how do we get from a one module gene with 8 introns to a four module gene with 3 unrelated introns by lamprey divergence? This in some ways may have been the critical step in the evolution of imaging eyes with their massive requirement for rapid retinol recycling that likely vastly exceeded that of the ancestral cephalochordate (note RPE65 is [http://www.ncbi.nlm.nih.gov/pubmed/19193895 rate-limiting]). IRBP co-evolved its interstitial location and shuttling function with the newly developed supporting role of the retinal pigmented epithelium, which together were essential for effective vertebrate imaging vision.
 
One hypothetical scenario is formation first of a retroprocessed intronless gene with one module. This may have displaced the nine-exon parental gene because of selection for higher throughput translation. The protein may have been initially a non-cyclic tetramer of discrete subunits. The gene dosage perhaps doubled via a tandem copy, again to meet the need of increased retinol cycling. Next the intervening untranslated region experienced deletions fusing the previously independent modules, leading to a dimer of the internal repeat dimer at the protein level.
 
The gene complex then doubled again perhaps through recombinational module mismatch, once again to meet the newly evolving need for rapid retinol recycling -- at this point all four modules may have bound retinol. New introns with were gained by an unexplained process that favored the 3' end of the gene. Finally a need for allosteric regulation or interaction with other proteins allowed subfunctionalization of other domains to non-retinol shuttling roles despite the apparent loss of previously selection for efficiency because RPE65 had become rate-limiting.
 
While this scenario is speculative and non-unique, elements of it are not uncommon in other genes, even in opsins. For example, a retroprocessed fish RHO1 [http://www.ncbi.nlm.nih.gov/pubmed/18466202 displaced] the parental 5-exon gene into the pineal and LWS repeated spawned secondary cone opsin genes that were initially tandem. A great many human proteins have internally repeated domains and some like titin quite large numbers of them. There may not exist sufficient surviving members of the cephalochordate, hagfish and lamprey clades to specifically illuminate what really happened here. The highest priority would be to study localization and function of RBP3_braFlo within that the visual systems of that organism.
 
>RBP3_braFlo Branchiostoma floridae Region: 9 exons; 1 domain: 83-381
0 MTRPSKVDIVFPIKPFTIPTAHEQVKGEGPVDINKNALCKSADEGHTHP 1
2 VSIAMAPTAYIVFVALVPTVLSVDWLD<font color="blue">VVMGIGDVMADHYLDQDLRALNDQSLLQRWNRTLVHRFQ 0
0 SWSQDDMSDSLRMEEGLTSELRNITGDETIK 0
0 VWDFGVYENTTQEPVPREFYNFSTFVDNFK 2
1 KNREKHINVTMLEGNVGYVSIRSMSHIVDIILPDPEMTEFFLSKMAALNESK 0
0 AIILDLRYNLGGDREGVVHWASFFFNATPSVPLSDVYYRDGVNQYWTLLE 0
0 VPGGIRFPDMPLYLLTSNRTSREAEEFAYAMQVVNRTTIIGETT 1
2 AGEEFTGMWFPIDQTDVHLLTRTNVVRNPITQDSWSGK 1
2 GVTPDIIVPSEKALTVALRKIQ</font>GSEDTKMAASSGNIEPPRWTVYLVFICTSIAILTYPTFM*
 
=== RBP3 (IRBP) use in marsupial phylogeny ===
The first three homology domains and part of the fourth are all encoded by the first large exon of 1090 amino acids. Sequenced fragments of this exon (often starting internally within module M1) has been [http://www.ncbi.nlm.nih.gov/pubmed/19249373 much used in marsupial phylogeny] (along with the first intron of transthyretin). Indeed the 96 marsupial species in 51 genera having partially determined IRBP sequences at GenBank include a Dec 2008 partial sequence for the extinct species [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=158668312 Thylacinus cynocephalus], as well as for [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=47117971 Sarcophilus harrisii] (replaced here by a full length sequence derived from the genome project).
 
The use of IRBP in phylogenetic trees requires a high level of sequence accuracy, particularly since 'informative' characters are precisely the differences. However the PCR survey sequences exhibit various discrepancies in comparison to very high coverage genomic sequences. Some differences could arise from valid polymorphisms in individual animals used as dna source or represent an acceptable (low) level of PCR sequencing error, but other discrepancies appear to be gross errors in GenBank submissions (all from the same research group).
 
The Sacrophilus entry AY532685 has 6 amino acids inconsistent with genomic data (too many for polymorphic variation) as well as a gross error affecting a 17 residue block. It seems likely in the rush to obtain enough 'informative' characters, a completely unworkable error rate has been tolerated. All marsupial phylogenetic studies based in part on analysis of IRBP thus come into question.
 
None of the fragmentary marsupial GenBank entries provide a numbering system relative to a full length marsupial IRBP gene (eg Monodelphis) or its modules; the 4x module repeat structure of the gene is conducive to erroneous module cross-alignment. cDNA sequences typically start at position 73 of M1 (beginning of first hyper-variable indel region) and continue half way through M2 (to position 143), for example EF028750 of Myrmecobius fasciatus (numbat). Thus the region commonly sequenced is poorly coordinated with internal modular structure or existing 3D data.
 
The closest matches to the thylacine IRBP are shown in the difference alignment of the first 60 residues below. These species all lie with the Dasyuromorphia. The indicated E-->K may be one of several phyloSNPs breaking this group into <font color="blue">blue</font> and <font color="green">green</font> subclades. The numbat <font color="red">Myrmecobius</font> fits implausibly (its amino terminal sequence [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=124054062 EF028750] needs verification) -- its affinities seem to lie with the <font color="brown">Didelphimorphia</font> in view of the shared Q.VV.K motif. Thylacinus is not basal within Dasyuromorphia relative to Myrmecobius using IRBP. This is not a case of mis-comparison of modules.  
   *          *                                    *<font color="blue">
STSKAPQHDSKFTNATQEELLALFQQIIKYQVLEGNVGYLRVDYIPGREMIEEVGEFLVN EU091365  0 Thylacinus cynocephalus
  .........P..A..................I............................ AY532676  3 Myoictis wallacei
  .........P..A..................I............................ AY532676  3 Myoictis wallacei
  ........NP..A............................................... AY532687  3 Neophascogale lorentzii
  ........NP..A............................................... AY532687  3 Neophascogale lorentzii
Line 38: Line 268:
  .IPET...VP.LA.I......T.L..M....................Q.VV.K....... AF257689 16 Thylamys pallidior</font>
  .IPET...VP.LA.I......T.L..M....................Q.VV.K....... AF257689 16 Thylamys pallidior</font>


Using Sarcophilus as probe in a different region, 721-900, we find this peculiar outcome: what appears to be a second very odd gene, XY difference, pseudogene, weird balanced polymorphism, nonhomologous recombination, sequence submission error, frameshifts, or systemic experimental error (eg Dasyurus maculatus AY532680 is identical to AY243439 outside the 15 amino acid block). However the genomic reads from individual Sarcophilus used in this project show no sign of this gene despite excellent coverage of the second type of gene.
Using Sarcophilus as probe in a different region, 721-900, we find a very peculiar outcome for numerous GenBank marsupial entries: the 17 residue region orthologous to 38-54 in M2 (VLTEEDLAAKLNAMLQA in M2_sacHar) has been replaced by a non-homologous 17 residue section copied over from 143-158 of M1 (SLVLDLQHSRGGEVSG in M2_myrFas), explaining non-alignment in the latter region (blue shows M2):


Macropus and Monodelphis genomes only contain the second type of gene. All Didelphimorphia and Diprotodontia are of this type, as are platypus and all placentals. With the Sarcophilus genome, this can be resolved as it should have both and be the such first genome. Perhaps the alignment above is a mixture of type 1 and type 2 genes (resp. alleles). The Myrmecobius anomaly makes it more likely two distinct genes are present.
myrFas:    61 DIWKKVMETSSL<font color="red">VLDLQHSRGGEVSG</font>IPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTL 120
              DIWKKVMETSSLVLDLQHSRGGEVSGIPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTL
sacHar:  154 DIWKKVMETSSLVLDLQHSRGGEVSGIPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTL 213
myrFas:  121 PQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKEMRRAIVVGEQTQGGVLDLRKLRIGQ 180
              PQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILK+MRRAIVVGEQTQGG LDLRKLRIGQ
sacHar:  214 PQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKKMRRAIVVGEQTQGGSLDLRKLRIGQ 273
myrFas:  181 SDFFITVPVARSLSPLGGGSQTLEGSGVVPCVGIPAEKALEKTLAILTLR<font color="blue">RARPGAIQRL 240
              SDFFITVPVARSLSPLGGGSQT EGSGVVPCVGIPAE+ALEK LAILTLR<font color="blue">RARPGAIQRL
sacHar:  274 SDFFITVPVARSLSPLGGGSQTWEGSGVVPCVGIPAEQALEKALAILTLR<font color="blue">RARPGAIQRL 333
myrFas:  241 MEILQKYYTLVDRVPALLHHLTAIDYSSSL<font color="red">VLDLQHSRGGEVSG</font>TVSEDPRLLVRVLRSE 300</font>
              MEILQKYYTLVDRVPALLHHLTAIDYSS L  +  ++  +  VSEDPRLLVRVLR E</font>
sacHar:  334 MEILQKYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAMLQAVSEDPRLLVRVLRPE 393</font>


A definite pecularity seen in blast searches is the occurence earlier in the sequence of a very homologous segment for this very block, likely the homologous part of another of the internal tandem repeats. It is seen in both types of genes. Possibly internal non-homologus recombination or gene conversion has inserted first repeat sequence again in this distal block in place of what was relatively diverged sequence. Internal gene conversion would make IRBP extremely difficult to use in alignment-based phylogeny. As rare genomic event, it unites the species that have it but species that don't have it would have to be re-examined to exclude the possiblity that only the type 2 gene happened to be sequenced.
The source of this error cannot plausibly be explained XY difference, pseudogene, balanced polymorphism, nonhomologous recombination, frameshifts, internal inversion, or systemic experimental error (eg Dasyurus maculatus AY532680 is identical to AY243439 outside the 15 amino acid block). Genomic reads from Sarcophilus, Macropus and Monodelphis show no sign of novel substitution gene despite excellent coverage. All Didelphimorphia and Diprotodontia entries at Genbank are normal; sauropods, platypus and dozens of placentals establish this as ancestral. For some marsupials, independent sequencing finds the normal version of the gene.


It emerges from direct tblastn that the Sacrophilus individual sequenced was female. That is, ATRX is well represented but not ATRY (though the situation is somewhat confused due to additional paralogs). Marsupial XY are [http://www.ncbi.nlm.nih.gov/pubmed/11173870,12508115,16209912,17333539,18185981,9215558 quite different] from placentals:
These peculiar sequences were all submitted by C. Krajewski on 23-JAN-2004 and utilized in a paper entitled "Molecular systematics of the enigmatic phascolosoricine marsupials of New Guinea" published in the Aust. J. Zool. 52, 389-415 (2004). Two similarly flawed sequences submitted the same day (AY532677, AY532679) were subsequently corrected on 25-SEP-2006 by the same individual resulting in GenBank entries being fixed. However many subsequent studies of IRBP may have used the 17 flawed sequences that were never corrected. The same authors resequenced species such as Pseudantechinus roryi (EU086689) obtaining the correct sequence in this region on 07-AUG-2007 but still did not fix their earlier entry AY532673.
<blockquote>
"Many or most genes on the mammal Y chromosome evolved a testis-specific function after diverging from an X-borne copy with a general function in both sexes. In marsupial but not eutherian mammals, a testis-specific orthologue (ATRY) of the widely expressed X-borne ATRX gene lies on the Y chromosome. Since mutations in human ATRX cause sex reversal, it is possible that one function of ATRY in marsupials is testicular differentiation. We report here the isolation and sequencing of the tammar wallaby (Macropus eugenii) ATRY cDNA, and comparison of its sequence with that of tammar ATRX. The evolution of a testis-specific function for the ATRY protein distinct from the general role of ATRX in both sexes has been accompanied by sequence changes in many protein domains that would alter protein binding partners. A large open reading frame encodes a 1771 amino acid ATRY protein that has diverged extensively from ATRX. The conservation and loss of particular motifs identify those required for testicular function (ATRY) and function in other tissues (ATRX)."</blockquote>
   
   
  AY532685 MEILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE <font color="blue">Sarcophilus harrisii</font>
  AY532685 MEILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE <font color="blue">Sarcophilus harrisii</font>
Line 112: Line 354:
           E LQ YYTLVDRVPALLHHL ++D+SS +  D  ++      VSEDPRLLV V+RS+
           E LQ YYTLVDRVPALLHHL ++D+SS +  D  ++      VSEDPRLLV V+RS+
  equCab    EALQDYYTLVDRVPALLHHLASMDFSSVVSEDDLVAKLNAGLQAVSEDPRLLVWVVRSK
  equCab    EALQDYYTLVDRVPALLHHLASMDFSSVVSEDDLVAKLNAGLQAVSEDPRLLVWVVRSK
It emerges from direct tblastn that the Sacrophilus individual sequenced was female. That is, ATRX is well represented but not ATRY (though the situation is somewhat confused due to additional paralogs). Marsupial XY are [http://www.ncbi.nlm.nih.gov/pubmed/11173870,12508115,16209912,17333539,18185981,9215558 quite different] from placentals:
<blockquote>
"Many or most genes on the mammal Y chromosome evolved a testis-specific function after diverging from an X-borne copy with a general function in both sexes. In marsupial but not eutherian mammals, a testis-specific ortholog (ATRY) of the widely expressed X-borne ATRX gene lies on the Y chromosome. Since mutations in human ATRX cause sex reversal, it is possible that one function of ATRY in marsupials is testicular differentiation. We report here the isolation and sequencing of the tammar wallaby (Macropus eugenii) ATRY cDNA, and comparison of its sequence with that of tammar ATRX. The evolution of a testis-specific function for the ATRY protein distinct from the general role of ATRX in both sexes has been accompanied by sequence changes in many protein domains that would alter protein binding partners. A large open reading frame encodes a 1771 amino acid ATRY protein that has diverged extensively from ATRX. The conservation and loss of particular motifs identify those required for testicular function (ATRY) and function in other tissues (ATRX)."</blockquote>


== Reference sequences ==
== Reference sequences ==


These are organized in three ways, as intronated genes showing position and phase of intron breaks, as parsed into functional modules (signal peptide and spacer residues are dropped), and as modules organized by type 1-4. All three sets are in phylogenetic order with respect to the canonical deuterostome tree.
These are organized both parsed into functional modules (signal peptide and spacer residues are dropped) as determined by global multiple alignment consistency and as intronated genes showing position and phase of intron breaks. Both sets are in phylogenetic order with respect to the canonical deuterostome tree.
 
=== RBP3 (IRBP) sequences parsed into structural modules ===
 
<pre>
>M1_homSap
LFQPSLVLDMAKVLLDNYCFPENLLGMQEAIQQAIKSHEILSISDPQTLASVLTAGVQSSLNDPRLVISYEPSTPEPPPQVPALTSLSEEELLAWLQRGLRHEVLEGNVGYLRVDSVPGQEVLSMMGEFLVAHVWGNLMGTSALVLDLRHCTGGQVSGIPYIISYLHPGNTILHVDTIYNRPSNTTTEIWTLPQVLGERYGADKDVVVLTSSQTRGVAEDIAHILKQMRRAIVVGERTGGGALDLRKLRIGESDFFFTVPVSRSLGPLGGGSQTWEGSGVLPCVGTPAEQALEKALAIL
>M1_bosTau
LFQPSLVLEMAQVLLDNYCFPENLMGMQGAIEQAIKSQEILSISDPQTLAHVLTAGVQSSLNDPRLVISYEPSTLEAPPRAPAVTNLTLEEIIAGLQDGLRHEILEGNVGYLRVDDIPGQEVMSKLRSFLVANVWRKLVNTSALVLDLRHCTGGHVSGIPYVISYLHPGSTVSHVDTVYDRPSNTTTEIWTLPEALGEKYSADKDVVVLTSSRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRVGQSDFFLTVPVSRSLGPLGEGSQTWEGSGVLPCVGTPAEQALEKALAVL
>M1_monDom
IFQPSLVRDMAKILLDNYCFPENLMGMQEVIEQAIKSGEILDISDPQMLASVLTAGVQGALNDPRLVISFEPSIPETPQHVPKLANVTQEELLILLQQMIKYQVLEGNVGYLRVDYIPGQEVVEKVGEFLVNNIWKKLMGTSSLVLDLQHSSGGEISGIPFVISYLHQGDILLHVDTVYDRPSNTTTEIWTLPQVLGERYGGEKDMVVLTSHRTVGVAEDIAYILKKLRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALGKALAIL
>M1_macEug
IFQPSLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLASVLTAGVQGSLNDPRLVISYEPSPAEAPQQSPKLTSLTQEELLTLLQQMIKYQVLDGNVGYLRVDYIPGQEVVEKVGEFLVNDIWKKLMGTSSLVLDLQHSTEGEVSGIPFVISYLHEGDILLHVDTVYDRPSNTTTEIWTLPQVLGERYSGEKDLVILTSHRTVGVAEDIAYILKKMRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALEKALAIL
>M1_sacHar
IFQPTLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLANVLTAGVQGSLNDPRLVISYEPSTSEAPQHDPKFANATQEELLALFQKIIKYQVLEDNVGYLRVDYIPGRDMIEEVGEFLVNDIWKKVMETSSLVLDLQHSRGGEVSGIPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTLPQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKKMRRAIVVGEQTQGGSLDLRKLRIGQSDFFITVPVARSLSPLGGGSQTWEGSGVVPCVGIPAEQALEKALAIL
>M1_ornAna
VSQPSMVLDVAKILLDNYCYPENLMGMQEAIEEAIQRGEILDIADPKRLASVLTAGVQGSLNDPRLVISYEPAPVAVSQQPPEPASLPAEQPLERLRPAVGSEVLEGNVGYLRVDRLPGREEIERVGAVLGRDIWEKLLGTSALVLDLRHSTGGHVSGIPFFISYFYPEGPALHVDTVYDRPSNATRQLWTLPRVLGARYAADKDVVVLTSRLTAGVAEDVAYILQQMRRAIVVGERTAGGPLVFRKLRVGLSDFFITVPVACSLGPLGGGGRSWEGSGVLPCVAVPADRALDEALDIL
>M1_galGal
IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPSLHAAPKQEAETYPTREQLLSLIEHVVIYDKLEGNVGYLRIDYIIGQEVVEKVGAFLVDKVWKTLINTSALVIDLRYSTGGQISGIPFIISYLHEADKMLHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITLGEKTAGGSLDIQKLRIGPSNFYMMVPVSRSVSPLSGGGQSWEVSGVMPCVASEAEQALKKSLDIL
>M1_taeGut
IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPLPHSGPKQEAEGSPTREQLLSLIEHVIMYDKLEGNVGYLRIDYIIGEEVVQKVGAFLVDKVWKTLIETSALVIDLRHSTGGQISGLPFIISYLHEQDKILHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITVGEKTAGGSLDIQKLRIGPSNFYMMVPVSRSVSPLSGGGQSWEVSGVMPCVATEAEQALQKSLDIL
>M1_anoCar
VLQSTLVLDMAKLLLDNYCLPENLVGMREAIEQAIKNGEVLDISDPKLLATVLTAGVQGALNDPRLVISYEPTAPAAPKQRMETSLTPEQLLSLIQHTVKYEVLDDNVGYLRIDYIMGQDIVQKIGSFLVEKVWKTLLGTSALILDLRYTTGGDVSGIPFIISYLYNGDKVLHVDTVYNRPSNTTVEILTLPKVLGVRYSKDKDVILLISKYTTGVAENVAYILKHMHRTIIVGEKSAGGSLDTQKMQIGNSQFYMTVPLSCSVSPLSGSGQSWEISGVTPCVVISAEQALDKALAIL
>M1_xenLae
LFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAVKGGEILHISDPDTLANVFTSGVQGYLNDPRLVVSYEPNYSGPQTEQSLELTPEQLKFLINHSVKYDILPGNIGYLRIDFIIGQDVVQKVGPHLVNNIWKKLMPTSALILDLRYSTQGEVSGIPFVVSYLCDSEIHIDSIYNRPSNTTTDLWTLPELMGERYGKVKDVVVLTSKYTKGVAEDASYILKHMNRAIVVGEKTAGGSLDTQKIKIGQSDFYITVPVSRSLSPLTGQSWEVSGVSPCVVVNAKDALDKAQAIL
>M1_xenTro
VFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAMKSGEILHISDPETLANVFTSGVQGFLNDPRLVVSYEPNYSGPRKEQSPEPTLEQLKFLLDHSVTYDLLPGNIGYLRIDFIIGQDVVQKVGPLLVNNIWKKLMPSSALILDLRYSTQGKVSGIPFVVSYLTDPQIHIDSIYNRPSNTTTDLWTLSELMGERYGKDKDVVVLTSKYTEGIAEGAAYILKHMSRAIVVGEKTAGGSLDIQKIKIGQSEFYITVPVSRSISPLTGQSWEVAGVFPCVVVNANNALNKAQGIL
>M1_tetNig
AFPPSLIADMAKIVLDNYCSPEKLAGMKEAIKAAGTNTEVLNIPDGESLARVLSAGVQGTVSDPRLMVSFQPNYVPAGPHKMPPLPPEHLVAVLQTSVKLDILEGNTGYLRIDHILGEEVADKVGPALIDLIWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPVVHIDSVYDRPSNTTTKLLSLPNLLGQRYGVSKPLIVLTSKNTKGIAEDVAYCLKNLKRATIVGEKTAGGSLKLDTFKVGDTDFYITVPTAKSINPITGSSWEIRGVTPHVEVNAEDALATAIKIV
>M1_takRub
AFPPSLITDMAKIVLDNYCSPEKLAGMKEAIEAAGTNTEVLNIPDGESLARVLSAGVQGTVSDSRLMVSYQPDYVPAVPPKMPPLPPEHLVAVLQTSIKLDLLEGNTGYLRIDHIIGEDVAEKVGPSLIDLIWNKILPTSALIFDLRYTSSGEISGIPYIVSYFTQAEPVVHIDSVYDRPSNTTTKLFSLSNLLGERYGITKPLIILTSKNTKGIAEDVAYCLKNLKRATIVGERTAGGSVKLDNFKVGSTDFYITVPTAKSINPVTGSSWEITGVKPDVEVNAEDALATAIKIV
>M1_gasAcu
GFAPNVIIDMAKIVIDNYCSPEKLAGMKEAIEAAGSNTEVLSIPDAETLANVLSAGVQTTVSDPRLMISYEPNYVPVVPPKMPPLPPDQVIAVLQTSIKLDILEGNIGYLRIDHILGEDVAEKVGPLLLDLVWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTEAGTPIHIDSIYDRPSNTTTKLFSMSTLLGERYSTSKPLIILTSKNTKGIAEDVAYCLQNLKRATIVGEKTAGGSVKVDKIQVRDTGFYVTVPTAKSVNPITGSTWEVTGVTPNVEVNAEDALATAIKIV
>M1_oryLat
SFPPSLITDLAKIVMDNYCSPEKLSGMKEDIATAGANTDVLNIPDGEALAKVLTDGVQTTVSDPRLRVSYEPNYVPVVPPQLPPEQLIAVLQTSIKLDILEGNIGYLRIDSIIGEEVAEKVGPLLLELVWSKILPTSALIFDLRYTSSGDITGIPYIISYLTDAKSEIHIDTIYDRPLNTTTKLLSMQSTLGQTYGGTKPLLVLTSKNTKDIAEDVAYCLKNLKRATIVGEKTAGGSAKIKKFRVGDTDFYVTLPTAKSINPITGSSWEVTGVKPNVEVNAEEALATALKII
>M1_danRer
NFSPTLIADMAKIFMDNYCSPEKLTGMEEAIDAASSNTEILSISDPTMLANVLTDGVKKTISDSRVKVTYEPDLILAAPPAMPDIPLEHLAAMIKGTVKVEILEGNIGYLKIQHIIGEEMAQKVGPLLLEYIWDKILPTSAMILDFRSTVTGELSGIPYIVSYFTDPEPLIHIDSVYDRTADLTIELWSMPTLLGKRYGTSKPLIILTSKDTLGIAEDVAYCLKNLKRATIVGENTAGGTVKMSKMKVGDTDFYVTVPVAKSINPITGKSWEINGVAPDVDVAAEDALDAAIAII
>M1_petMar
KFDTAVVLHLAKVLLDNYCIPENLVGMDEAIQRAVDNGELLGVSDPESAASALTEGIQAALNDPRIAVSYVPDVDDDGDREEGDAEGWDAGEQHRPTTFEELLATIPQKTSFAVLDGNVGYLRADEIISEATIKKLGPVIVQRIWNRLVDTDTFVLDLRYNSHGDITGLPYLVSCFCEPRPVVHLDTVYYRPTNESKEIWSLPDLQGARFAKHKDVFVLVSANTEGVAENVAYVLKHLHRATVIGEQTAGGSLEVERFRLGDSRFFVTVPTARSQSPLTGRSWELTGVFPCVSAPSERALDKALEIL
 
>M1x_takRu
FYQHTLVLEMAKLLLENYCIPENLVGMQEAIQRAIKSREILQISDRKTLATVLTVGVQGALNDPRLSVSYEPSFSPLPLQALSSLPVEQQLRLLRNSIKLDILDSDVGYLRIDRIIDEETLLKFGPLLRENVWDKAAQTSSLILDLRFSTAGGWSGIPSIVSYFTEPHSLVHIDTVYDRPSNTTTELWTMSSVRGKTFGGKKDMIVLIGRRTAGAAEAVAYTLKHLNRAIVVGERSAGGSLKVRKFRIAESDFYITMPVARSVSPITGKSWEVSGISPTVNVAAREALAKAQTFL
>M1x_danRe
SFQSALVLDMAKILLDNYCFPENLIGMQEAIQQAINSGEILHISDRKTLASVLTAGVQGALNDPRLTVSYEPNYTLITPPALHSLPTEQLIRLIRSTVKLEVMDNNIGYLRIDRIIGQETVVKLGRLLHNNIWKKVAHTSAMIFDLRFSTAGELSGLPYIVSYFSDSDPLLHIDTIYERPTNITRELWTLPTLLGERFGKRKDLIVLISKRTIGAAEGVAYILKHLKRAVIIGERSAGGSVRVDKLKIGDSGFYITVPVARSVNPVTGQSWEVSGVAPSVTVNPKESIAKAKSLI
 
>M2_homSap
SALPGVVHCLQEVLKDYYTLVDRVPTLLQHLASMDFSTVVSEEDLVTKLNAGLQAASEDPRLLVRAIGPTETPSWPAPDAAAEDSPGVAPELPEDEAIRQALVDSVFQVSVLPGNVGYLRFDSFADASVLGVLAPYVLRQVWEPLQDTEHLIMDLRHNPGGPSSAVPLLLSYFQGPEAGPVHLFTTYDRRTNITQEHFSHMELPGPRYSTQRGVYLLTSHRTATAAEEFAFLMQSLGWATLVGEITAGNLLHTRTVPLLDTPEGSLALTVPVLTFIDNHGEAWLGGGVVPDAIVLAEEALDKAQEVL
>M2_bosTau
RALPGVIQRLQEALREYYTLVDRVPALLSHLAAMDLSSVVSEDDLVTKLNAGLQAVSEDPRLQVQVVRPKEASSGPEEEAEEPPEAVPEVPEDEAVRRALVDSVFQVSVLPGNVGYLRFDSFADASVLEVLGPYILHQVWEPLQDTEHLIMDLRQNPGGPSSAVPLLLSYFQSPDASPVRLFSTYDRRTNITREHFSQTELLGRPYGTQRGVYLLTSHRTATAAEELAFLMQSLGWATLVGEITAGSLLHTHTVSLLETPEGGLALTVPVLTFIDNHGECWLGGGVVPDAIVLAEEALDRAQEVL
>M2_monDom
RARPGAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATMGSEASEEEDATPAANSLPEDESQRQALVDSVFQVSVLPGNVGYLRFDEFADSSVLGTLAPYVIRQVWEPLQDTNHLIMDLRYNPGGPSSAVPLLLSYFQDPAAGPIRLFTTYDRQTNQTQEHLSRAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGNLVLTVPILTFIDNNGECWLGGGVVPDAIVLAEEALDKAKEVL
>M2_macEug
RARPAAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATAGAESREEAATAAPVPLPDGESQRQALVNSVFQVSVLPGNVGYLRFDEFADSSVLGALAPYVLQQVWEPLQDTDHLIMDLRYNPGGPSSAVPLLLSYFQDPAAGPVRLFATYDRQTNQTREYRSQAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGNLMHTRTFSLLQPPDGSLVLTVPILTFIDNHGECWLGGGVVPDAIVLAEEALDKAKEVI
>M2_sacHar
RARPGAIQRLMEILQKYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAMLQAVSEDPRLLVRVLRPEEATVEAEPGEESATPASVSLPESDAERQALIDSVFQVSVLPGNVGYLRFDEFADNSVLGTLAPYVLRQVWEPLQDTDHLIMDLRYNPGGPSSAVPLLLSYFQDPSAGPVRLFATYDRQTNQTQEYRSRAELLGKPYGAERGVYLLTSYHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGSLVLTVPTLTFIDNHGECWLGGGVVPDAIVLAEEALDKAKEVL
>M2_ornAna
GAVPGAVAHLADLLRDYYALVDRVPALLRHLAALDLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPEEAERGPPRKEEEQKEEEEEDQPSPGASILPGDGSSLFRVSVLPGNVGYLCFDEFPEASALERLGPLLGRRVWEPLEATDHLMVDLRNNPGGPSSAVPLLLSYFQDPAAGPIRLFTTYNRPADVTREYASRAGALEKPYGARRGVYLLTSHRTATAAEEFAYLMQALGRATLVGEITAGRLLHSRTFPLLRPPWEGLVLTVPFLTLFDPHGEGWLGGGVVPDAIVLAEEALEKAGEVL
>M2_galGal
RAVPGTLSRLTDILKDYYSLVERVPVLLRHLTTSDFSSVQSAEDLATKLNTEMQTLSEDPRLLVRTMMPGEAAAPPAEMPIAMAANLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYIVKKVWEPLQNTENLIMDLRYNPGGPSSSAVPMLISYFQDPTAGPVHLFTTYDRRTNHTQEHNSQAELLAQPYGAQRGIYVLTSRHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTCTFPLVQPEQGITRGLTITVPVITFIDNHGESWMGGGVVPDAIVLAEDALEKAEEVL
>M2_taeGut
RAVPGTISHLKNILKDYYSLVERVPALLRRLTTSDFSSVQSSEDLATKLNTELQALSDDPRLMVRVMMPGEAADSPAEKPVGMAADLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYLVHKVWEPLQNTENLIMDLRYNLGGPSSSAVPVLLSYFQDPAAGPVHLFTTYDRRTNHTQEHNSQAELLGQSYGAKRGVYLLTSHHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTRTFPLLQPGPGITRGLTITVPVITFIDNHGESWMGGGVVPDAIVLAEDALEKAEEVL
>M2_anoCar
KAIPNSMSYLVDIIKNNYSMLEQVPVLLQHLSTFDYSSVLSVKDLASKLNAELQTISEDPRLFLRVPASDEAVTSQTDEKVAMASDLPNNEQLMKALVMTVFKVSVLPGNVGYMRFDEFGDATVLVKLGPYLLQHVWEPLQATDYLIIDLRYNIGGPSSSAVPVLLSYFQDPSAGPVHFFTTYNRLTNQTQAYSSSAEMVGKPYGARRGVYLLTSHNTATAAEEFAYLMQTLGRATLVGEITAGSLSHTHTFCILELGGGCGLLINVPVITLIDNHGEYWLGGGVVPDSIVLADEALEKAREVL
>M2_xenTro
SSITHILLQLSEILVNNYAFSERIPTLLQHLPNLDYSSVISEEDITAKLNYELQSLTEDPRLVLKSKTDSLVMPEDSTQVENLPDDEATLQALVNTVFKVSILPGNIGYLRFDEFADVSVLAKLGPYIVNTVWDPITVTENLIIDLRYNIGGSSTSIPLLLSYFQEPENRIHLFTIYNRQQNSTNEVYSLPKVLGKPYGSKKGVYVLTSHETATAAEEFAYLMQSLSRATIIGEITSGNLMHSKAFPLDGTRLSVTVPIMNFIDNNGDYWLGGGVVPDAIVLADEALDKAKEII
>M2_xenLae
SSVTHVLHQLCDILANNYAFSERIPTLLQHLPNLDYSTVISEEDIAAKLNYELQSLTEDPRLVLKSKTDTLVMPGDSIQAENIPEDEAMLQALVNTVFKVSILPGNIGYLRFDQFADVSVIAKLAPFIVNTVWEPITITENLIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFDGTQLSVTVPIINFIDSNGDYWLGGGVVPDAIVLADEALDKAKEII
>M2_petMar
GVARKAVEAAGELLLSSYTFVERASAIADHLSWSEYGSVVSVEDLTSKLTQDLQSVAEDPRLVVSNREPEWPPLAQPIPPGPPAPLPDDEQMLEAIVDSAFKVEVLEGNIGYLRFDEFGDASAVMKLRKQLVSKVWERIHPTDDVIIDLRYNLGGSSTAIPIVLSYFQDASPPVHFYTVYDRLRNVTAEFHTVSNLTSQLYGSKKGVYLLTSQHTATAAEEFTYLMQSLNRATIVGEITSGRLAHSLAFRLSDTGLYMTVPIVNFIDNNDEYWLGGGVVPDAIVLAENALDAAKEII
 
>M2x_takRu
SRIPKVLQIVLDIIGRFYAFADRVQALLQQLESADLFSVVSEEDLAARLNHDLQTASEDPRLIIRHKRDNIPRAEEEPELHAANDHDGELVEGFTVQVLPHNTGYLRLDRFVRCSEGDKLEEIVAEKVWGPLKDTQNLIIDLRHNTGGSSTSVALLLSYLRDPLPKRHFFTIYDSVQNTTTEYGSRPHIPGPSYGSERGVYVLTSHYTAGAAEEFAYLIQSLHFGTVVGEITSGTLMHSKTFQVEGTDIFITVPFINFLDNNGEYWLGGGVVPDAIVLAEEALEHVNRTA   
>M2x_danRe
KTIPKAVRRVSDIIKRYYSFKDKIPALLNQLAKADYFTVVSEEDLAGKLNHEMQSVFEDPRLLIKATQVLTDDASSEDRSSSDDLTDPLFKLEMISGNNGYLRFDRFPTPEVLLRLEDHIKKKIWQPVQETENLVIDLRFNTGGSTEALPILLSYMFDTSSSTYLFSIYDSIKNTTFDFHTLNNISGPSYGSTKGVYVLTSYYTAEAGEEFAYLMQSLHRGTVIGEITSGMLLHSKTFQIEQTSLAITVPIINFIDVNGECWLGGGVVPDAIVLAEEALERAHEII


=== RBP3 from human to amphioxus ===
>M3_homSap
QSLGALVEGTGHLLEAHYARPEVVGQTSALLRAKLAQGAYRTAVDLESLASQLTADLQEVSGDHRLLVFHSPGELVVEEAPPPPPAVPSPEELTYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVRLVWQQLVDTAALVIDLRYNPGSYSTAIPLLCSYFFEAEPRQHLYSVFDRATSKVTEVWTLPQVAGQRYGSHKDLYILMSHTSGSAAEAFAHTMQDLQRATVIGEPTAGGALSVGIYQVGSSPLYASMPTQMAMSATTGKAWDLAGVEPDITVPMSEALSIAQDIV
>M3_bosTau
RSLGELVEGTGRLLEAHYARPEVVGQMGALLRAKLAQGAYRTAVDLESLASQLTADLQEMSGDHRLLVFHSPGEMVAEEAPPPPPVVPSPEELSYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVQLVWQKLVDTAALVVDLRYNPGSYSTAVPLLCSYFFEAEPRRHLYSVFDRATSRVTEVWTLPHVTGQRYGSHKDLYVLVSHTSGSAAEAFAHTMQDLQRATIIGEPTAGGALSVGIYQVGSSALYASMPTQMAMSASTGEAWDLAGVEPDITVPMSVALSTARDIV
>M3_monDom
QRLGALVEGTGHLLEAHYALPEVVGQASALLKAKLEHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPVSEELTPPQKGVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIAPQLVELVWEKLVHTEALVVDLRYNPGGYSTAVPLLCSYFFEAEPRRHLYTIFDRAASQLTEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFVHTMKDQHRATVIGEPTGGGALSVGIYQVENSPLYASMPTQVAISPVTGKAWDMAGVEPDVSVLSSEALMTTQGIV
>M3_macEug
QRLGALVEDAGHLLEAHYALPEVVGQASALLRARLVHGTYRTAVDFESLASQLTSDLQEVSGDHRVHVFHSPGELIPEELSPPQNVVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIGPQLIELVWEKLVNTEALVVDLRYNPGSYSTSVPLLCSYFFEAEPRKHLYTIFDRAASQATEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFAHAMKDLRRATVIGEPTAGGALSVGIYQVSNSPLYASMPTQVAISPVTGKAWDIAGVEPDVSVPAREALITTQGIV
>M3_sacHar
QRLGALVEGTGHLVEAHYALPEVVGQASAFLRATLAHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPVPEESSPPHKGVPSPEELTYLIEALFKTDVLPQLGYLRFDMMAEVETVRAIGPQLVELVWEKLVNTEALVVDLRYNPGSYSTTVPLLCSYFFEAEPRKHLYTVFDRATSQFTEVWTLPQVTGERYGSQKDLYILISHTSGSAAEAFAHIMKDLQRATVIGEPTAGGALSVGIYQVGDSPLYVSMPTQVALSPVTGKAWDMAGVEPDVSVLANEALITAQGIV
>M3_taeGut
KNMGVLLEGTGQLLEDHYAIPEVAAKASAMLSTKRAQGGYRSAIDSETLASQLTSDLQEASGDHRLHVFHSHVEPTPEEQLPNVIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLLQMVWNKLVDTDAMIIDMRYNTGGYSTAIPILCSYFFDPEPRKHLYTVFDRSTSRSTEVWTLPQLAGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVVGEPTVGGSLSVGIYRVGNSSLYASIPSQVVLSPVTGKVWSVSGVEPHITIQASEAMAAAQHIA
>M3_galGal
RKMGILLESTGQLLEAHYAIPEVAEKASVMLSTKRVQGGYRSAVDFETLASQLTSDLQEASGDHRLHVFHSHVEPTPEEQLPNMIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLVQMVWNKLVDTDAMIIDMRYNTGGYSTAVPILCSYFFEPEPRQHLYTVFDRSTSRSTEVWTLPKVTGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVIGEPTVGGSLSVGIYRVGNSSLYRSIPSQVVLSPVTGKVWSVSGAEPHITIQASEALAAAKHIA
>M3_anoCar
KGMGSLIERVGQLLEAHYAIPEMARRVSSMLNSKLAQGGYRTAVDFETLASQLTNDLQETSGDHQLHVFHSHVEPSLEEQSPFKTLTPEELNFIIEALFKVDVLPGNVGYLRFDMMAEFESVKTIEPQILHMVWEKLVETSAMIVDMRYNTGSYSTAVPMFCSYFFDAEPQQHLYTIIDRSTSQSTEVWTSSQVSGKRYGSTKDLYILISHASGSAAEAFTRSLKDLHRATVIGEPTVGGSLSASIYNIGSTPLYASIPSQIVLSPVSGKVWSLSGIQPHVTTQSNEALASAQNII
>M3_xenTro
PSVFALVEGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASQLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIPSAEELNYIIDALFKIEVLQGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSSGTDIWTLPEVVGERYGSTKDIYILTSHMTGSAAEVFTRSMKELNRATIIGEPTSGVSLSVGMYKVGESNLYVSIPNQVVISSVTGKVWSVSGVEPHVIAQASEAMNVAHHII
>M3_xenLae
PSIFPLVKGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASLLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIPSPEELNYIIDALFKIEVLPGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSTGKDIWTLPEVFGERYGSTKDIYILTSHMTGSAAEVFTRSLKDLNRATLIGEPTSGVSLSVGMYKVGDSNLYVTIPNQVVISSVTGKVWSVSGVEPHVIIQANEAMNIAHRII
>M3_petMar
AKMASLLELAGALVEGYYAMLSDGENATAEILLKYREGWYRSVVDYEALASQLTSDLHEIWGDHRLHAFYSDLQIERMDEDKTPSVPSPEELSVLIDTVFKVDILANNVGYLRFDMMTDAEVLKHVGPQLVEKVWNKISSTRSLVIDVRYNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDSRLYVFIPNQAGVSPSGGRTWSVAGVEPHVQTKASEALQSALRMV
 
>M3x_takRu
QGLRSLIGRTGELLEKHYAIQEVAQKVGEVLLSKWAEGLYRSVVDLESLASQLTADLQEASGDHRLHVFRCDVELESLHGVPKIAAVEEAGFVIDALFKSELLPRNVGYLRFDTMADIEAAKGAAPRLVKSVWNKLVDTDSLIIDMRYNAGGSSTAVPLWCSYFVDGEPLQHLYTVYDRTTKTRVEVMTLPEVSGQRYDPGKDVYILTSHMTGSAAEAFVRAMRDLNRVTIVGEPTAGGSLSSATYQIGESVLYASIPNQVVTSAATGKLWSISGVEPDVFAQARDALPVAQRII
>M3x_danRr
KNIQGLVQEAGDLLEKHYSVPEVAAKVSRLLQSKLTEGLYRSVVDYESLASQLTSDLQETSGDQRLHIFYCETEPETLHDTPKIPSPEEAGFIVEALFKVDVMSGNIGYLRFDMMEDIKVLQAINPEFLKVVWNKLVNTDMLIIDVRYNTGGYSTAIPLLCTYFFDAQPLTHIYTLFDRSTATVTKVTTLPDVLGQKYSSQKDVYILTSHITGSAAEAFTRTMKDLKRATVIGEPTIGGALSSGTYQIGNSILYASIPNQAVLNAVTGKPWSISGVEPHIVAQASDALIVAQKII
 
>M4_homSap
AKVPTVLQTAGKLVADNYASAELGAKMATKLSGLQSRYSRVTSEVALAEILGADLQMLSGDPHLKAAHIPENAKDRIPGIVPMQIPSPEVFEELIKFSFHTNVLEDNIGYLRFDMFGDGELLTQVSRLLVEHIWKKIMHTDAMIIDMRFNIGGPTSSIPILCSYFFDEGPPVLLDKIYSRPDDSVSELWTHAQVVGERYGSKKSMVILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTNLYLTIPTARSVGASDGSSWEGVGVTPHVVVPAEEALARAKEML
>M4_bosTau
AKVPTVLQTAGKLVADNYASPELGVKMAAELSGLQSRYARVTSEAALAELLQADLQVLSGDPHLKTAHIPEDAKDRIPGIVPMQIPSPEVFEDLIKFSFHTNVLEGNVGYLRFDMFGDCELLTQVSELLVEHVWKKIVHTDALIVDMRFNIGGPTSSISALCSYFFDEGPPILLDKIYNRPNNSVSELWTLSQLEGERYGSKKSMVILTSTLTAGAAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTDLYLTIPTARSVGAADGSSWEGVGVVPDVAVPAEAALTRAQEML
>M4_monDom
AKVPTILQTAGKLVADNYASLEVGSRVASKLAKLQTQYRQVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAKDRIPGIVPMQLPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDMRFNIGGPTSSISALCSYFFDEGQEVLLDQIYNRPNDSISEIWTQSQVAGERYGSKKSVIILTSSMTAGAAEEFVYVMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTARSVGSGDKPSWEGVGVAPHVEVPADQALSKAKEMF
>M4_macEug lower case: sacHar fix
SKVPTILQTAGKLVADNYASPEVGSRVAAKLARLQTQYRQVTSEGELADMLGADLQTLSGDSHLKTAHIPEDSKDRIPGIVPMQlpspeafedlikfsFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDMRFNIGGPTSSISALCSYFFDEGQKVLLDRIYNRPNDSIVEIWTQPHVTGERYGSKKSVIILTSSTTAGAAEEFVYIMQGLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTAQSVGSGDRPSWEGIGVTPHVEVPADQALSKAKEMF
>M4_sacHar
AKVPTILQTAGKLVADNYASPEVGSRVAAKLASLQIQYGKVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAKDRIPGIVPMQLPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLIQVSDLLVEHVWKKVMHTDGMIIDMRFNIGGPTSSISAMCSYFFDEGQGVLLDRIYNRPNDSISEIWTQPQVIGERYGSKKTVVILTSSMTAGAAEEFVYIMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTTRSVVSGDKSSWEGVGVVPHMEVPADQALSKAKEMF
>M4_ornAna
SKVPTVLRTAAKLVADNYAFRETGAGVAAQMGGLQARCGRVTSEGALAEVLGAHLRALSGDPHLQMVYIPEDAKDRIPGVVPMQIPSAETFEDLIKFSFHTSVMEGNIGYLRFDMFGDCELLTQVSELMVEHVWKKIVHTDGLIIDMRNIGGPTSSISALCSYFFDEDHPVLLDKIYNRPNDSISEIWTHSHIAGERYGSRKSVVILTSNMTAGAAEEFVSIMKRLGRALVVGEVTGGGCHPPQTYHVDDTHLYITIPTSRSVGSEDGSSWEGVGVTPHLVVPADVALSRAKDLF
>M4_taeGut
AQVPQILQTVGKLVADNYAFVNTGTVIASNLTKNIHKDNYKRINTEEDLAGKVTAILQALSDDKHLKLLYIPEHAKDSIPGIMPKQIPPPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDSELLTQLSDLMIEHVWKKIFHTDALIIDLRYNIGGSTTPIAILCSYFFDEGHPVLLDRVYDRPSDSVKEIWTQPQLKGERYGSQKGLVILTSAVTAGAAEEFVYIMKRLSRALIIGEQTSGGCHSPQTYQVDETNFYVVIPTSRSVTSADSTSWEGKGVSPHIETPAETALIKAKEML
>M4_galGal
TQVPQIVQTVGKLVAENYAFVDIGTDIASNLTKSVNKENYKRINSEKELARKLTAILQALSDDEHLKILYIPEHAKDSIPGILPKQIPSPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDCELLTQVSDLLVEHVWKKIVHTDALIIDMRYNIGGYTNSIPILCSYFFDEGHQVLLDKVYDRPSDSVKEIWTQPQLRGERYGSQKGLIILTSAVTAGAAEEFVFIMKRLGRALIIGEQTSGGSHSPQTYQVDDTNFYIIIPTARSVISAESASWEGKGVPPHMETPAVTALIKAKEVL
>M4_anoCar
TKLPSVLNTIGKLVADNYAFADIGATVAAKFADYAKKGTYRKINSEIELSGKLAADLKALSGDRHLMISHIPERSKGRILGLVPMQQIPPPEILEDLIKFSLHTNVFENNIGYLRFDMFGDCELMSQVSELLVQHVWNKIVNTDALIIDMRYNVGGPACSVPLLCSYFFDEGHPILLDKVYNRPNDTTSNIWTVSKLAGKRYGLNKGLIILTSSVTSGAAEEFAHIMKRLGRAFIIGQKTSGGCHPPQTFHVDGTNLYITTPVSRSVFSVNDSWEGVGVSPHLDVSTDVALIKAKEML
>M4_xenLae
TKIPTVIQTAAKLVADNYAFADTGANVASKFIALVDKIDYKMIKSEVELAEKINDDLQSLSKDFHLKAVYIPENSKDRIPGVVPMQIPSPELFEELIKFSFHTDVFEKNIGYIRFDMFADSDLLNQVSDLLVEHVWKKVVDQDALIIDMRFNIGGPTSSIPIFCSYFFDEGTPVLLDKIYSRTSNAMTDIWTLPDLVGKTFGSKKPLIILTSSLTEGAAEEFVYIMKRLGRAYVVGEVTSGGCHPPQTYHVDDTHLYLTIPTSRSASAEPGESWEGKGVLPDLEISSETALLKAKEIL
>M4_xenTro
TKIPSVIQTAGKLVADNYAFADTGADVASKLIALVDKINYKMIKSEVELAEKLNYDLQSLSKDVHLKAVYIPENSKDRIPGVVPMQIPSPEMFEDLIKFSFHTDVFEKNLGYIRFDMFADSDLLNQVSDLLVEHVWKKVVNQDALIIDMRFNIGGPTSSIPTFCSYFFDEGTPVLLDKIYSRTTNAITDVWTLPHLVGNAFGSKKPVIILTSSLTEGAAEEFVYIMKRLGRAYVIGEVTSGGCHPPQTYHVDDTHLYLTIPTSRSASAKPGESWEGKGVLPDLEITSETALMKAKEIL
>M4_tetNig
AQIPAIIEGTAALVANNYAFEATGADVAKELRELQANGQYSSVVSKESLEAALSADLQRLSGDKSLKTTPNTPVLPPMDYTPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDLRNNVGGPTTAIAGFCSYFFDADKQNRVGQAVRQASGTTTELLTLSELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQTFRVGETDVFLLIPTVHSDTGAGPAWEGAGIAPHIPASAEAALGTARAIL 
>M4_takRub
AQIPAIIEGAATLIAKNYAFEATGADVATKLRELLAKGQYNSVVSSESLEVALSADLQRLSGDKSLKATQNAPVLPPMDYSPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDLRNNVGGPTTAIAGFCSYFFDADKLIVLDKLHDRPSGTTTELLTLPELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQVFSVGEIGIFLSIPTVHSDTAAGPAWEGTGITPHIPVSAEAALGTAKGIL 
>M4_gasAcu
NRVPAIIEGSATLIADNYAFEDIGAAVAEKLKGLLANGEYSKVVSKDSLEMKLSADLRTLSGDKSLKTTSNVPALPPMNYSPEMYIELIKVSFHTDVFEDNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDAMIVDLRNNIGGPTTAIAGFCSYFFDSDKQIVLDRLYDRPSGTTTELRTLPELTGTRYGSKKSLVMLTSRATAGAAEEFVYIMKKLGRAMIVGETTAGTSHPPKTFRVGETDIFLSIPTVHSDTAAGPAWEGAGVAPHIPVPADAALETAKGIF
>M4_oryLat
LQVPAIIEESATLVANNYAFESTAADVAEKLKGHLANGDYNMVVSKESLEAKLSADLQSLSGDKSLTVSSNTGAPPPMEYTPEMYIELIKISFHTDVFENNIGYLRFDMFGDFEEVKAIAQVIVEHVWNKVLHTDAMIIDLRNNVGGPTTAIAGFCSYFFDGDKQILLDKLYDRSTGTTTDLLTLGELTGERYGSKKSLIILASRATAGAAEEFVYIMKRLGRAMIVGETTAGASHPPKVFQVGESDIFLSIPTVHSDTSAGPGWEGAGVAPHIPVAAGAALETAKAIL 
>M4_danRer
AEIPALAQAAATLIADNYAFPSIGEHVAEKLEAVVAGGEYNLISTKEDLEERLSEDLLKLSEDKCLKTTSNIPALPPMNPTPEMFIALIKSSFQTDVFENNIGYLRFDMFGDFEHVATIAQIIVEHVWNKVVDTDALIIDLRNNIGGHASSIAGFCSYFFDADKQIVLDHIYDRPSNTTRDLQTLEQLTGRRYGSKKSVVILTSGVTAGAAEEFVFIMKRLGRAMIIGETTHGGCQPPETFAVGESDIFLSIPISHSTAQGPSWEGAGIAPHIPVPAGAALDTAKGML 
>M4_petMar
ADAPSILRTVGKLVADGYSRAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHLKAVCVPEHATDRMPGIVPMQMPPTESFEDLIKFSFITDVLEGNIGYLRFDLFSDLEALEHVAHLLVEHVWKKICDTEILIIDLR 
 
>Mn_braFlo RALNDQSL SKAIILD LNEL insertions omitted
VDWLDVVMGIGDVMADHYLDQDLLQRWNRTLVHRFQSWSQDDMSDSLRMEEGLTSELRNITGDETIKVWDFGVYENTTQEPVPREFYNFSTFVDNFKKNINVTMLEGNVGYVSIRSMSHIVDIILPDPEMTEFFLSKMAASKAIILDLRYNLGGDREGVVHWASFFFNATPSVPLSDVYYRDGVNQYWTLLEVPGGIRFPDMPLYLLTSNRTSREAEEFAYAMQVVNRTTIIGETTAGEEFTGMWFPIDQTDVHLLTRTNVVRNPITQDSWSGKGVTPDIIVPSEKALTVALRKI
</pre>
 
=== RBP3 (IRBP) sequences from human to amphioxus ===
<pre>
<pre>
>RPB3_homSap human
>RPB3_homSap human
Line 153: Line 539:
HVPKLANVTQEELLILLQQMIKYQVLEGNVGYLRVDYIPGQEVVEKVGEFLVNNIWKKLMGTSSLVLDLQHSSGGEISGIPFVISYLHQGDILLHVDTVY
HVPKLANVTQEELLILLQQMIKYQVLEGNVGYLRVDYIPGQEVVEKVGEFLVNNIWKKLMGTSSLVLDLQHSSGGEISGIPFVISYLHQGDILLHVDTVY
DRPSNTTTEIWTLPQVLGERYGGEKDMVVLTSHRTVGVAEDIAYILKKLRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSG
DRPSNTTTEIWTLPQVLGERYGGEKDMVVLTSHRTVGVAEDIAYILKKLRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSG
VLPCVGIPAEQALGKALAILTLRRARPGAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATMGEA
VLPCVGIPAEQALGKALAILTLRRARPGAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATMGSEASEEEDATPAANS
EEEDATPAANSLPEDESQRQALVDSVFQVSVLPGNVGYLRFDEFADSSVLGTLAPYVIRQVWEPLQDTNHLIMDLRYNPGGPSSAVPLLLSYFQDPAAGP
LPEDESQRQALVDSVFQVSVLPGNVGYLRFDEFADSSVLGTLAPYVIRQVWEPLQDTNHLIMDLRYNPGGPSSAVPLLLSYFQDPAAGP
IRLFTTYDRQTNQTQEHLSRAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGNLVLTVPILTFIDNNG
IRLFTTYDRQTNQTQEHLSRAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGNLVLTVPILTFIDNNG
ECWLGGGVVPDAIVLAEEALDKAKEVLEFHQRLGALVEGTGHLLEAHYALPEVVGQASALLKAKLEHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFH
ECWLGGGVVPDAIVLAEEALDKAKEVLEFHQRLGALVEGTGHLLEAHYALPEVVGQASALLKAKLEHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFH
Line 164: Line 550:
1 FNIGGPTSSISALCSYFFDEGQEVLLDQIYNRPNDSISEIWTQSQVA 1
1 FNIGGPTSSISALCSYFFDEGQEVLLDQIYNRPNDSISEIWTQSQVA 1
2 GERYGSKKSVIILTSSMTAGAAEEFVYVMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTARSVGSGDKPSWEGVGVAPHVEVPADQALSKAKEMFNHHLQRAK* 0
2 GERYGSKKSVIILTSSMTAGAAEEFVYVMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTARSVGSGDKPSWEGVGVAPHVEVPADQALSKAKEMFNHHLQRAK* 0
>RBP3_sacHar Sarcophilus harrisii
0 MTSQCLLLFSALLFSLAHGEEIFQPTLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLANVLTAGVQGSLNDPRLVISYEPSTSEAPQ
HDPKFANATQEELLALFQKIIKYQVLEDNVGYLRVDYIPGRDMIEEVGEFLVNDIWKKVMETSSLVLDLQHSR
GGEVSGIPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTLPQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKKMRRAIVVGEQTQGGSLDLRKLRIGQSDFFITVPVARSLSPLGGGSQTWEGSG
VVPCVGIPAEQALEKALAILTLRRARPGAIQRLMEILQKYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAMLQAVSEDPRLLVRVLRPEEATVEAEPGEESATPASVSLPESDAERQALI
DSVFQVSVLPGNVGYLRFDEFADNSVLGTLAPYVLRQVWEPLQDTDHLIMDLRYNPGGPSSAVPLLLSYFQDPSAGPVRLFATYDRQTNQ
TQEYRSRAELLGKPYGAERGVYLLTSYHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGSLVLTVPTLTFIDNHGECWLGGGVVPDAIVLAEEALDKAKEVLEFHQRL
GALVEGTGHLVEAHYALPEVVGQASAFLRATLAHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPVPEESSPPHKGVPSPEELTYLIEALFKTDVLP
QLGYLRFDMMAEVETVRAIGPQLVELVWEKLVNTEALVVDLRYNPGSYSTTVPLLCSYFFEAEPRKHLYTVFDRATSQFTEVWTLPQVTGERYGSQKDLYILISHTSGSA
AEAFAHIMKDLQRATVIGEPTAGGALSVGIYQVGDSPLYVSMPTQVALSPVTGKAWDMAGVEPDVSVLANEALITAQGIVALRAKVPTILQTAGKLVADNYA
SPEVGSRVAAKLASLQIQYGKVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAKDRIPGIVPMQ 0
0 LPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLIQVSDLLVEHVWKKVMHTDGMIIDMR 2
1 FNIGGPTSSISAMCSYFFDEGQGVLLDRIYNRPNDSISEIWTQPQVI 1
2 GERYGSKKTVVILTSSMTAGAAEEFVYIMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTTRSVVSGDKSSWEGVGVVPHMEVPADQALSKAKEMFTHQLQKTK* 0
>RBP3_macEug wallaby 3 alleles to FJ603206 Macropus eugenii frag exon 2 lower case: sacHar fix
0 MTSQCLLLFSALLLSLAHAEQIFQPSLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLASVLTAGVQGSLNDPRLVISYEPSPAEAPQQSPKLTSLTQEELLTLLQQM
IKYQVLDGNVGYLRVDYIPGQEVVEKVGEFLVNDIWKKLMGTSSLVLDLQHSTEGEVSGIPFVISYLHEGDILLHVDTVYDRPSNTTTEIWTLPQVLGERYSGEKDLVILTSHRTVGVAE
DIAYILKKMRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALEKALAILTLRRARPAAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYS
SVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATAGAESREEAATAAPVPLPDGESQRQALVNSVFQVSVLPGNVGYLRFDEFADSSVLGALAPYVLQQVWEPLQDTDHLIMDLRYNP
GGPSSAVPLLLSYFQDPAAGPVRLFATYDRQTNQTREYRSQAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGNLMHTRTFSLLQPPDGSLVLTVPILTFIDNH
GECWLGGGVVPDAIVLAEEALDKAKEVIEFHQRLGALVEDAGHLLEAHYALPEVVGQASALLRARLVHGTYRTAVDFESLASQLTSDLQEVSGDHRVHVFHSPGELIPEELSPPQNVVPS
PEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIGPQLIELVWEKLVNTEALVVDLRYNPGSYSTSVPLLCSYFFEAEPRKHLYTIFDRAASQATEVWTLPQVAGERYGSQKDLYI
LISHTSGSAAEAFAHAMKDLRRATVIGEPTAGGALSVGIYQVSNSPLYASMPTQVAISPVTGKAWDIAGVEPDVSVPAREALITTQGIVTLRSKVPTILQTAGKLVADNYASPEVGSRVA
AKLARLQTQYRQVTSEGELADMLGADLQTLSGDSHLKTAHIPEDSKDRIPGIVPMQ 0
0 lpspeafedlikfsFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDMR 2
1 FNIGGPTSSISALCSYFFDEGQKVLLDRIYNRPNDSIVEIWTQPHVT 1
2 GERYGSKKSVIILTSSTTAGAAEEFVYIMQGLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTAQSVGSGDRPSWEGIGVTPHVEVPADQALSKAKEMFIHHLQRAD* 0


>RBP3_ornAna platypus genome rife with frameshifts, dels, misassembly frag
>RBP3_ornAna platypus genome rife with frameshifts, dels, misassembly frag
Line 170: Line 585:
DRPSNATRQLWTLPRVLGARYAADKDVVVLTSRLTAGVAEDVAYILQQMRRAIVVGERTAGGPLVFRKLRVGLSDFFITVPVACSLGPLGGGGRSWEGSG
DRPSNATRQLWTLPRVLGARYAADKDVVVLTSRLTAGVAEDVAYILQQMRRAIVVGERTAGGPLVFRKLRVGLSDFFITVPVACSLGPLGGGGRSWEGSG
VLPCVAVPADRALDEALDILALRGAVPGAVAHLADLLRDYYALVDRVPALLRHLAALDLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPEEAERGPP
VLPCVAVPADRALDEALDILALRGAVPGAVAHLADLLRDYYALVDRVPALLRHLAALDLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPEEAERGPP
RKEEEQKEEEEEDQPSPGASILPGDGSSREAPLFRVSVLPGNVGYLCFDEFPEASALERLGPLLGRRVWEPLEATDHLMVDLRNNPGGPSSAVPLLLSYF
RKEEEQKEEEEEDQPSPGASILPGDGSSLFRVSVLPGNVGYLCFDEFPEASALERLGPLLGRRVWEPLEATDHLMVDLRNNPGGPSSAVPLLLSYF
QDPAAGPIRLFTTYNRPADVTREYASRAGALEKPYGARRGVYLLTSHRTATAAEEFAYLMQALGRATLVGEITAGRLLHSRTFPLLRPPWEGLVLTVPFL
QDPAAGPIRLFTTYNRPADVTREYASRAGALEKPYGARRGVYLLTSHRTATAAEEFAYLMQALGRATLVGEITAGRLLHSRTFPLLRPPWEGLVLTVPFL
TLFDPHGEGWLGGGVVPDAIVLAEEALEKAGEVLAFHQTLEALVETTGHLLEAHYCFPAGARRAGAQPWPVAGVEPDVMAQAAEALAVAQGIAALRSKVP
TLFDPHGEGWLGGGVVPDAIVLAEEALEKAGEVLAFHQTLEALVETTGHLLEAHYCFPAGARRAGAQPWPVAGVEPDVMAQAAEALAVAQGIAALRSKVP
Line 221: Line 636:
QHLYTIIDRSTSQSTEVWTSSQVSGKRYGSTKDLYILISHASGSAAEAFTRSLKDLHRATVIGEPTVGGSLSASIYNIGSTPLYASIPSQIVLSPVSGKV
QHLYTIIDRSTSQSTEVWTSSQVSGKRYGSTKDLYILISHASGSAAEAFTRSLKDLHRATVIGEPTVGGSLSASIYNIGSTPLYASIPSQIVLSPVSGKV
WSLSGIQPHVTTQSNEALASAQNIILFRTKLPSVLNTIGKLVADNYAFADIGATVAAKFADYAKKGTYRKINSEIELSGKLAADLKALSGDRHLMISHIP
WSLSGIQPHVTTQSNEALASAQNIILFRTKLPSVLNTIGKLVADNYAFADIGATVAAKFADYAKKGTYRKINSEIELSGKLAADLKALSGDRHLMISHIP
ERSKGRILGLVPMQ 0
ERSKGRILGLVPM 0
0 QIPPPEILEDLIKFSLHTNVFENNIGYLRFDMFGDCELMSQVSELLVQHVWNKIVNTDALIIDMR 2
0 QIPPPEILEDLIKFSLHTNVFENNIGYLRFDMFGDCELMSQVSELLVQHVWNKIVNTDALIIDMR 2
1 YNVGGPACSVPLLCSYFFDEGHPILLDKVYNRPNDTTSNIWTVSKLA 1
1 YNVGGPACSVPLLCSYFFDEGHPILLDKVYNRPNDTTSNIWTVSKLA 1
Line 337: Line 752:
2  * 0
2  * 0


>RBP3_petMar lamprey exon3/4 fused, exon4 run-on, fixed genomic frameshift; four domains: 34-312,327-615,625-914,916-1217
>RBP3_petMar lamprey fragment exon3/4 missing, fixed genomic frameshift; four domains: 34-312,327-615,625-914,916-1217
0 MAGSREQRTAFSTRLLLLLLLPLATCPSQAPYKFDTAVVLHLAKVLLDNYCIPENLVGMDEAIQRAVDNGELLGVSDPESAASALTEGIQAALNDPRIAV
0 MAGSREQRTAFSTRLLLLLLLPLATCPSQAPYKFDTAVVLHLAKVLLDNYCIPENLVGMDEAIQRAVDNGELLGVSDPESAASALTEGIQAALNDPRIAVSYVPDVDDDGDREEGDAEGW
SYVAPPHTFEELLATIPQKTSFAVLDGNVGYLRADEIISEATIKKLGPVIVQRIWNRLVDTDTFVLDLRYNSHGDITGLPYLVSCFCEPRPVVHLDTVYY
DAGEQHRPTTFEELLATIPQKTSFAVLDGNVGYLRADEIISEATIKKLGPVIVQRIWNRLVDTDTFVLDLRYNSHGDITGLPYLVSCFCEPRPVVHLDTVYYRPTNESKEIWSLPDLQGA
RPTNESKEIWSLPDLQGARFAKHKDVFVLVSANTEGVAENVAYVLKHLHRATVIGEQTAGGSLEVERFRLGDSRFFVTVPTARSEPADRSWGVFPCVSAP
RFAKHKDVFVLVSANTEGVAENVAYVLKHLHRATVIGEQTAGGSLEVERFRLGDSRFFVTVPTARSQSPLTGRSWELTGVFPCVSAPSERALDKALEILNARGVARKAVEAAGELLLSSY
SERALDKALEILNARGVARKAVEAAGELLLSSYTFVERASAIADHLSWSEYGSVVSVEDLTSKLTQDLQSVAEDPRLVVSNREPEWVGAADPPGPPAPLP
TFVERASAIADHLSWSEYGSVVSVEDLTSKLTQDLQSVAEDPRLVVSNREPEWPPLAQPIPPGPPAPLPDDEQMLEAIVDSAFKVEVLEGNIGYLRFDEFGDASAVMKLRKQLVSKVWER
DDEQMLEAIVDSAFKVEVLEGNIGYLRFDEFGDASAVMKLRKQLVSKVWERIHPTDDVIIDLRYNLGGSSTAIPIVLSYFQDVAPVHFYTVYDRLRNVTA
IHPTDDVIIDLRYNLGGSSTAIPIVLSYFQDASPPVHFYTVYDRLRNVTAEFHTVSNLTSQLYGSKKGVYLLTSQHTATAAEEFTYLMQSLNRATIVGEITSGRLAHSLAFRLSDTGLYMT
EFHTVSNLTSQLYGSKKGVYLLTSQHTATAAEEFTYLMQSLNRATIVGEITSGRLAHSLAFRLSDTGLYMTVPIVNFIDNNDEYWLGGGVVPDAIVLAENALDAAKEIIEFHAKMASL
VPIVNFIDNNDEYWLGGGVVPDAIVLAENALDAAKEIIEFHAKMASLLELAGALVEGYYAMLSDGENATAEILLKYREGWYRSVVDYEALASQLTSDLHEIWGDHRLHAFYSDLQIERMD
LELAGALVEGYYAMLSDGENATAEILLKYREGWYRSVVDYEALASQLTSDLHEIWGDHRLHAFYSDLQIERMDEDKTPSVPSPEELSVLIDTVFKVDILANNVGYLRFDMMTDAEVLKHV
EDKTPSVPSPEELSVLIDTVFKVDILANNVGYLRFDMMTDAEVLKHVGPQLVEKVWNKISSTRSLVIDVRYNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVLGQR
GPQLVEKVWNKISSTRSLVIDVRYNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTG
YGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDSRLYVFIPNQAGVSPSGGRTWSVAGVEPHVQTKASEALQSALRMVALRADAPSILRTVGKLVADGYS
TYRIGDSRLYVFIPNQAGVSPSGGRTWSVAGVEPHVQTKASEALQSALRMVALRADAPSILRTVGKLVADGYSRAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHL
RAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHLKAVCVPEHATDRMPGIVPMQ 0
KAVCVPEHATDRMPGIVPMQ 0
0 MPPTESFEDLIKFSFITDVLEGNIGYLRFDLFSDLEALEHVAHLLVEHVWKKICDTEILIIDLR 2
0 MPPTESFEDLIKFSFITDVLEGNIGYLRFDLFSDLEALEHVAHLLVEHVWKKICDTEILIIDLR 2
1 YNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVL 1^2 GQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDSRLYVFIPNQAGVSPSGGRTWSVAGVEPHVQTKASEALQSALRMVALRADAPSILRTVGKLVADGYSRAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHLKAVCVPEHATDRMPGIVPMQVNVVRTRI* 0


>RBP3_braFlo Branchiostoma floridae Region: 9 exons 1 domain: 83-381 ClpP/crotonase e-38 419-630; misfused to PAPS sulfotransferase
>RBP3_braFlo Branchiostoma floridae Region: 9 exons 1 domain: 83-381 ClpP/crotonase e-38 419-630; misfused to PAPS sulfotransferase
Line 363: Line 776:
</pre>
</pre>


=== RBP3 proteins parsed into constituent modules ===
'''See also:''' [[Opsin_evolution|Curated Sequences]] | [[Opsin_evolution:_RPE65|RPE65]] | [[Opsin_evolution:_transducins|Transducins]] | [[USH2A_SNPs|Usher: USH2A]] | [[CDH23_SNPs|Usher: CDH23]] | [[LOXHD1_SNPs|LOXHD1]] | [[Opsin_evolution:_update_blog|Update Blog]]
<pre>
>M1_homSap 
GPTHPALTSLSEEELLAWLQRGLRHEVLEGNVGYLRVDSVPGQEVLSMMGEFLVAHVWGNLMGTSALVLDLRHCTGGQVSGIPYIISYLHPGNTILHVDTIYNRPSNTTTEIWTLPQVLG
ERYGADKDVVVLTSSQTRGVAEDIAHILKQMRRAIVVGERTGGGALDLRKLRIGESDFFFTVPVSRSLGPLGGGSQTWEGSGVLPCVGTPAEQALEKALAIL
>M2_homSap
TLRSALPGVVHCLQ
EVLKDYYTLVDRVPTLLQHLASMDFSTVVSEEDLVTKLNAGLQAASEDPRLLVRAIGPTETPSWPAPDAAAEDSPGVAPELPEDEAIRQALVDSVFQVSVLPGNVGYLRFDSFADA
SVLGVLAPYVLRQVWEPLQDTEHLIMDLRHNPGGPSSAVPLLLSYFQGPEAGPVHLFTTYDRRTNITQEHFSHMELPGPRYSTQRGVYLLTSHRTATAAEEFAFLMQSLGWATLVG
EITAGNLLHTRTVPLLDTPEGSLALTVPVLTFIDNHGEAWLGGGVVPDAIVLAEEALDKAQEVL
>M3_homSap
EFHQSLGALVEGTGHLLEAHYARPEVVGQTSALLRAKLAQGAYRTAVDLESL
ASQLTADLQEVSGDHRLLVFHSPGELVVEEAPPPPPAVPSPEELTYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVRLVWQQLVDTAALVIDLRYNPGSYSTAIPLLCS
YFFEAEPRQHLYSVFDRATSKVTEVWTLPQVAGQRYGSHKDLYILMSHTSGSAAEAFAHTMQDLQRATVIGEPTAGGALSVGIYQVGSSPLYASMPTQMAMSATTGKAWDLAGVEP
DITVPMSEALSIAQDIV
>M4_homSap
ALRAKVPTVLQTAGKLVADNYASAELGAKMATKLSGLQSRYSRVTSEVALAEILGADLQMLSGDPHLKAAHIPENAKDRIPGIVPMQ
IPSPEVFEELIKFSFHTNVLEDNIGYLRFDMFGDGELLTQVSRLLVEHIWKKIMHTDAMIIDMR
FNIGGPTSSIPILCSYFFDEGPPVLLDKIYSRPDDSVSELWTHAQVV
GERYGSKKSMVILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTNLYLTIPTARSVGASDGSSWEGVGVTPHVVVPAEEALARAKEML 
 
>M1_bosTau 
LFQPSLVLEMAQVLLDNYCFPENLMGMQGAIEQAIKSQEILSISDPQTLAHVLTAGVQSSLNDPRLVISYEPSTLEAPP
RAPAVTNLTLEEIIAGLQDGLRHEILEGNVGYLRVDDIPGQEVMSKLRSFLVANVWRKLVNTSALVLDLRHCTGGHVSGIPYVISYLHPGSTVSHVDTVY
DRPSNTTTEIWTLPEALGEKYSADKDVVVLTSSRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRVGQSDFFLTVPVSRSLGPLGEGSQTWEGSG
VLPCVGTPAEQALEKALAVL
>M2_bosTau
LRRALPGVIQRLQEALREYYTLVDRVPALLSHLAAMDLSSVVSEDDLVTKLNAGLQAVSEDPRLQVQVVRPKEASSGPE
EEAEEPPEAVPEVPEDEAVRRALVDSVFQVSVLPGNVGYLRFDSFADASVLEVLGPYILHQVWEPLQDTEHLIMDLRQNPGGPSSAVPLLLSYFQSPDAS
PVRLFSTYDRRTNITREHFSQTELLGRPYGTQRGVYLLTSHRTATAAEELAFLMQSLGWATLVGEITAGSLLHTHTVSLLETPEGGLALTVPVLTFIDNH
GECWLGGGVVPDAIVLAEEALDRAQEVL
>M3_bosTau
EFHRSLGELVEGTGRLLEAHYARPEVVGQMGALLRAKLAQGAYRTAVDLESLASQLTADLQEMSGDHRLLVF
HSPGEMVAEEAPPPPPVVPSPEELSYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVQLVWQKLVDTAALVVDLRYNPGSYSTAVPLLCSYFFE
AEPRRHLYSVFDRATSRVTEVWTLPHVTGQRYGSHKDLYVLVSHTSGSAAEAFAHTMQDLQRATIIGEPTAGGALSVGIYQVGSSALYASMPTQMAMSAS
TGEAWDLAGVEPDITVPMSVALSTARDI
>M4_bosTau
LRAKVPTVLQTAGKLVADNYASPELGVKMAAELSGLQSRYARVTSEAALAELLQADLQVLSGDPHLKTAH
IPEDAKDRIPGIVPMQIPSPEVFEDLIKFSFHTNVLEGNVGYLRFDMFGDCELLTQVSELLVEHVWKKIVHTDALIVDMRFNIGGPTSSISALCSYFFDE
GPPILLDKIYNRPNNSVSELWTLSQLEGERYGSKKSMVILTSTLTAGAAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTDLYLTIPTARSVGAAD
GSSWEGVGVVPDVAVPAEAALTRAQEML
 
>M1_monDom
IFQPSLVRDMAKILLDNYCFPENLMGMQEVIEQAIKSGEILDISDPQMLASVLTAGVQGALNDPRLVISFEPSIPETPQ
HVPKLANVTQEELLILLQQMIKYQVLEGNVGYLRVDYIPGQEVVEKVGEFLVNNIWKKLMGTSSLVLDLQHSSGGEISGIPFVISYLHQGDILLHVDTVY
DRPSNTTTEIWTLPQVLGERYGGEKDMVVLTSHRTVGVAEDIAYILKKLRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSG
VLPCVGIPAEQALGKALAIL
>M2_monDom
LRRARPGAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATMGEA
EEEDATPAANSLPEDESQRQALVDSVFQVSVLPGNVGYLRFDEFADSSVLGTLAPYVIRQVWEPLQDTNHLIMDLRYNPGGPSSAVPLLLSYFQDPAAGP
IRLFTTYDRQTNQTQEHLSRAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGNLVLTVPILTFIDNNG
ECWLGGGVVPDAIVLAEEALDKAKEVL
>M3_monDom
EFHQRLGALVEGTGHLLEAHYALPEVVGQASALLKAKLEHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFH
SPGEPVSEELTPPQKGVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIAPQLVELVWEKLVHTEALVVDLRYNPGGYSTAVPLLCSYFFEA
EPRRHLYTIFDRAASQLTEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFVHTMKDQHRATVIGEPTGGGALSVGIYQVENSPLYASMPTQVAISPVT
GKAWDMAGVEPDVSVLSSEALMTTQGI
>M4_monDom
LRAKVPTILQTAGKLVADNYASLEVGSRVASKLAKLQTQYRQVTSEGELADMLGADLQTLSGDRHLKTAHI
PEDAKDRIPGIVPMQLPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDMR
FNIGGPTSSISALCSYFFDEGQEVLLDQIYNRPNDSISEIWTQSQVA
GERYGSKKSVIILTSSMTAGAAEEFVYVMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTARSVGSGDKPSWEGVGVAPHVEVPADQALSKAKEM 
 
>M1_ornAna genome rife with frameshifts, dels, misassembly
SQPSMVLDVAKILLDNYCYPENLMGMQEAIEEAIQRGEILDIADPKRLASVLTAGVQGSLNDPRLVISYEPAPVAVSQ
QPPEPASLPAEQPLERLRPAVGSEVLEGNVGYLRVDRLPGREEIERVGAVLGRDIWEKLLGTSALVLDLRHSTGGHVSGIPFFISYFYPEGPALHVDTVY
DRPSNATRQLWTLPRVLGARYAADKDVVVLTSRLTAGVAEDVAYILQQMRRAIVVGERTAGGPLVFRKLRVGLSDFFITVPVACSLGPLGGGGRSWEGSG
VLPCVAVPADRALDEALDIL
>M2_ornAna 
LRGAVPGAVAHLADLLRDYYALVDRVPALLRHLAALDLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPEEAERGPPRKEEEQKEEE
EEDQPSPGASILPGDGSSREAPLFRVSVLPGNVGYLCFDEFPEASALERLGPLLGRRVWEPLEATDHLMVDLRNNPGGPSSAVPLLLSYFQDPAAGPIRLFTTYNRPADVTREYASRAGA
LEKPYGARRGVYLLTSHRTATAAEEFAYLMQALGRATLVGEITAGRLLHSRTFPLLRPPWEGLVLTVPFLTLFDPHGEGWLGGGVVPDAIVLAEEALEKAGEVL
>M3_ornAna frag
FHQTLEALVETTGHLLEAHYCFPAGARRAGAQPWPVAGVEPDVMAQAAEALAVAQGIAA
>M4_ornAna
LRSKVPTVLRTAAKLVADNYAFRETGAGVAAQMGGLQARCGRVTSEGALAEVLGAHLRALSGDPHLQMVYIPEDAKDRIPGVVPMQ
IPSAETFEDLIKFSFHTSVMEGNIGYLRFDMFGDCELLTQVSELMVEHVWKKIVHTDGLIIDMR
NIGGPTSSISALCSYFFDEDHPVLLDKIYNRPNDSISEIWTHSHIA
GERYGSRKSVVILTSNMTAGAAEEFVSIMKRLGRALVVGEVTGGGCHPPQTYHVDDTHLYITIPTSRSVGSEDGSSWEGVGVTPHLVVPADVALSRAKDL 
 
>M1_taeGut Taeniopygia guttata
IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPLPHSGPK
QEAEGSPTREQLLSLIEHVIMYDKLEGNVGYLRIDYIIGEEVVQKVGAFLVDKVWKTLIETSALVIDLRHSTGGQISGLPFIISYLHEQDKILHVETVYN
RPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITVGEKTAGGSLDIQKLRIGPSNFYMMVPVSRSVSPLSGGGQSWEVSGV
MPCVATEAEQALQKSLDIL
>M2_taeGut 
VRRAVPGTISHLKNILKDYYSLVERVPALLRRLTTSDFSSVQSSEDLATKLNTELQALSDDPRLMVRVMMPGEAADSPAE
KPVGMAADLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYLVHKVWEPLQNTENLIMDLRYNLGGPSSSAVPVLLSYFQDPAAGPVH
LFTTYDRRTNHTQEHNSQAELLGQSYGAKRGVYLLTSHHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTRTFPLLQPGPGITRGLTITVPVITFIDNH
GESWMGGGVVPDAIVLAEDALEKAEEVLA
>M3_taeGut
FHKNMGVLLEGTGQLLEDHYAIPEVAAKASAMLSTKRAQGGYRSAIDSETLASQLTSDLQEASGDHRLHVF
HSHVEPTPEEQLPNVIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLLQMVWNKLVDTDAMIIDMRYNTGGYSTAIPILCSYFFDPE
PRKHLYTVFDRSTSRSTEVWTLPQLAGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVVGEPTVGGSLSVGIYRVGNSSLYASIPSQVVLSPVTG
KVWSVSGVEPHITIQASEAMAAAQHI
>M4_taeGut
ANLRAQVPQILQTVGKLVADNYAFVNTGTVIASNLTKNIHKDNYKRINTEEDLAGKVTAILQALSDDKHLKLLY
IPEHAKDSIPGIMPK
QIPPPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDSELLTQLSDLMIEHVWKKIFHTDALIIDLR
YNIGGSTTPIAILCSYFFDEGHPVLLDRVYDRPSDSVKEIWTQPQLK
GERYGSQKGLVILTSAVTAGAAEEFVYIMKRLSRALIIGEQTSGGCHSPQTYQVDETNFYVVIPTSRSVTSADSTSWEGKGVSPHIETPAETALIKAKEM 
 
>M1_galGal 
IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPSLHAAPKQ
EAETYPTREQLLSLIEHVVIYDKLEGNVGYLRIDYIIGQEVVEKVGAFLVDKVWKTLINTSALVIDLRYSTGGQISGIPFIISYLHEADKMLHVETVYNR
PSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITLGEKTAGGSLDIQKLRIGPSNFYMMVPVSRSVSPLSGGGQSWEVSGVM
PCVASEAEQALKKSLDIL
>M2_galGal 
AVRRAVPGTLSRLTDILKDYYSLVERVPVLLRHLTTSDFSSVQSAEDLATKLNTEMQTLSEDPRLLVRTMMPGEAAAPPAEM
PIAMAANLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYIVKKVWEPLQNTENLIMDLRYNPGGPSSSAVPMLISYFQDPTAGPVHL
FTTYDRRTNHTQEHNSQAELLAQPYGAQRGIYVLTSRHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTCTFPLVQPEQGITRGLTITVPVITFIDNHG
ESWMGGGVVPDAIVLAEDALEKAEEVL
>M3_galGal 
LLESTGQLLEAHYAIPEVAEKASVMLSTKRVQGGYRSAVDFETLASQLTSDLQEASGDHRLHVFH
SHVEPTPEEQLPNMIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLVQMVWNKLVDTDAMIIDMRYNTGGYSTAVPILCSYFFEPEP
RQHLYTVFDRSTSRSTEVWTLPKVTGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVIGEPTVGGSLSVGIYRVGNSSLYRSIPSQVVLSPVTGK
VWSVSGAEPHITIQASEALAAAKHI
>M4_galGal 
ASLRTQVPQIVQTVGKLVAENYAFVDIGTDIASNLTKSVNKENYKRINSEKELARKLTAILQALSDDEHLKILYI
PEHAKDSIPGILPK
QIPSPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDCELLTQVSDLLVEHVWKKIVHTDALIIDMR
YNIGGYTNSIPILCSYFFDEGHQVLLDKVYDRPSDSVKEIWTQPQLR
GERYGSQKGLIILTSAVTAGAAEEFVFIMKRLGRALIIGEQTSGGSHSPQTYQVDDTNFYIIIPTARSVISAESASWEGKGVPPHMETPAVTALIKAKEVL 
 
>M1_anoCar
VLQSTLVLDMAKLLLDNYCLPENLVGMREAIEQAIKNGEVLDISDPKLLATVLTAGVQGALNDPRLVISYEPTAPAAPK
QRMETSLTPEQLLSLIQHTVKYEVLDDNVGYLRIDYIMGQDIVQKIGSFLVEKVWKTLLGTSALILDLRYTTGGDVSGIPFIISYLYNGDKVLHVDTVYN
RPSNTTVEILTLPKVLGVRYSKDKDVILLISKYTTGVAENVAYILKHMHRTIIVGEKSAGGSLDTQKMQIGNSQFYMTVPLSCSVSPLSGSGQSWEISGV
TPCVVISAEQALDKALAIL
>M2_anoCar
SLRKAIPNSMSYLVDIIKNNYSMLEQVPVLLQHLSTFDYSSVLSVKDLASKLNAELQTISEDPRLFLRVPASDEAVTSQTD
EKVAMASDLPNNEQLMKALVMTVFKVSVLPGNVGYMRFDEFGDATVLVKLGPYLLQHVWEPLQATDYLIIDLRYNIGGPSSSAVPVLLSYFQDPSAGPVH
FFTTYNRLTNQTQAYSSSAEMVGKPYGARRGVYLLTSHNTATAAEEFAYLMQTLGRATLVGEITAGSLSHTHTFCILELGGGCGLLINVPVITLIDNHGE
YWLGGGVVPDSIVLADEALEKAREVLE
>M3_anoCar
EAHYAIPEMARRVSSMLNSKLAQGGYRTAVDFETLASQLTNDLQETSGDHQLHVFHS
HVEPSLEEQSPFKTLTPEELNFIIEALFKVDVLPGNVGYLRFDMMAEFESVKTIEPQILHMVWEKLVETSAMIVDMRYNTGSYSTAVPMFCSYFFDAEPQ
QHLYTIIDRSTSQSTEVWTSSQVSGKRYGSTKDLYILISHASGSAAEAFTRSLKDLHRATVIGEPTVGGSLSASIYNIGSTPLYASIPSQIVLSPVSGKV
WSLSGIQPHVTTQSNEALASAQNII
>M4_anoCar
LFRTKLPSVLNTIGKLVADNYAFADIGATVAAKFADYAKKGTYRKINSEIELSGKLAADLKALSGDRHLMISHIP
ERSKGRILGLVPMQ
QIPPPEILEDLIKFSLHTNVFENNIGYLRFDMFGDCELMSQVSELLVQHVWNKIVNTDALIIDMR
YNVGGPACSVPLLCSYFFDEGHPILLDKVYNRPNDTTSNIWTVSKLA
GKRYGLNKGLIILTSSVTSGAAEEFAHIMKRLGRAFIIGQKTSGGCHPPQTFHVDGTNLYITTPVSRSVFSVNDSWEGVGVSPHLDVSTDVALIKAKEML 
 
>M1_xenLae Xenopus laevis
LFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAVKGGEILHISDPDTLANVFTSGVQGYLNDPRLVVSYEPNYSGPQT
EQSLELTPEQLKFLINHSVKYDILPGNIGYLRIDFIIGQDVVQKVGPHLVNNIWKKLMPTSALILDLRYSTQGEVSGIPFVVSYLCDSEIHIDSIYNRPS
NTTTDLWTLPELMGERYGKVKDVVVLTSKYTKGVAEDASYILKHMNRAIVVGEKTAGGSLDTQKIKIGQSDFYITVPVSRSLSPLTGQSWEVSGVSPCVV
VNAKDALDKAQAIL
>M2_xenLae
AVRSSVTHVLHQLCDILANNYAFSERIPTLLQHLPNLDYSTVISEEDIAAKLNYELQSLTEDPRLVLKSKTDTLVMPGDSIQAENI
PEDEAMLQALVNTVFKVSILPGNIGYLRFDQFADVSVIAKLAPFIVNTVWEPITITENLIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNS
TDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFDGTQLSVTVPIINFIDSNGDYWLGGGVVPDAIVLA
DEALDKAKEII
>M3_xenLae
FHPSIFPLVKGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASLLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIP
SPEELNYIIDALFKIEVLPGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSTGK
DIWTLPEVFGERYGSTKDIYILTSHMTGSAAEVFTRSLKDLNRATLIGEPTSGVSLSVGMYKVGDSNLYVTIPNQVVISSVTGKVWSVSGVEPHVIIQAN
EAMNIAHRII
>M4_xenLae
KLRTKIPTVIQTAAKLVADNYAFADTGANVASKFIALVDKIDYKMIKSEVELAEKINDDLQSLSKDFHLKAVYIPENSKDRIPGVVPM
QIPSPELFEELIKFSFHTDVFEKNIGYIRFDMFADSDLLNQVSDLLVEHVWKKVVDQDALIIDMR
FNIGGPTSSIPIFCSYFFDEGTPVLLDKIYSRTSNAMTDIWTLPDLV
GKTFGSKKPLIILTSSLTEGAAEEFVYIMKRLGRAYVVGEVTSGGCHPPQTYHVDDTHLYLTIPTSRSASAEPGESWEGKGVLPDLEISSETALLKAKEIL 
 
>M1_xenTro Xenopus tropicalis 89% xenLae
VFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAMKSGEILHISDPETLANVFTSGVQGFLNDPRLVVSYEPNYSGPRK
EQSPEPTLEQLKFLLDHSVTYDLLPGNIGYLRIDFIIGQDVVQKVGPLLVNNIWKKLMPSSALILDLRYSTQGKVSGIPFVVSYLTDPQIHIDSIYNRPS
NTTTDLWTLSELMGERYGKDKDVVVLTSKYTEGIAEGAAYILKHMSRAIVVGEKTAGGSLDIQKIKIGQSEFYITVPVSRSISPLTGQSWEVAGVFPCVV
VNANNALNKAQGIL
>M2_xenTro
AVRSSITHILLQLSEILVNNYAFSERIPTLLQHLPNLDYSSVISEEDITAKLNYELQSLTEDPRLVLKSKTDSLVMPEDSTQVENL
PDDEATLQALVNTVFKVSILPGNIGYLRFDEFADVSVLAKLGPYIVNTVWDPITVTENLIIDLRYNIGGSSTSIPLLLSYFQEPENRIHLFTIYNRQQNS
TNEVYSLPKVLGKPYGSKKGVYVLTSHETATAAEEFAYLMQSLSRATIIGEITSGNLMHSKAFPLDGTRLSVTVPIMNFIDNNGDYWLGGGVVPDAIVLA
DEALDKAKEII
>M3_xenTro
FHPSVFALVEGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASQLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIP
SAEELNYIIDALFKIEVLQGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSSGT
DIWTLPEVVGERYGSTKDIYILTSHMTGSAAEVFTRSMKELNRATIIGEPTSGVSLSVGMYKVGESNLYVSIPNQVVISSVTGKVWSVSGVEPHVIAQAS
EAMNVAHHII
>M4_xenTro
KLRTKIPSVIQTAGKLVADNYAFADTGADVASKLIALVDKINYKMIKSEVELAEKLNYDLQSLSKDVHLKAVYIPENSKDRIPGVVPMQ
IPSPEMFEDLIKFSFHTDVFEKNLGYIRFDMFADSDLLNQVSDLLVEHVWKKVVNQDALIIDMr
FNIGGPTSSIPTFCSYFFDEGTPVLLDKIYSRTTNAITDVWTLPHLV
GNAFGSKKPVIILTSSLTEGAAEEFVYIMKRLGRAYVIGEVTSGGCHPPQTYHVDDTHLYLTIPTSRSASAKPGESWEGKGVLPDLEITSETALMKAKEIL 
 
>M1_tetNig  
AFPPSLIADMAKIVLDNYCSPEKLAGMKEAIKAAGTNTEVLNIPDGESLARVLSAGVQGTVSDPRLMVSFQPNYVPAG
PHKMPPLPPEHLVAVLQTSVKLDILEGNTGYLRIDHILGEEVADKVGPALIDLIWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPVVHIDSVYD
RPSNTTTKLLSLPNLLGQRYGVSKPLIVLTSKNTKGIAEDVAYCLKNLKRATIVGEKTAGGSLKLDTFKVGDTDFYITVPTAKSINPITGSSWEIRGVTP
HVEVNAEDALATAIKIV
>M4_tetNig 
LRAQIPAIIEGTAALVANNYAFEATGADVAKELRELQANGQYSSVVSKESLEAALSADLQRLSGDKSLKTTPNTPVLPPM
DYTPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDLr
NNVGGPTTAIAGFCSYFFDADKQNRVGQAVRQASGTTTELLTLSELT
GVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQTFRVGETDVFLLIPTVHSDTGAGPAWEGAGIAPHIPASAEAALGTAR 
 
>M1_takRub two domains: 3-324,326-61plus upstream dup
AFPPSLITDMAKIVLDNYCSPEKLAGMKEAIEAAGTNTEVLNIPDGESLARVLSAGVQGTVSDSRLMVSYQPDYVPAV
PPKMPPLPPEHLVAVLQTSIKLDLLEGNTGYLRIDHIIGEDVAEKVGPSLIDLIWNKILPTSALIFDLRYTSSGEISGIPYIVSYFTQAEPVVHIDSVYD
RPSNTTTKLFSLSNLLGERYGITKPLIILTSKNTKGIAEDVAYCLKNLKRATIVGERTAGGSVKLDNFKVGSTDFYITVPTAKSINPVTGSSWEITGVKP
DVEVNAEDALATAIKIV
>M4_takRub
LRAQIPAIIEGAATLIAKNYAFEATGADVATKLRELLAKGQYNSVVSSESLEVALSADLQRLSGDKSLKATQNAPVLPPM
DYSPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDLR
NNVGGPTTAIAGFCSYFFDADKLIVLDKLHDRPSGTTTELLTLPELT
GVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQVFSVGEIGIFLSIPTVHSDTAAGPAWEGTGITPHIPVSAEAALGTAK
 
>M1_gasAcu two domains:7-317,323-61no upstream dup
FAPNVIIDMAKIVIDNYCSPEKLAGMKEAIEAAGSNTEVLSIPDAETLANVLSAGVQTTVSDPRLMISYEPNYVPVV
PPKMPPLPPDQVIAVLQTSIKLDILEGNIGYLRIDHILGEDVAEKVGPLLLDLVWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTEAGTPIHIDSIYD
RPSNTTTKLFSMSTLLGERYSTSKPLIILTSKNTKGIAEDVAYCLQNLKRATIVGEKTAGGSVKVDKIQVRDTGFYVTVPTAKSVNPITGSTWEVTGVTP
NVEVNAEDALATAIKIV
DALATAIKIV
>M4_gasAcu 
TLLNRVPAIIEGSATLIADNYAFEDIGAAVAEKLKGLLANGEYSKVVSKDSLEMKLSADLRTLSGDKSLKTTSNVPALPPM
NYSPEMYIELIKVSFHTDVFEDNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDAMIVDLR
NNIGGPTTAIAGFCSYFFDSDKQIVLDRLYDRPSGTTTELRTLPELT
GTRYGSKKSLVMLTSRATAGAAEEFVYIMKKLGRAMIVGETTAGTSHPPKTFRVGETDIFLSIPTVHSDTAAGPAWEGAGVAPHIPVPADAALETAKGIFKKHFAGQK
 
>M1_oryLat two domains:8-314,320-605 no upstream dup
SFPPSLITDLAKIVMDNYCSPEKLSGMKEDIATAGANTDVLNIPDGEALAKVLTDGVQTTVSDPRLRVSYEPNYVPVV
PPQLPPEQLIAVLQTSIKLDILEGNIGYLRIDSIIGEEVAEKVGPLLLELVWSKILPTSALIFDLRYTSSGDITGIPYIISYLTDAKSEIHIDTIYDRPL
NTTTKLLSMQSTLGQTYGGTKPLLVLTSKNTKDIAEDVAYCLKNLKRATIVGEKTAGGSAKIKKFRVGDTDFYVTLPTAKSINPITGSSWEVTGVKPNVE
VNAEEALATALKII
>M4_oryLat
LRLQVPAIIEESATLVANNYAFESTAADVAEKLKGHLANGDYNMVVSKESLEAKLSADLQSLSGDKSLTVSSNTGAPPPM
EYTPEMYIELIKISFHTDVFENNIGYLRFDMFGDFEEVKAIAQVIVEHVWNKVLHTDAMIIDLR
NNVGGPTTAIAGFCSYFFDGDKQILLDKLYDRSTGTTTDLLTLGELT
GERYGSKKSLIILASRATAGAAEEFVYIMKRLGRAMIVGETTAGASHPPKVFQVGESDIFLSIPTVHSDTSAGPGWEGAGVAPHIPVAAGAALETAK
 
>M1_danRer upstream frag as well two domains:2-322,324-609
FSPTLIADMAKIFMDNYCSPEKLTGMEEAIDAASSNTEILSISDPTMLANVLTDGVKKTISDSRVKVTYEPDLILAAPP
AMPDIPLEHLAAMIKGTVKVEILEGNIGYLKIQHIIGEEMAQKVGPLLLEYIWDKILPTSAMILDFRSTVTGELSGIPYIVSYFTDPEPLIHIDSVYDRT
ADLTIELWSMPTLLGKRYGTSKPLIILTSKDTLGIAEDVAYCLKNLKRATIVGENTAGGTVKMSKMKVGDTDFYVTVPVAKSINPITGKSWEINGVAPDV
DVAAEDALDAAIAII
>M4_danRer
KLRAEIPALAQAAATLIADNYAFPSIGEHVAEKLEAVVAGGEYNLISTKEDLEERLSEDLLKLSEDKCLKTTSNIPALPPM
NPTPEMFIALIKSSFQTDVFENNIGYLRFDMFGDFEHVATIAQIIVEHVWNKVVDTDALIIDLr
NNIGGHASSIAGFCSYFFDADKQIVLDHIYDRPSNTTRDLQTLEQLT
GRRYGSKKSVVILTSGVTAGAAEEFVFIMKRLGRAMIIGETTHGGCQPPETFAVGESDIFLSIPISHSTAQGPSWEGAGIAPHIPVPAGAALDTAK
 
>M1x_takRub single upstream exon 42% frameshift no transcripts three domains:3-323,325-615,618-907
TLVLEMAKLLLENYCIPENLVGMQEAIQRAIKSREILQISDRKTLATVLTVGVQGALNDPRLSVSYEPSFSPLPLQALSSLPVEQQLRLLRN
SIKLDILDSDVGYLRIDRIIDEETLLKFGPLLRENVWDKAAQTSSLILDLRFSTAGGWSGIPSIVSYFTEPHSLVHIDTVYDRPSNTTTELWTMSSVRGK
TFGGKKDMIVLIGRRTAGAAEAVAYTLKHLNRAIVVGERSAGGSLKVRKFRIAESDFYITMPVARSVSPITGKSWEVSGISPTVNVAAREALAKAQTFL
>M2x_takRub
AVRSRIPKVLQIVLDIIGRFYAFADRVQALLQQLESADLFSVVSEEDLAARLNHDLQTASEDPRLIIRHKRDNIPRAEEEPELHAANDHDGELVEGFTVQV
LPHNTGYLRLDRFVRCSEGDKLEEIVAEKVWGPLKDTQNLIIDLRHNTGGSSTSVALLLSYLRDPLPKRHFFTIYDSVQNTTTEYGSRPHIPGPSYGSER
GVYVLTSHYTAGAAEEFAYLIQSLHFGTVVGEITSGTLMHSKTFQVEGTDIFITVPFINFLDNNGEYWLGGGVVPDAIVLAEEALE 
>M3x_takRub
FHQGLRSLIGRTGELLEKHYAIQEVAQKVGEV
LLSKWAEGLYRSVVDLESLASQLTADLQEASGDHRLHVFRCDVELESLHGVPKIAAVEEAGFVIDALFKSELLPRNVGYLRFDTMADIEAAKGAAPRLVKSVWNKLVDTDSLIIDMRYNA
GGSSTAVPLWCSYFVDGEPLQHLYTVYDRTTKTRVEVMTLPEVSGQRYDPGKDVYILTSHMTGSAAEAFVRAMRDLNRVTIVGEPTAGGSLSSATYQIGESVLYASIPNQVVTSAATGKL
WSISGVEPDVFAQARDALPVAQRII
 
>M1x_danRer  
FQSALVLDMAKILLDNYCFPENLIGMQEAIQQAINSGEILHISDRKTLASVLTAGVQGALNDPRLTVSYEPNYTLITPPA
LHSLPTEQLIRLIRSTVKLEVMDNNIGYLRIDRIIGQETVVKLGRLLHNNIWKKVAHTSAMIFDLRFSTAGELSGLPYIVSYFSDSDPLLHIDTIYERPT
NITRELWTLPTLLGERFGKRKDLIVLISKRTIGAAEGVAYILKHLKRAVIIGERSAGGSVRVDKLKIGDSGFYITVPVARSVNPVTGQSWEVSGVAPSVTVNPKESIAKAKSLI
>M2x_danRer
SVRKTIPKAVRRVSDIIKRYYSFKDKIPALLNQLAKADYFTVVSEEDLAGKLNHEMQSVFEDPRLLIKATQVLTDDASSEDRSSSD
DLTDPLFKLEMISGNNGYLRFDRFPTPEVLLRLEDHIKKKIWQPVQETENLVIDLRFNTGGSTEALPILLSYMFDTSSSTYLFSIYDSIKNTTFDFHTLN
NISGPSYGSTKGVYVLTSYYTAEAGEEFAYLMQSLHRGTVIGEITSGMLLHSKTFQIEQTSLAITVPIINFIDVNGECWLGGGVVPDAIVLAEEALERAHEII
>M3x_danRer
FHKNIQGLVQEAGDLLEKHYSVPEVAAKVSRLLQSKLTEGLYRSVVDYESLASQLTSDLQETSGDQRLHIFYCETEPETLHDTPKIPSPEEAGFIV
EALFKVDVMSGNIGYLRFDMMEDIKVLQAINPEFLKVVWNKLVNTDMLIIDVRYNTGGYSTAIPLLCTYFFDAQPLTHIYTLFDRSTATVTKVTTLPDVL
GQKYSSQKDVYILTSHITGSAAEAFTRTMKDLKRATVIGEPTIGGALSSGTYQIGNSILYASIPNQAVLNAVTGKPWSISGVEPHIVAQASDALIVAQKII
 
>M2_calMil frag domains 6-243,334-531
VTRESSPTSDKLPEDPTFLQALVDTVFKVSVLPDNTGYFRFDEFPEISVMSKLVQYIIEKVWLPVKDTDRLIVDLRHNVGGHSSVVPLLLSYFYDPEP
PVGLFTVYNRLTNTTSHTTLPGVGQHVYGSRKDIYVLTSHRTATAAEELAYLLQSLNRATIVGEITSGSLLHSRSFQIPSTHLVITIPFINFMDNHGECW
LGGGVVPDSIVLAEDTLERTKEII
>M3_calMil frag
GFHAQVAELVESTGKLLAVHYAIPEVAAEVSAVLSAKLTQGLYRSVVDWESLASRLTVDLQETSVWSVSGAEPHVI
VQANEAMTVALGIIN
>M4_calMil frag
LRAKIPSIFQAAGKLVADNYAFAQTGAGVAETIADLIEGTGYGMINTEGKLAEVLSDTLQQLSGDKHLKAVHIPGDSKHQTPGIAMIQ
QMPPPEILEDLVKFSYQTKVLENNVGYLRFDMFGDNEMITQVSELMAKHVWNVIASTSSLIVDLR
YNIGGPTSSIPILCSYFFDDDKTVLLDTVYSRPTDTISEMKAIPQVAGNGSTESSVHSYI
 
 
>M1_petMar  exon3/4 fused, exon4 run-on, fixed genomic frameshift; four domains: 34-312,327-615,625-914,916-1217
KFDTAVVLHLAKVLLDNYCIPENLVGMDEAIQRAVDNGELLGVSDPESAASALTEGIQAALNDPRIAV
SYVAPPHTFEELLATIPQKTSFAVLDGNVGYLRADEIISEATIKKLGPVIVQRIWNRLVDTDTFVLDLRYNSHGDITGLPYLVSCFCEPRPVVHLDTVYY
RPTNESKEIWSLPDLQGARFAKHKDVFVLVSANTEGVAENVAYVLKHLHRATVIGEQTAGGSLEVERFRLGDSRFFVTVPTARSEPADRSWGVFPCVSAP
SERALDKALEIL
>M2_petMar 
ELLLSSYTFVERASAIADHLSWSEYGSVVSVEDLTSKLTQDLQSVAEDPRLVVSNREPEWVGAADPPGPPAPLP
DDEQMLEAIVDSAFKVEVLEGNIGYLRFDEFGDASAVMKLRKQLVSKVWERIHPTDDVIIDLRYNLGGSSTAIPIVLSYFQDVAPVHFYTVYDRLRNVTA
EFHTVSNLTSQLYGSKKGVYLLTSQHTATAAEEFTYLMQSLNRATIVGEITSGRLAHSLAFRLSDTGLYMTVPIVNFIDNNDEYWLGGGVVPDAIVLAENALDAAKEII
>M3_petMar 
FHAKMASL
LELAGALVEGYYAMLSDGENATAEILLKYREGWYRSVVDYEALASQLTSDLHEIWGDHRLHAFYSDLQIERMDEDKTPSVPSPEELSVLIDTVFKVDILANNVGYLRFDMMTDAEVLKHV
GPQLVEKVWNKISSTRSLVIDVRYNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTG
TYRIGDSRLYVFIPNQAGVSPSGGRTWSVAGVEPHVQTKASEALQSALRMV
>M4_petMar 
ALRADAPSILRTVGKLVADGYSRAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHLKAVCVPEHATDRMPGIVPMQ
MPPTESFEDLIKFSFITDVLEGNIGYLRFDLFSDLEALEHVAHLLVEHVWKKICDTEILIIDLR
YNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDSRLYVFIPNQAGVSPSGGRTWSVAGVEPHVQTKASEALQSA
 
>M3/4_braFlo Branchiostoma floridae Region: 9 exons 
VVMGIGDVMADHYLDQDLRALNDQSLLQRWNRTLVHRFQ
SWSQDDMSDSLRMEEGLTSELRNITGDETIK
VWDFGVYENTTQEPVPREFYNFSTFVDNFK
KNREKHINVTMLEGNVGYVSIRSMSHIVDIILPDPEMTEFFLSKMAALNESK
AIILDLRYNLGGDREGVVHWASFFFNATPSVPLSDVYYRDGVNQYWTLLE
VPGGIRFPDMPLYLLTSNRTSREAEEFAYAMQVVNRTTIIGETT
AGEEFTGMWFPIDQTDVHLLTRTNVVRNPITQDSWSGK
GVTPDIIVPSEKALTVALRK
</pre>
 
=== RBP3 proteins parsed by module class ===
<font color="blue">
>M1_homSap
GPTHPALTSLSEEELLAWLQRGLRHEVLEGNVGYLRVDSVPGQEVLSMMGEFLVAHVWGNLMGTSALVLDLRHCTGGQVSGIPYIISYLHPGNTILHVDTIYNRPSNTTTEIWTLPQVLGERYGADK
DVVVLTSSQTRGVAEDIAHILKQMRRAIVVGERTGGGALDLRKLRIGESDFFFTVPVSRSLGPLGGGSQTWEGSGVLPCVGTPAEQALEKALAIL
>M1_bosTau
LFQPSLVLEMAQVLLDNYCFPENLMGMQGAIEQAIKSQEILSISDPQTLAHVLTAGVQSSLNDPRLVISYEPSTLEAPPRAPAVTNLTLEEIIAGLQDGLRHEILEGNVGYLRVDDIPGQEVMSKLR
SFLVANVWRKLVNTSALVLDLRHCTGGHVSGIPYVISYLHPGSTVSHVDTVYDRPSNTTTEIWTLPEALGEKYSADKDVVVLTSSRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRVGQSDF
>M1_monDom
IFQPSLVRDMAKILLDNYCFPENLMGMQEVIEQAIKSGEILDISDPQMLASVLTAGVQGALNDPRLVISFEPSIPETPQHVPKLANVTQEELLILLQQMIKYQVLEGNVGYLRVDYIPGQEVVEKVG
EFLVNNIWKKLMGTSSLVLDLQHSSGGEISGIPFVISYLHQGDILLHVDTVYDRPSNTTTEIWTLPQVLGERYGGEKDMVVLTSHRTVGVAEDIAYILKKLRRAIVVGEQTLGGALDLRKLRIGQSDF
>M1_ornAna genome rife with frameshifts, dels, misassembly
SQPSMVLDVAKILLDNYCYPENLMGMQEAIEEAIQRGEILDIADPKRLASVLTAGVQGSLNDPRLVISYEPAPVAVSQQPPEPASLPAEQPLERLRPAVGSEVLEGNVGYLRVDRLPGREEIERVGA
VLGRDIWEKLLGTSALVLDLRHSTGGHVSGIPFFISYFYPEGPALHVDTVYDRPSNATRQLWTLPRVLGARYAADKDVVVLTSRLTAGVAEDVAYILQQMRRAIVVGERTAGGPLVFRKLRVGLSDFF
>M1_galGal
IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPSLHAAPKQEAETYPTREQLLSLIEHVVIYDKLEGNVGYLRIDYIIGQEVVEKVGA
FLVDKVWKTLINTSALVIDLRYSTGGQISGIPFIISYLHEADKMLHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITLGEKTAGGSLDIQKLRIGPSNFY
>M1_taeGut Taeniopygia guttata
IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPLPHSGPKQEAEGSPTREQLLSLIEHVIMYDKLEGNVGYLRIDYIIGEEVVQKVGA
FLVDKVWKTLIETSALVIDLRHSTGGQISGLPFIISYLHEQDKILHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITVGEKTAGGSLDIQKLRIGPSNFY
>M1_anoCar
VLQSTLVLDMAKLLLDNYCLPENLVGMREAIEQAIKNGEVLDISDPKLLATVLTAGVQGALNDPRLVISYEPTAPAAPKQRMETSLTPEQLLSLIQHTVKYEVLDDNVGYLRIDYIMGQDIVQKIGS
FLVEKVWKTLLGTSALILDLRYTTGGDVSGIPFIISYLYNGDKVLHVDTVYNRPSNTTVEILTLPKVLGVRYSKDKDVILLISKYTTGVAENVAYILKHMHRTIIVGEKSAGGSLDTQKMQIGNSQFY
>M1_xenTro Xenopus tropicalis 89% xenLae
VFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAMKSGEILHISDPETLANVFTSGVQGFLNDPRLVVSYEPNYSGPRKEQSPEPTLEQLKFLLDHSVTYDLLPGNIGYLRIDFIIGQDVVQKVGPL
LVNNIWKKLMPSSALILDLRYSTQGKVSGIPFVVSYLTDPQIHIDSIYNRPSNTTTDLWTLSELMGERYGKDKDVVVLTSKYTEGIAEGAAYILKHMSRAIVVGEKTAGGSLDIQKIKIGQSEFYITV
>M1_xenLae Xenopus laevis
LFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAVKGGEILHISDPDTLANVFTSGVQGYLNDPRLVVSYEPNYSGPQTEQSLELTPEQLKFLINHSVKYDILPGNIGYLRIDFIIGQDVVQKVGPH
LVNNIWKKLMPTSALILDLRYSTQGEVSGIPFVVSYLCDSEIHIDSIYNRPSNTTTDLWTLPELMGERYGKVKDVVVLTSKYTKGVAEDASYILKHMNRAIVVGEKTAGGSLDTQKIKIGQSDFYITV
>M1_danRer upstream frag as well two domains: 22-322,324-609
FSPTLIADMAKIFMDNYCSPEKLTGMEEAIDAASSNTEILSISDPTMLANVLTDGVKKTISDSRVKVTYEPDLILAAPPAMPDIPLEHLAAMIKGTVKVEILEGNIGYLKIQHIIGEEMAQKVGPLL
LEYIWDKILPTSAMILDFRSTVTGELSGIPYIVSYFTDPEPLIHIDSVYDRTADLTIELWSMPTLLGKRYGTSKPLIILTSKDTLGIAEDVAYCLKNLKRATIVGENTAGGTVKMSKMKVGDTDFYVT
>M1_takRub two domains: 23-324,326-612 plus upstream dup
AFPPSLITDMAKIVLDNYCSPEKLAGMKEAIEAAGTNTEVLNIPDGESLARVLSAGVQGTVSDSRLMVSYQPDYVPAVPPKMPPLPPEHLVAVLQTSIKLDLLEGNTGYLRIDHIIGEDVAEKVGPS
LIDLIWNKILPTSALIFDLRYTSSGEISGIPYIVSYFTQAEPVVHIDSVYDRPSNTTTKLFSLSNLLGERYGITKPLIILTSKNTKGIAEDVAYCLKNLKRATIVGERTAGGSVKLDNFKVGSTDFYI
>M1_gasAcu two domains: 27-317,323-612 no upstream dup
FAPNVIIDMAKIVIDNYCSPEKLAGMKEAIEAAGSNTEVLSIPDAETLANVLSAGVQTTVSDPRLMISYEPNYVPVVPPKMPPLPPDQVIAVLQTSIKLDILEGNIGYLRIDHILGEDVAEKVGPLL
LDLVWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTEAGTPIHIDSIYDRPSNTTTKLFSMSTLLGERYSTSKPLIILTSKNTKGIAEDVAYCLQNLKRATIVGEKTAGGSVKVDKIQVRDTGFYVT
>M1_tetNig
AFPPSLIADMAKIVLDNYCSPEKLAGMKEAIKAAGTNTEVLNIPDGESLARVLSAGVQGTVSDPRLMVSFQPNYVPAGPHKMPPLPPEHLVAVLQTSVKLDILEGNTGYLRIDHILGEEVADKVGPA
LIDLIWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPVVHIDSVYDRPSNTTTKLLSLPNLLGQRYGVSKPLIVLTSKNTKGIAEDVAYCLKNLKRATIVGEKTAGGSLKLDTFKVGDTDFYI
>M1_oryLat two domains: 28-314,320-605 no upstream dup
SFPPSLITDLAKIVMDNYCSPEKLSGMKEDIATAGANTDVLNIPDGEALAKVLTDGVQTTVSDPRLRVSYEPNYVPVVPPQLPPEQLIAVLQTSIKLDILEGNIGYLRIDSIIGEEVAEKVGPLLLE
LVWSKILPTSALIFDLRYTSSGDITGIPYIISYLTDAKSEIHIDTIYDRPLNTTTKLLSMQSTLGQTYGGTKPLLVLTSKNTKDIAEDVAYCLKNLKRATIVGEKTAGGSAKIKKFRVGDTDFYVTLP
>M1_petMar exon3/4 fused, exon4 run-on, fixed genomic frameshift; four domains: 34-312,327-615,625-914,916-1217
KFDTAVVLHLAKVLLDNYCIPENLVGMDEAIQRAVDNGELLGVSDPESAASALTEGIQAALNDPRIAVSYVAPPHTFEELLATIPQKTSFAVLDGNVGYLRADEIISEATIKKLGPVIVQRIWNRLV
DTDTFVLDLRYNSHGDITGLPYLVSCFCEPRPVVHLDTVYYRPTNESKEIWSLPDLQGARFAKHKDVFVLVSANTEGVAENVAYVLKHLHRATVIGEQTAGGSLEVERFRLGDSRFFVTVPTARSEPA
>M1x_danRer
FQSALVLDMAKILLDNYCFPENLIGMQEAIQQAINSGEILHISDRKTLASVLTAGVQGALNDPRLTVSYEPNYTLITPPALHSLPTEQLIRLIRSTVKLEVMDNNIGYLRIDRIIGQETVVKLGRLL
HNNIWKKVAHTSAMIFDLRFSTAGELSGLPYIVSYFSDSDPLLHIDTIYERPTNITRELWTLPTLLGERFGKRKDLIVLISKRTIGAAEGVAYILKHLKRAVIIGERSAGGSVRVDKLKIGDSGFYIT
>M1x_takRub single upstream exon 42% frameshift no transcripts three domains: 23-323,325-615,618-907
TLVLEMAKLLLENYCIPENLVGMQEAIQRAIKSREILQISDRKTLATVLTVGVQGALNDPRLSVSYEPSFSPLPLQALSSLPVEQQLRLLRNSIKLDILDSDVGYLRIDRIIDEETLLKFGPLLREN
VWDKAAQTSSLILDLRFSTAGGWSGIPSIVSYFTEPHSLVHIDTVYDRPSNTTTELWTMSSVRGKTFGGKKDMIVLIGRRTAGAAEAVAYTLKHLNRAIVVGERSAGGSLKVRKFRIAESDFYITMPV
  </font><font color="brown">
>M2_homSap
TLRSALPGVVHCLQEVLKDYYTLVDRVPTLLQHLASMDFSTVVSEEDLVTKLNAGLQAASEDPRLLVRAIGPTETPSWPAPDAAAEDSPGVAPELPEDEAIRQALVDSVFQVSVLPGNVGYLRFDSF
ADASVLGVLAPYVLRQVWEPLQDTEHLIMDLRHNPGGPSSAVPLLLSYFQGPEAGPVHLFTTYDRRTNITQEHFSHMELPGPRYSTQRGVYLLTSHRTATAAEEFAFLMQSLGWATLVGEITAGNLLH
>M2_bosTau
LRRALPGVIQRLQEALREYYTLVDRVPALLSHLAAMDLSSVVSEDDLVTKLNAGLQAVSEDPRLQVQVVRPKEASSGPEEEAEEPPEAVPEVPEDEAVRRALVDSVFQVSVLPGNVGYLRFDSFADA
SVLEVLGPYILHQVWEPLQDTEHLIMDLRQNPGGPSSAVPLLLSYFQSPDASPVRLFSTYDRRTNITREHFSQTELLGRPYGTQRGVYLLTSHRTATAAEELAFLMQSLGWATLVGEITAGSLLHTHT
>M2_monDom
LRRARPGAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATMGEAEEEDATPAANSLPEDESQRQALVDSVFQVSVLPGNVGYLRFDEFADSS
VLGTLAPYVIRQVWEPLQDTNHLIMDLRYNPGGPSSAVPLLLSYFQDPAAGPIRLFTTYDRQTNQTQEHLSRAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTF
>M2_ornAna
LRGAVPGAVAHLADLLRDYYALVDRVPALLRHLAALDLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPEEAERGPPRKEEEQKEEEEEDQPSPGASILPGDGSSREAPLFRVSVLPGNVGYLCF
DEFPEASALERLGPLLGRRVWEPLEATDHLMVDLRNNPGGPSSAVPLLLSYFQDPAAGPIRLFTTYNRPADVTREYASRAGALEKPYGARRGVYLLTSHRTATAAEEFAYLMQALGRATLVGEITAGR
>M2_galGal
AVRRAVPGTLSRLTDILKDYYSLVERVPVLLRHLTTSDFSSVQSAEDLATKLNTEMQTLSEDPRLLVRTMMPGEAAAPPAEMPIAMAANLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASV
LVKLGPYIVKKVWEPLQNTENLIMDLRYNPGGPSSSAVPMLISYFQDPTAGPVHLFTTYDRRTNHTQEHNSQAELLAQPYGAQRGIYVLTSRHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTCTF
>M2_taeGut
VRRAVPGTISHLKNILKDYYSLVERVPALLRRLTTSDFSSVQSSEDLATKLNTELQALSDDPRLMVRVMMPGEAADSPAEKPVGMAADLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVL
VKLGPYLVHKVWEPLQNTENLIMDLRYNLGGPSSSAVPVLLSYFQDPAAGPVHLFTTYDRRTNHTQEHNSQAELLGQSYGAKRGVYLLTSHHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTRTFP
>M2_anoCar
SLRKAIPNSMSYLVDIIKNNYSMLEQVPVLLQHLSTFDYSSVLSVKDLASKLNAELQTISEDPRLFLRVPASDEAVTSQTDEKVAMASDLPNNEQLMKALVMTVFKVSVLPGNVGYMRFDEFGDATV
LVKLGPYLLQHVWEPLQATDYLIIDLRYNIGGPSSSAVPVLLSYFQDPSAGPVHFFTTYNRLTNQTQAYSSSAEMVGKPYGARRGVYLLTSHNTATAAEEFAYLMQTLGRATLVGEITAGSLSHTHTF
>M2_xenTro
AVRSSITHILLQLSEILVNNYAFSERIPTLLQHLPNLDYSSVISEEDITAKLNYELQSLTEDPRLVLKSKTDSLVMPEDSTQVENLPDDEATLQALVNTVFKVSILPGNIGYLRFDEFADVSVLAKL
GPYIVNTVWDPITVTENLIIDLRYNIGGSSTSIPLLLSYFQEPENRIHLFTIYNRQQNSTNEVYSLPKVLGKPYGSKKGVYVLTSHETATAAEEFAYLMQSLSRATIIGEITSGNLMHSKAFPLDGTR
>M2_xenLae
AVRSSVTHVLHQLCDILANNYAFSERIPTLLQHLPNLDYSTVISEEDIAAKLNYELQSLTEDPRLVLKSKTDTLVMPGDSIQAENIPEDEAMLQALVNTVFKVSILPGNIGYLRFDQFADVSVIAKL
APFIVNTVWEPITITENLIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFDGTQ
>M2_calMil frag 2 domains 6-243,334-531
VTRESSPTSDKLPEDPTFLQALVDTVFKVSVLPDNTGYFRFDEFPEISVMSKLVQYIIEKVWLPVKDTDRLIVDLRHNVGGHSSVVPLLLSYFYDPEPPVGLFTVYNRLTNTTSHTTLPGVGQHVYG
SRKDIYVLTSHRTATAAEELAYLLQSLNRATIVGEITSGSLLHSRSFQIPSTHLVITIPFINFMDNHGECWLGGGVVPDSIVLAEDTLERTKEII
>M2_petMar
ELLLSSYTFVERASAIADHLSWSEYGSVVSVEDLTSKLTQDLQSVAEDPRLVVSNREPEWVGAADPPGPPAPLPDDEQMLEAIVDSAFKVEVLEGNIGYLRFDEFGDASAVMKLRKQLVSKVWERIH
PTDDVIIDLRYNLGGSSTAIPIVLSYFQDVAPVHFYTVYDRLRNVTAEFHTVSNLTSQLYGSKKGVYLLTSQHTATAAEEFTYLMQSLNRATIVGEITSGRLAHSLAFRLSDTGLYMTVPIVNFIDNN
>M2x_danRer
SVRKTIPKAVRRVSDIIKRYYSFKDKIPALLNQLAKADYFTVVSEEDLAGKLNHEMQSVFEDPRLLIKATQVLTDDASSEDRSSSDDLTDPLFKLEMISGNNGYLRFDRFPTPEVLLRLEDHIKKKI
WQPVQETENLVIDLRFNTGGSTEALPILLSYMFDTSSSTYLFSIYDSIKNTTFDFHTLNNISGPSYGSTKGVYVLTSYYTAEAGEEFAYLMQSLHRGTVIGEITSGMLLHSKTFQIEQTSLAITVPII
>M2x_takRub
AVRSRIPKVLQIVLDIIGRFYAFADRVQALLQQLESADLFSVVSEEDLAARLNHDLQTASEDPRLIIRHKRDNIPRAEEEPELHAANDHDGELVEGFTVQVLPHNTGYLRLDRFVRCSEGDKLEEIV
AEKVWGPLKDTQNLIIDLRHNTGGSSTSVALLLSYLRDPLPKRHFFTIYDSVQNTTTEYGSRPHIPGPSYGSERGVYVLTSHYTAGAAEEFAYLIQSLHFGTVVGEITSGTLMHSKTFQVEGTDIFIT
  </font><font color="green">
>M3_homSap
EFHQSLGALVEGTGHLLEAHYARPEVVGQTSALLRAKLAQGAYRTAVDLESLASQLTADLQEVSGDHRLLVFHSPGELVVEEAPPPPPAVPSPEELTYLIEALFKTEVLPGQLGYLRFDAMAELETV
KAVGPQLVRLVWQQLVDTAALVIDLRYNPGSYSTAIPLLCSYFFEAEPRQHLYSVFDRATSKVTEVWTLPQVAGQRYGSHKDLYILMSHTSGSAAEAFAHTMQDLQRATVIGEPTAGGALSVGIYQVG
>M3_bosTau
EFHRSLGELVEGTGRLLEAHYARPEVVGQMGALLRAKLAQGAYRTAVDLESLASQLTADLQEMSGDHRLLVFHSPGEMVAEEAPPPPPVVPSPEELSYLIEALFKTEVLPGQLGYLRFDAMAELETV
KAVGPQLVQLVWQKLVDTAALVVDLRYNPGSYSTAVPLLCSYFFEAEPRRHLYSVFDRATSRVTEVWTLPHVTGQRYGSHKDLYVLVSHTSGSAAEAFAHTMQDLQRATIIGEPTAGGALSVGIYQVG
>M3_monDom
EFHQRLGALVEGTGHLLEAHYALPEVVGQASALLKAKLEHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPVSEELTPPQKGVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETV
RAIAPQLVELVWEKLVHTEALVVDLRYNPGGYSTAVPLLCSYFFEAEPRRHLYTIFDRAASQLTEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFVHTMKDQHRATVIGEPTGGGALSVGIYQVE
>M3_ornAna frag
FHQTLEALVETTGHLLEAHYCFPAGARRAGAQPWPVAGVEPDVMAQAAEALAVAQGIAA
>M3_galGal
LLESTGQLLEAHYAIPEVAEKASVMLSTKRVQGGYRSAVDFETLASQLTSDLQEASGDHRLHVFHSHVEPTPEEQLPNMIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLVQM
VWNKLVDTDAMIIDMRYNTGGYSTAVPILCSYFFEPEPRQHLYTVFDRSTSRSTEVWTLPKVTGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVIGEPTVGGSLSVGIYRVGNSSLYRSIPS
>M3_taeGut
FHKNMGVLLEGTGQLLEDHYAIPEVAAKASAMLSTKRAQGGYRSAIDSETLASQLTSDLQEASGDHRLHVFHSHVEPTPEEQLPNVIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAI
GPQLLQMVWNKLVDTDAMIIDMRYNTGGYSTAIPILCSYFFDPEPRKHLYTVFDRSTSRSTEVWTLPQLAGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVVGEPTVGGSLSVGIYRVGNSS
>M3_anoCar
EAHYAIPEMARRVSSMLNSKLAQGGYRTAVDFETLASQLTNDLQETSGDHQLHVFHSHVEPSLEEQSPFKTLTPEELNFIIEALFKVDVLPGNVGYLRFDMMAEFESVKTIEPQILHMVWEKLVETS
AMIVDMRYNTGSYSTAVPMFCSYFFDAEPQQHLYTIIDRSTSQSTEVWTSSQVSGKRYGSTKDLYILISHASGSAAEAFTRSLKDLHRATVIGEPTVGGSLSASIYNIGSTPLYASIPSQIVLSPVSG
>M3_xenTro
FHPSVFALVEGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASQLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIPSAEELNYIIDALFKIEVLQGNVGYLRFDMMADTEIIKAI
GPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSSGTDIWTLPEVVGERYGSTKDIYILTSHMTGSAAEVFTRSMKELNRATIIGEPTSGVSLSVGMYKVGESN
>M3_xenLae
FHPSIFPLVKGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASLLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIPSPEELNYIIDALFKIEVLPGNVGYLRFDMMADTEIIKAI
GPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSTGKDIWTLPEVFGERYGSTKDIYILTSHMTGSAAEVFTRSLKDLNRATLIGEPTSGVSLSVGMYKVGDSN
>M3_calMil frag
GFHAQVAELVESTGKLLAVHYAIPEVAAEVSAVLSAKLTQGLYRSVVDWESLASRLTVDLQETSVWSVSGAEPHVIVQANEAMTVALGIIN
>M3_petMar
FHAKMASLLELAGALVEGYYAMLSDGENATAEILLKYREGWYRSVVDYEALASQLTSDLHEIWGDHRLHAFYSDLQIERMDEDKTPSVPSPEELSVLIDTVFKVDILANNVGYLRFDMMTDAEVLKH
VGPQLVEKVWNKISSTRSLVIDVRYNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDS
>M3/4_braFlo Branchiostoma floridae Region: 9 exons
MTRPSKVDIVFPIKPFTIPTAHEQVKGEGPVDINKNALCKSADEGHTHPVSIAMAPTAYIVFVALVPTVLSVDWLDVVMGIGDVMADHYLDQDLRALNDQSLLQRWNRTLVHRFQSWSQDDMSDSLR
MEEGLTSELRNITGDETIKVWDFGVYENTTQEPVPREFYNFSTFVDNFKKNREKHINVTMLEGNVGYVSIRSMSHIVDIILPDPEMTEFFLSKMAALNESKAIILDLRYNLGGDREGVVHWASFFFNA
>M3x_takRub
FHQGLRSLIGRTGELLEKHYAIQEVAQKVGEVLLSKWAEGLYRSVVDLESLASQLTADLQEASGDHRLHVFRCDVELESLHGVPKIAAVEEAGFVIDALFKSELLPRNVGYLRFDTMADIEAAKGAA
PRLVKSVWNKLVDTDSLIIDMRYNAGGSSTAVPLWCSYFVDGEPLQHLYTVYDRTTKTRVEVMTLPEVSGQRYDPGKDVYILTSHMTGSAAEAFVRAMRDLNRVTIVGEPTAGGSLSSATYQIGESVL
>M3x_danRer
FHKNIQGLVQEAGDLLEKHYSVPEVAAKVSRLLQSKLTEGLYRSVVDYESLASQLTSDLQETSGDQRLHIFYCETEPETLHDTPKIPSPEEAGFIVEALFKVDVMSGNIGYLRFDMMEDIKVLQAIN
PEFLKVVWNKLVNTDMLIIDVRYNTGGYSTAIPLLCTYFFDAQPLTHIYTLFDRSTATVTKVTTLPDVLGQKYSSQKDVYILTSHITGSAAEAFTRTMKDLKRATVIGEPTIGGALSSGTYQIGNSIL
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>M4_homSap
ALRAKVPTVLQTAGKLVADNYASAELGAKMATKLSGLQSRYSRVTSEVALAEILGADLQMLSGDPHLKAAHIPENAKDRIPGIVPMQIPSPEVFEELIKFSFHTNVLEDNIGYLRFDMFGDGELLTQ
VSRLLVEHIWKKIMHTDAMIIDMRFNIGGPTSSIPILCSYFFDEGPPVLLDKIYSRPDDSVSELWTHAQVVGERYGSKKSMVILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDT
>M4_bosTau
LRAKVPTVLQTAGKLVADNYASPELGVKMAAELSGLQSRYARVTSEAALAELLQADLQVLSGDPHLKTAHIPEDAKDRIPGIVPMQIPSPEVFEDLIKFSFHTNVLEGNVGYLRFDMFGDCELLTQV
SELLVEHVWKKIVHTDALIVDMRFNIGGPTSSISALCSYFFDEGPPILLDKIYNRPNNSVSELWTLSQLEGERYGSKKSMVILTSTLTAGAAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTD
>M4_monDom
LRAKVPTILQTAGKLVADNYASLEVGSRVASKLAKLQTQYRQVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAKDRIPGIVPMQLPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLTQV
SDLLVEHVWKKVVHTDGMIIDMRFNIGGPTSSISALCSYFFDEGQEVLLDQIYNRPNDSISEIWTQSQVAGERYGSKKSVIILTSSMTAGAAEEFVYVMQRLGRALVIGEVTSGGCQPPQTYHVDDTD
>M4_ornAna
LRSKVPTVLRTAAKLVADNYAFRETGAGVAAQMGGLQARCGRVTSEGALAEVLGAHLRALSGDPHLQMVYIPEDAKDRIPGVVPMQIPSAETFEDLIKFSFHTSVMEGNIGYLRFDMFGDCELLTQV
SELMVEHVWKKIVHTDGLIIDMRNIGGPTSSISALCSYFFDEDHPVLLDKIYNRPNDSISEIWTHSHIAGERYGSRKSVVILTSNMTAGAAEEFVSIMKRLGRALVVGEVTGGGCHPPQTYHVDDTHL
>M4_galGal
ASLRTQVPQIVQTVGKLVAENYAFVDIGTDIASNLTKSVNKENYKRINSEKELARKLTAILQALSDDEHLKILYIPEHAKDSIPGILPKQIPSPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDCEL
LTQVSDLLVEHVWKKIVHTDALIIDMRYNIGGYTNSIPILCSYFFDEGHQVLLDKVYDRPSDSVKEIWTQPQLRGERYGSQKGLIILTSAVTAGAAEEFVFIMKRLGRALIIGEQTSGGSHSPQTYQV
>M4_taeGut
ANLRAQVPQILQTVGKLVADNYAFVNTGTVIASNLTKNIHKDNYKRINTEEDLAGKVTAILQALSDDKHLKLLYIPEHAKDSIPGIMPKQIPPPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDSEL
LTQLSDLMIEHVWKKIFHTDALIIDLRYNIGGSTTPIAILCSYFFDEGHPVLLDRVYDRPSDSVKEIWTQPQLKGERYGSQKGLVILTSAVTAGAAEEFVYIMKRLSRALIIGEQTSGGCHSPQTYQV
>M4_anoCar
LFRTKLPSVLNTIGKLVADNYAFADIGATVAAKFADYAKKGTYRKINSEIELSGKLAADLKALSGDRHLMISHIPERSKGRILGLVPMQQIPPPEILEDLIKFSLHTNVFENNIGYLRFDMFGDCEL
MSQVSELLVQHVWNKIVNTDALIIDMRYNVGGPACSVPLLCSYFFDEGHPILLDKVYNRPNDTTSNIWTVSKLAGKRYGLNKGLIILTSSVTSGAAEEFAHIMKRLGRAFIIGQKTSGGCHPPQTFHV
>M4_xenTro
KLRTKIPSVIQTAGKLVADNYAFADTGADVASKLIALVDKINYKMIKSEVELAEKLNYDLQSLSKDVHLKAVYIPENSKDRIPGVVPMQIPSPEMFEDLIKFSFHTDVFEKNLGYIRFDMFADSDLL
NQVSDLLVEHVWKKVVNQDALIIDMrFNIGGPTSSIPTFCSYFFDEGTPVLLDKIYSRTTNAITDVWTLPHLVGNAFGSKKPVIILTSSLTEGAAEEFVYIMKRLGRAYVIGEVTSGGCHPPQTYHVD
>M4_xenLae
KLRTKIPTVIQTAAKLVADNYAFADTGANVASKFIALVDKIDYKMIKSEVELAEKINDDLQSLSKDFHLKAVYIPENSKDRIPGVVPMQIPSPELFEELIKFSFHTDVFEKNIGYIRFDMFADSDLL
NQVSDLLVEHVWKKVVDQDALIIDMRFNIGGPTSSIPIFCSYFFDEGTPVLLDKIYSRTSNAMTDIWTLPDLVGKTFGSKKPLIILTSSLTEGAAEEFVYIMKRLGRAYVVGEVTSGGCHPPQTYHVD
>M4_danRer
KLRAEIPALAQAAATLIADNYAFPSIGEHVAEKLEAVVAGGEYNLISTKEDLEERLSEDLLKLSEDKCLKTTSNIPALPPMNPTPEMFIALIKSSFQTDVFENNIGYLRFDMFGDFEHVATIAQIIV
EHVWNKVVDTDALIIDLrNNIGGHASSIAGFCSYFFDADKQIVLDHIYDRPSNTTRDLQTLEQLTGRRYGSKKSVVILTSGVTAGAAEEFVFIMKRLGRAMIIGETTHGGCQPPETFAVGESDIFLSI
>M4_takRub
LRAQIPAIIEGAATLIAKNYAFEATGADVATKLRELLAKGQYNSVVSSESLEVALSADLQRLSGDKSLKATQNAPVLPPMDYSPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVE
HVWNKVVNTDALILDLRNNVGGPTTAIAGFCSYFFDADKLIVLDKLHDRPSGTTTELLTLPELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQVFSVGEIGIFLSIP
>M4_tetNig
LRAQIPAIIEGTAALVANNYAFEATGADVAKELRELQANGQYSSVVSKESLEAALSADLQRLSGDKSLKTTPNTPVLPPMDYTPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVE
HVWNKVVNTDALILDLrNNVGGPTTAIAGFCSYFFDADKQNRVGQAVRQASGTTTELLTLSELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQTFRVGETDVFLLIP
>M4_gasAcu
TLLNRVPAIIEGSATLIADNYAFEDIGAAVAEKLKGLLANGEYSKVVSKDSLEMKLSADLRTLSGDKSLKTTSNVPALPPMNYSPEMYIELIKVSFHTDVFEDNIGYLRFDMFGDFEEVKAIAQIIV
EHVWNKVVNTDAMIVDLRNNIGGPTTAIAGFCSYFFDSDKQIVLDRLYDRPSGTTTELRTLPELTGTRYGSKKSLVMLTSRATAGAAEEFVYIMKKLGRAMIVGETTAGTSHPPKTFRVGETDIFLSI
>M4_oryLat
LRLQVPAIIEESATLVANNYAFESTAADVAEKLKGHLANGDYNMVVSKESLEAKLSADLQSLSGDKSLTVSSNTGAPPPMEYTPEMYIELIKISFHTDVFENNIGYLRFDMFGDFEEVKAIAQVIVE
HVWNKVLHTDAMIIDLRNNVGGPTTAIAGFCSYFFDGDKQILLDKLYDRSTGTTTDLLTLGELTGERYGSKKSLIILASRATAGAAEEFVYIMKRLGRAMIVGETTAGASHPPKVFQVGESDIFLSIP
>M4_calMil frag
LRAKIPSIFQAAGKLVADNYAFAQTGAGVAETIADLIEGTGYGMINTEGKLAEVLSDTLQQLSGDKHLKAVHIPGDSKHQTPGIAMIQQMPPPEILEDLVKFSYQTKVLENNVGYLRFDMFGDNEMI
TQVSELMAKHVWNVIASTSSLIVDLRYNIGGPTSSIPILCSYFFDDDKTVLLDTVYSRPTDTISEMKAIPQVAGNGSTESSVHSYI
>M4_petMar
ALRADAPSILRTVGKLVADGYSRAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHLKAVCVPEHATDRMPGIVPMQMPPTESFEDLIKFSFITDVLEGNIGYLRFDLFSDLEAL
EHVAHLLVEHVWKKICDTEILIIDLRYNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRI
</font>
 
 


[[Category:Comparative Genomics]]
[[Category:Comparative Genomics]]

Latest revision as of 11:47, 23 March 2010

See also: Curated Sequences | RPE65 | Transducins | Usher: USH2A | Usher: CDH23 | LOXHD1 | Update Blog

RPB3 (IRBP): introduction

Interstitial retinol-binding protein, inexplicably named by RBP3 by HGNC despite a lack of paralogs RBP1 or RBP2, likely confusion with ribosomal binding protein genes and widespread prior use of the protein name IRBP, is a 4 exon 1247 residue glycoprotein thought to shuttle retinoids interstitially between the photoreceptor cells and the retinal pigment epithelium. This role would only make sense for ciliary opsin systems that are unable to regenerate cis-retinal without an auxiliary pathway in an anatomically separate tissue (here RPE). Consequently -- since nearly all protein folds are extremely ancient -- RPB3 must have been co-opted from some other role.

The protein's size results from four ancient internal tandem duplications that became established prior to intronation (that is, the gene structure does not reflect the repeat structure; the repeats happened first, introns were inserted randomly later within the fourth repeat). Any given repeat module clusters markedly better to the same-numbered repeat in other species than to any of the internal repeats, establishing that repeats had arisen and diverged already prior to speciation rather than arising independently in descendent lineages (like RHO1 and RHO2 in lamprey).

It was initially expected that IRBP as a self-contained homotetramer would load four molecules of trans-retinol to accomplish its passive shuttling efficiently. However experiments decisively show this to be false -- the subunits are quite inequivalent and only one molecule is transported. The structure of module 2 of frog was [determined in 2002 (PDB: 1J7X); it consists of two sub-domains and a cleft. The fold matches obscure proteases and hydrolases found in little-studied bacteria; this might represent convergent evolution as seen in TIM beta barrels rather than provide valid clues to ancestral function. A structural determination of the entire molecule is reportedly underway.

Fragments of the protein have been sequenced from an immense number of species for phylogenetic purposes. That's because it evolves fast enough to provide a large number of seemingly informative sites and these can be obtained conveniently exploiting the large size of the first reading frame. While there is minimal risk of accidentally cross-matching different modules, the internal repeat structure implies that residues might not be evolving independently. While the modules might seem too diverged for cross-module gene conversion to still be operative, they retain patches of near identity.

Some very odd aspects of marsupial RBP3 are investigated below because of the implications in a gene so widely used in taxonomy. Teleost fish further raise the question of inhomogeneous recombination events arising from module mix-up. In fish, the ancestral four-module gene has given rise to a two-module gene (M1 and M4) accompanied by an intronless upstream tandem fragment duplicate of M1-M3 without any indication of M4 in the residual 10 residues. Both genes are transcribed and apparently functional since the establishment event occurred prior to zebrafish and fugu divergence, though the upstream gene has been lost in many lineages including tetraodon, medaka, and stickleback but not cichlids.

The upstream fragment suggests a truncated version of the first large exon. The lack of intron does not suggest retroprocessing in view of their lack in the parental gene and the locational adjacency but rather standard recombinational or flanking retroposon-driven tandem duplicating. The loss of M2 and M3 in the downstream gene but retention of standard introns again suggests recombinant loss, either as part of the initial tandem event or subsequent to it as a consequence of the new potential for exact misalignment. Note otherwise the four modules would have been quite diverged from each other prior to the emergence of rayfinned fish.

Conceivably whole genome or segmental duplication in fish set the stage for inhomogeneous recombination (as modelled by Nickerson), though simple local tandem duplication event mediated by retroposons during replication is another option. A great many tandem loci exist in genomes such as human for which wholesale duplication is inapplicable. This could possibly be resolved by sequencing basal teleost fish that diverged prior to the putative genome duplication to determine if the odd arrangement of genes was already established.

IRBP module alignment, conservation and structural aspects

The image below aligns the four module types from human to lamprey and amphioxus, with yellow showing exceptionally conserved residues and cyan moderately conserved. The number of species shown could be greatly expanded especially for module 1 but for clarity only a phylogenetically representative set is displayed. Module boundaries vary slightly according to the bioinformatics tool used to define the domain (eg crystallographic homology transfer, SuperFamily, Pfam, SwissProt, blastp of reference domains) but can be standardized by counting back a fixed number of residues N-terminally from the universally conserved tyrosine and forward from the C-terminal alanines because conserved residues must occupy near-identical positions within the tertiary structure.

It can be seen that M2 has two variable length insertional regions, no doubt relatively disordered loops. Amphioxus additionally has inserted residues in three regions that are suppressed in the figure -- observe that although its overall identity is low, identity is high in conserved residues. The modules each have distinctive class indels and characteristic residues that allow them to be readily distinguished from each other. These features were most likely established prior to lamprey divergence rather than later by convergence. Only two conserved patches are observed, GNvGLYRvD and RAivVGErT in human; other conserved residues are dispersed (at least within the linear structure).

IRBPsstruc.png

The sole structural determination to date, 1J7X_A the single module M2 of Xenopus laevis to 1.8 Å, describes two domains separated by a hydrophobic binding cleft (based on analogy to very similar protease and hydrolase folds). The smaller domain A is an an amino terminal three helix bundle that extends 8 residues past the M2 insertion region (to PGDSIQAEN in xenLae) . M2 was an unfortunate choice because it is most diverged and bares the least resemblance to early-diverging or ancestral sequence.

The observed fold similarities could not plausibly have arisen by chance. Crotonase has a binding site for hydrophobic chains of fatty acids and isomerizes them, with possible relevance in RBP3 to cis and trans retinoid stabilization and transport; however IRBP does not appear to be an enzyme or isomerase itself and RPE65 carries out the regenerative isomerization reaction.

M2 may have two distinct binding sites, one in the cleft between domains A and B and the other solely inside domain B. The assignment of conserved tryptophans to these sites and other conserved residues to the surface (suggesting a protein binding partner, possibly intra-module binding) has to be revisited in view of the much deeper phylogenetic array of sequences now available.

A peculiar feature of full four-module protein (after discounting a couple dozen residues for signal peptide and carboxy terminal wander) is the cheek-to-jowl adjacency of consecutive modules -- in human at most 3 amino acids separate the modules from each other.

This is far too short a bridge to allow many arrangement options for module-module quasi-homodimerization (or allosteric regulation of the binding subunit). Instead the modules must be arranged more as beads on a string. Linear donor-receptor docking in a M1-M2-M3-M4 arrangement risks endless polymerization unless the donor in M4 docks to the receptor in M1. However the bridge sequences are too short to permit closure into a tetrameric cycle.

Despite subunits quite diverged in sequence, a more likely arrangement is an anti-parallel dimer of M1-M2-M3-M4 to M4-M3-M2-M1 (as seen in actinin spectrin repeats). This arrangement allows each module to dimerize with the quasi dihedral symmetry, leaving no docking sites vacant. Because the binding patches are in paralogous modules, this explains why observed surface residue conservation in frog M2 carries over to the other modules.

If true, this implies co-evolution of amino acids in these binding patches on top of what already occurs internally to an individual module. All phylogenetic software assumes -- ridiculously -- independent evolution of sites. However like morphological characters, molecular characters can have dependencies that amount to couplings and coordination between individual reduced alphabets. Here the much studied M1 module has surface residues co-evolving with counterparts on M4.

IRBP has only a single site with glycosylation potential (in beta strand 8 of the hinge region of domain B at residues 204 and 515 which are paralogous under module alignment). Although the NxT motif occurs with excellent phylogenetic conservation depth (human to lamprey, also in fish fragmentary genes), only modules M1 and M2 exhibit it. Given the interstitial location and experimental support for glycoprotein nature, IRBP is very likely glycosylated. Bulky carbohydrate chains need to be out of the way of the putative dimerization patches.

IRBPglycosyl.png

The situation with cysteines is not so clear. Here M1 has a cysteine at position 19 that is conserved back to lamprey (also in fish fragmentary genes) but A/T/S in other modules. A second conserved cysteine is found only in modules M2 and M3 at position 163 (human M1 numbering, residue is I). M4 has no conserved cysteines. A few other cysteines occur elsewhere but only sporadically in the comparative genomics sense. The cysteines at M2 and M3 could potentially form a disulfide in the antiparallel dimer model discussed above. Inter-modular disulfides are not feasible if modules are arranged linearly. No explanation is currently available for the conserved cysteine in M1.

An initial study of knockout mice disastrously used a strain carrying a severe mutation at L450 in RPE65, the enzyme catalyzing the rate-limiting isomerization step in the visual regeneration cycle. Lack of IRBP alone delays transfer of both bleached from photoreceptor cells and newly regenerated chromophore from RPE to photoreceptors.

A single known disease mutation D1080N causes a very rare recessive retinitis pigmentosa. This aspartate may disrupt an internal salt bridge according to the Xenopus M2 structure (and homology transfer to other modules]. It lies in M4 near the end of the second exon. This residue is conserved back to lamprey and amphioxus, indeed to crotonase and other weakly aligning homologs. 

    *
AIILDLRYNLGGDREGVVHWASFFF RBP3_braFlo
A+I+D+R+N+GG    +    S+FF
AMIIDMRFNIGGPTSSIPILCSYFF RBP3_homSap
 +IID+R+N+GG ++SIPILCSYFF
ILIIDLRYNMGGYSTSIPILCSYFF RBP3_petMar

IRBPconserved.png 

M1_homSap  LFQPSLVLDMAKVLLDNYCFPENLLGMQEAIQQAIKSHEILSISDPQTLASVLTAGVQSSLNDPRLVISYEPST-----------PEPPPQVPALTSLSEEELLAWLQRGLRHEVLEGNVGYLRVDSVPGQEVLSMMGEFLVAHVWGNLMGTSALVLDL
M1_bosTau  LFQPSLVLEMAQVLLDNYCFPENLMGMQGAIEQAIKSQEILSISDPQTLAHVLTAGVQSSLNDPRLVISYEPST-----------LEAPPRAPAVTNLTLEEIIAGLQDGLRHEILEGNVGYLRVDDIPGQEVMSKLRSFLVANVWRKLVNTSALVLDL
M1_monDom  IFQPSLVRDMAKILLDNYCFPENLMGMQEVIEQAIKSGEILDISDPQMLASVLTAGVQGALNDPRLVISFEPSI-----------PETPQHVPKLANVTQEELLILLQQMIKYQVLEGNVGYLRVDYIPGQEVVEKVGEFLVNNIWKKLMGTSSLVLDL
M1_macEug  IFQPSLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLASVLTAGVQGSLNDPRLVISYEPSP-----------AEAPQQSPKLTSLTQEELLTLLQQMIKYQVLDGNVGYLRVDYIPGQEVVEKVGEFLVNDIWKKLMGTSSLVLDL
M1_sacHar  IFQPTLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLANVLTAGVQGSLNDPRLVISYEPST-----------SEAPQHDPKFANATQEELLALFQKIIKYQVLEDNVGYLRVDYIPGRDMIEEVGEFLVNDIWKKVMETSSLVLDL
M1_ornAna  VSQPSMVLDVAKILLDNYCYPENLMGMQEAIEEAIQRGEILDIADPKRLASVLTAGVQGSLNDPRLVISYEPAP-----------VAVSQQPPEPASLPAEQPLERLRPAVGSEVLEGNVGYLRVDRLPGREEIERVGAVLGRDIWEKLLGTSALVLDL
M1_galGal  IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPSL-----------HAAPKQEAE-TYPTREQLLSLIEHVVIYDKLEGNVGYLRIDYIIGQEVVEKVGAFLVDKVWKTLINTSALVIDL
M1_taeGut  IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPLP-----------HSGPKQEAE-GSPTREQLLSLIEHVIMYDKLEGNVGYLRIDYIIGEEVVQKVGAFLVDKVWKTLIETSALVIDL
M1_anoCar  VLQSTLVLDMAKLLLDNYCLPENLVGMREAIEQAIKNGEVLDISDPKLLATVLTAGVQGALNDPRLVISYEPTA-----------PAAPKQRME-TSLTPEQLLSLIQHTVKYEVLDDNVGYLRIDYIMGQDIVQKIGSFLVEKVWKTLLGTSALILDL
M1_xenLae  LFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAVKGGEILHISDPDTLANVFTSGVQGYLNDPRLVVSYEPN-------------YSGPQTEQSLELTPEQLKFLINHSVKYDILPGNIGYLRIDFIIGQDVVQKVGPHLVNNIWKKLMPTSALILDL
M1_xenTro  VFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAMKSGEILHISDPETLANVFTSGVQGFLNDPRLVVSYEPN-------------YSGPRKEQSPEPTLEQLKFLLDHSVTYDLLPGNIGYLRIDFIIGQDVVQKVGPLLVNNIWKKLMPSSALILDL
M1_tetNig  AFPPSLIADMAKIVLDNYCSPEKLAGMKEAIKAAGTNTEVLNIPDGESLARVLSAGVQGTVSDPRLMVSFQPN-------------YVPAGPHKMPPLPPEHLVAVLQTSVKLDILEGNTGYLRIDHILGEEVADKVGPALIDLIWNKILPTSALIFDL
M1_takRub  AFPPSLITDMAKIVLDNYCSPEKLAGMKEAIEAAGTNTEVLNIPDGESLARVLSAGVQGTVSDSRLMVSYQPD-------------YVPAVPPKMPPLPPEHLVAVLQTSIKLDLLEGNTGYLRIDHIIGEDVAEKVGPSLIDLIWNKILPTSALIFDL
M1_gasAcu  GFAPNVIIDMAKIVIDNYCSPEKLAGMKEAIEAAGSNTEVLSIPDAETLANVLSAGVQTTVSDPRLMISYEPN-------------YVPVVPPKMPPLPPDQVIAVLQTSIKLDILEGNIGYLRIDHILGEDVAEKVGPLLLDLVWNKILPTSALIFDL
M1_oryLat  SFPPSLITDLAKIVMDNYCSPEKLSGMKEDIATAGANTDVLNIPDGEALAKVLTDGVQTTVSDPRLRVSYEPN-------------YVPVVP---PQLPPEQLIAVLQTSIKLDILEGNIGYLRIDSIIGEEVAEKVGPLLLELVWSKILPTSALIFDL
M1_danRer  NFSPTLIADMAKIFMDNYCSPEKLTGMEEAIDAASSNTEILSISDPTMLANVLTDGVKKTISDSRVKVTYEPD-------------LILAAPPAMPDIPLEHLAAMIKGTVKVEILEGNIGYLKIQHIIGEEMAQKVGPLLLEYIWDKILPTSAMILDF
M1_petMar  KFDTAVVLHLAKVLLDNYCIPENLVGMDEAIQRAVDNGELLGVSDPESAASALTEGIQAALNDPRIAVSYVA-----------------------PPHTFEELLATIPQKTSFAVLDGNVGYLRADEIISEATIKKLGPVIVQRIWNRLVDTDTFVLDL
M1x_takRu  FYQHTLVLEMAKLLLENYCIPENLVGMQEAIQRAIKSREILQISDRKTLATVLTVGVQGALNDPRLSVSYEPS-------------FSPLPLQALSSLPVEQQLRLLRNSIKLDILDSDVGYLRIDRIIDEETLLKFGPLLRENVWDKAAQTSSLILDL
M1x_danRe  SFQSALVLDMAKILLDNYCFPENLIGMQEAIQQAINSGEILHISDRKTLASVLTAGVQGALNDPRLTVSYEPN-------------YTLITPPALHSLPTEQLIRLIRSTVKLEVMDNNIGYLRIDRIIGQETVVKLGRLLHNNIWKKVAHTSAMIFDL
M2_homSap  SALPGVVHCLQEVLKDYYTLVDRVPTLLQHLASM----DFSTVVSEEDLVTKLNAGLQAASEDPRLLVRAIGPTETPSWPAPDAAAEDSPGVAPELPEDEAIRQALVDSVFQVSVLPGNVGYLRFDSFADASVLGVLAPYVLRQVWEPLQDTEHLIMDL
M2_bosTau  RALPGVIQRLQEALREYYTLVDRVPALLSHLAAM----DLSSVVSEDDLVTKLNAGLQAVSEDPRLQVQVVRPKEASS--GPEEEAEEPPEAVPEVPEDEAVRRALVDSVFQVSVLPGNVGYLRFDSFADASVLEVLGPYILHQVWEPLQDTEHLIMDL
M2_monDom  RARPGAIQRLMEVLQNYYTLVDRVPALLHHLTAI----DYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATM-GSEASEEEDATPAANSLPEDESQRQALVDSVFQVSVLPGNVGYLRFDEFADSSVLGTLAPYVIRQVWEPLQDTNHLIMDL
M2_sacHar  RARPGAIQRLMEILQKYYTLVDRVPALLHHLTAI----DYSSVLTEEDLAAKLNAMLQAVSEDPRLLVRVLRPEEATV--EAEPGEESATPASVSLPESDAERQALIDSVFQVSVLPGNVGYLRFDEFADNSVLGTLAPYVLRQVWEPLQDTDHLIMDL
M2_macEug  RARPAAIQRLMEVLQNYYTLVDRVPALLHHLTAI----DYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATA--GAESREEAATAAPVPLPDGESQRQALVNSVFQVSVLPGNVGYLRFDEFADSSVLGALAPYVLQQVWEPLQDTDHLIMDL
M2_ornAna  GAVPGAVAHLADLLRDYYALVDRVPALLRHLAAL----DLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPEEAERGPPRKEEEQKEEEEEDQPSPGASILPGDGSSLFRVSVLPGNVGYLCFDEFPEASALERLGPLLGRRVWEPLEATDHLMVDL
M2_galGal  RAVPGTLSRLTDILKDYYSLVERVPVLLRHLTTS----DFSSVQSAEDLATKLNTEMQTLSEDPRLLVRTMMPGEA-----AAPPAEMPIAMAANLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYIVKKVWEPLQNTENLIMDL
M2_taeGut  RAVPGTISHLKNILKDYYSLVERVPALLRRLTTS----DFSSVQSSEDLATKLNTELQALSDDPRLMVRVMMPGEA-----ADSPAEKPVGMAADLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYLVHKVWEPLQNTENLIMDL
M2_anoCar  KAIPNSMSYLVDIIKNNYSMLEQVPVLLQHLSTF----DYSSVLSVKDLASKLNAELQTISEDPRLFLRVPASDEA-----VTSQTDEKVAMASDLPNNEQLMKALVMTVFKVSVLPGNVGYMRFDEFGDATVLVKLGPYLLQHVWEPLQATDYLIIDL
M2_xenTro  SSITHILLQLSEILVNNYAFSERIPTLLQHLPNL----DYSSVISEEDITAKLNYELQSLTEDPRLVLKSKTDSLV---------MPEDSTQVENLPDDEATLQALVNTVFKVSILPGNIGYLRFDEFADVSVLAKLGPYIVNTVWDPITVTENLIIDL
M2_xenLae  SSVTHVLHQLCDILANNYAFSERIPTLLQHLPNL----DYSTVISEEDIAAKLNYELQSLTEDPRLVLKSKTDTLV---------MPGDSIQAENIPEDEAMLQALVNTVFKVSILPGNIGYLRFDQFADVSVIAKLAPFIVNTVWEPITITENLIIDL
M2_petMar  GVARKAVEAAGELLLSSYTFVERASAIADHLSWS----EYGSVVSVEDLTSKLTQDLQSVAEDPRLVVSNREPEWV--------GAADPPGPPAPLPDDEQMLEAIVDSAFKVEVLEGNIGYLRFDEFGDASAVMKLRKQLVSKVWERIHPTDDVIIDL
M2x_takRu  SRIPKVLQIVLDIIGRFYAFADRVQALLQQLESA----DLFSVVSEEDLAARLNHDLQTASEDPRLIIRHKRDNI------------PRAEEEPELHAANDHDGELVEG-FTVQVLPHNTGYLRLDRFVRCSEGDKLEEIVAEKVWGPLKDTQNLIIDL
M2x_danRe  KTIPKAVRRVSDIIKRYYSFKDKIPALLNQLAKA----DYFTVVSEEDLAGKLNHEMQSVFEDPRLLIKATQVLT------------DDASSE-DRSSSDDLTDPL----FKLEMISGNNGYLRFDRFPTPEVLLRLEDHIKKKIWQPVQETENLVIDL
M3_homSap  QSLGALVEGTGHLLEAHYARPEVVGQTSALLRAKLAQGAYRTAVDLESLASQLTADLQEVSGDHRLLVFHSPGELV---------VEEAP-PPPPAVPSPEELTYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVRLVWQQLVDTAALVIDL
M3_bosTau  RSLGELVEGTGRLLEAHYARPEVVGQMGALLRAKLAQGAYRTAVDLESLASQLTADLQEMSGDHRLLVFHSPGEMV---------AEEAP-PPPPVVPSPEELSYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVQLVWQKLVDTAALVVDL
M3_monDom  QRLGALVEGTGHLLEAHYALPEVVGQASALLKAKLEHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPV---------SEELT-PPQKGVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIAPQLVELVWEKLVHTEALVVDL
M3_macEug  QRLGALVEDAGHLLEAHYALPEVVGQASALLRARLVHGTYRTAVDFESLASQLTSDLQEVSGDHRVHVFHSPGELI---------PEELS-PPQNVVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIGPQLIELVWEKLVNTEALVVDL
M3_sacHar  QRLGALVEGTGHLVEAHYALPEVVGQASAFLRATLAHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPV---------PEESS-PPHKGVPSPEELTYLIEALFKTDVLP-QLGYLRFDMMAEVETVRAIGPQLVELVWEKLVNTEALVVDL
M3_taeGut  KNMGVLLEGTGQLLEDHYAIPEVAAKASAMLSTKRAQGGYRSAIDSETLASQLTSDLQEASGDHRLHVFHSHVEPT---------PEEQL-PNV--IPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLLQMVWNKLVDTDAMIIDM
M3_galGal  RKMGILLESTGQLLEAHYAIPEVAEKASVMLSTKRVQGGYRSAVDFETLASQLTSDLQEASGDHRLHVFHSHVEPT---------PEEQL-PNM--IPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLVQMVWNKLVDTDAMIIDM
M3_anoCar  KGMGSLIERVGQLLEAHYAIPEMARRVSSMLNSKLAQGGYRTAVDFETLASQLTNDLQETSGDHQLHVFHSHVEPS---------LEEQS-PFK--TLTPEELNFIIEALFKVDVLPGNVGYLRFDMMAEFESVKTIEPQILHMVWEKLVETSAMIVDM
M3_xenTro  PSVFALVEGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASQLTSEMQENSGDHRLHVFYSDTEPE---------ILEDQ-PPK--IPSAEELNYIIDALFKIEVLQGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDM
M3_xenLae  PSIFPLVKGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASLLTSEMQENSGDHRLHVFYSDTEPE---------ILEDQ-PPK--IPSPEELNYIIDALFKIEVLPGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDM
M3_petMar  AKMASLLELAGALVEGYYAMLSDGENATAEILLKYREGWYRSVVDYEALASQLTSDLHEIWGDHRLHAF-YSDLQI---------ERMDE-DKTPSVPSPEELSVLIDTVFKVDILANNVGYLRFDMMTDAEVLKHVGPQLVEKVWNKISSTRSLVIDV
M3x_takRu  QGLRSLIGRTGELLEKHYAIQEVAQKVGEVLLSKWAEGLYRSVVDLESLASQLTADLQEASGDHRLHVFRCDVELE---------SLHGV-PK---IAAVEEAGFVIDALFKSELLPRNVGYLRFDTMADIEAAKGAAPRLVKSVWNKLVDTDSLIIDM
M3x_danRr  KNIQGLVQEAGDLLEKHYSVPEVAAKVSRLLQSKLTEGLYRSVVDYESLASQLTSDLQETSGDQRLHIFYCETEPE---------TLHDT-PK---IPSPEEAGFIVEALFKVDVMSGNIGYLRFDMMEDIKVLQAINPEFLKVVWNKLVNTDMLIIDV
M4_petMar  ADAPSILRTVGKLVADGYSRAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHLKAVCVPEHAT---------DRMPG-IVPMQMPPTESFEDLIKFSFITDVLEGNIGYLRFDLFSDLEALEHVAHLLVEHVWKKICDTEILIIDL
M4_homSap  AKVPTVLQTAGKLVADNYASAELGAKMATKLSGL--QSRYSRVTSEVALAEILGADLQMLSGDPHLKAAHIPENAK---------DRIPGIVPMQ-IPSPEVFEELIKFSFHTNVLEDNIGYLRFDMFGDGELLTQVSRLLVEHIWKKIMHTDAMRIID
M4_bosTau  AKVPTVLQTAGKLVADNYASPELGVKMAAELSGL--QSRYARVTSEAALAELLQADLQVLSGDPHLKTAHIPEDAK---------DRIPGIVPMQ-IPSPEVFEDLIKFSFHTNVLEGNVGYLRFDMFGDCELLTQVSELLVEHVWKKIVHTDALIVDM
M4_monDom  AKVPTILQTAGKLVADNYASLEVGSRVASKLAKL--QTQYRQVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAK---------DRIPGIVPMQ-LPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDM
M4_macEug  SKVPTILQTAGKLVADNYASPEVGSRVAAKLARL--QTQYRQVTSEGELADMLGADLQTLSGDSHLKTAHIPEDSK---------DRIPGIVPMQ-LPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDM
M4_sacHar  AKVPTILQTAGKLVADNYASPEVGSRVAAKLASL--QIQYGKVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAK---------DRIPGIVPMQ-LPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLIQVSDLLVEHVWKKVMHTDGMIIDM
M4_ornAna  SKVPTVLRTAAKLVADNYAFRETGAGVAAQMGGL--QARCGRVTSEGALAEVLGAHLRALSGDPHLQMVYIPEDAK---------DRIPGVVPMQ-IPSAETFEDLIKFSFHTSVMEGNIGYLRFDMFGDCELLTQVSELMVEHVWKKIVHTDGLIIDM
M4_xenLae  TKIPTVIQTAAKLVADNYAFADTGANVASKFIALVDKIDYKMIKSEVELAEKINDDLQSLSKDFHLKAVYIPENSK---------DRIPGVVPMQ-IPSPELFEELIKFSFHTDVFEKNIGYIRFDMFADSDLLNQVSDLLVEHVWKKVVDQDALIIDM
M4_xenTro  TKIPSVIQTAGKLVADNYAFADTGADVASKLIALVDKINYKMIKSEVELAEKLNYDLQSLSKDVHLKAVYIPENSK---------DRIPGVVPMQ-IPSPEMFEDLIKFSFHTDVFEKNLGYIRFDMFADSDLLNQVSDLLVEHVWKKVVNQDALIIDM
M4_taeGut  AQVPQILQTVGKLVADNYAFVNTGTVIASNLTKNIHKDNYKRINTEEDLAGKVTAILQALSDDKHLKLLYIPEHAK---------DSIPGIMPKQ-IPPPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDSELLTQLSDLMIEHVWKKIFHTDALIIDL
M4_galGal  TQVPQIVQTVGKLVAENYAFVDIGTDIASNLTKSVNKENYKRINSEKELARKLTAILQALSDDEHLKILYIPEHAK---------DSIPGILPKQ-IPSPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDCELLTQVSDLLVEHVWKKIVHTDALIIDM
M4_anoCar  TKLPSVLNTIGKLVADNYAFADIGATVAAKFADYAKKGTYRKINSEIELSGKLAADLKALSGDRHLMISHIPERSK---------GRILGLVPMQQIPPPEILEDLIKFSLHTNVFENNIGYLRFDMFGDCELMSQVSELLVQHVWNKIVNTDALIIDM
M4_tetNig  AQIPAIIEGTAALVANNYAFEATGADVAKELRELQANGQYSSVVSKESLEAALSADLQRLSGDKSLKTT----------------PNTPVLPPMD--YTPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDL
M4_takRub  AQIPAIIEGAATLIAKNYAFEATGADVATKLRELLAKGQYNSVVSSESLEVALSADLQRLSGDKSLKAT----------------QNAPVLPPMD--YSPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDL
M4_gasAcu  NRVPAIIEGSATLIADNYAFEDIGAAVAEKLKGLLANGEYSKVVSKDSLEMKLSADLRTLSGDKSLKTT----------------SNVPALPPMN--YSPEMYIELIKVSFHTDVFEDNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDAMIVDL
M4_oryLat  LQVPAIIEESATLVANNYAFESTAADVAEKLKGHLANGDYNMVVSKESLEAKLSADLQSLSGDKSLTVS----------------SNTGAPPPME--YTPEMYIELIKISFHTDVFENNIGYLRFDMFGDFEEVKAIAQVIVEHVWNKVLHTDAMIIDL
M4_danRer  AEIPALAQAAATLIADNYAFPSIGEHVAEKLEAVVAGGEYNLISTKEDLEERLSEDLLKLSEDKCLKTT----------------SNIPALPPMN--PTPEMFIALIKSSFQTDVFENNIGYLRFDMFGDFEHVATIAQIIVEHVWNKVVDTDALIIDL

M1_homSap  RHCTGGQVS-GIPYIISYLHPGN-TILHVDTIYNRPSNTTTEIWTLPQVLGERYGADKDVVVLTSSQTRGVAEDIAHILKQMRRAIVVGERTGGGALDLRKLRIGES------DFFFTVPVSRSLGPLGGGSQTWEGSGVLPCVGTPAEQALEKALAIL
M1_bosTau  RHCTGGHVS-GIPYVISYLHPGS-TVSHVDTVYDRPSNTTTEIWTLPEALGEKYSADKDVVVLTSSRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRVGQS------DFFLTVPVSRSLGPLGEGSQTWEGSGVLPCVGTPAEQALEKALAVL
M1_monDom  QHSSGGEIS-GIPFVISYLHQGD-ILLHVDTVYDRPSNTTTEIWTLPQVLGERYGGEKDMVVLTSHRTVGVAEDIAYILKKLRRAIVVGEQTLGGALDLRKLRIGQS------DFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALGKALAIL
M1_macEug  QHSTEGEVS-GIPFVISYLHEGD-ILLHVDTVYDRPSNTTTEIWTLPQVLGERYSGEKDLVILTSHRTVGVAEDIAYILKKMRRAIVVGEQTLGGALDLRKLRIGQS------DFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALEKALAIL
M1_sacHar  QHSRGGEVS-GIPFVISYLHQGD-ILLHVDTIYDRPSNTTTEIWTLPQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKKMRRAIVVGEQTQGGSLDLRKLRIGQS------DFFITVPVARSLSPLGGGSQTWEGSGVVPCVGIPAEQALEKALAIL
M1_galGal  RYSTGGQIS-GIPFIISYLHEAD-KMLHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITLGEKTAGGSLDIQKLRIGPS------NFYMMVPVSRSVSPLSGGGQSWEVSGVMPCVASEAEQALKKSLDIL
M1_taeGut  RHSTGGQIS-GLPFIISYLHEQD-KILHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITVGEKTAGGSLDIQKLRIGPS------NFYMMVPVSRSVSPLSGGGQSWEVSGVMPCVATEAEQALQKSLDIL
M1_anoCar  RYTTGGDVS-GIPFIISYLYNGD-KVLHVDTVYNRPSNTTVEILTLPKVLGVRYSKDKDVILLISKYTTGVAENVAYILKHMHRTIIVGEKSAGGSLDTQKMQIGNS------QFYMTVPLSCSVSPLSGSGQSWEISGVTPCVVISAEQALDKALAIL
M1_ornAna  RHSTGGHVS-GIPFFISYFYPEG-PALHVDTVYDRPSNATRQLWTLPRVLGARYAADKDVVVLTSRLTAGVAEDVAYILQQMRRAIVVGERTAGGPLVFRKLRVGLS------DFFITVPVACSLGPLGGGGRSWEGSGVLPCVAVPADRALDEALDIL
M1_xenLae  RYSTQGEVS-GIPFVVSYL--CD-SEIHIDSIYNRPSNTTTDLWTLPELMGERYGKVKDVVVLTSKYTKGVAEDASYILKHMNRAIVVGEKTAGGSLDTQKIKIGQS------DFYITVPVSRSLSPLTG--QSWEVSGVSPCVVVNAKDALDKAQAIL
M1_xenTro  RYSTQGKVS-GIPFVVSYL--TD-PQIHIDSIYNRPSNTTTDLWTLSELMGERYGKDKDVVVLTSKYTEGIAEGAAYILKHMSRAIVVGEKTAGGSLDIQKIKIGQS------EFYITVPVSRSISPLTG--QSWEVAGVFPCVVVNANNALNKAQGIL
M1_tetNig  RYTSSGDIS-GIPYIVSYFTQAE-PVVHIDSVYDRPSNTTTKLLSLPNLLGQRYGVSKPLIVLTSKNTKGIAEDVAYCLKNLKRATIVGEKTAGGSLKLDTFKVGDT------DFYITVPTAKSINPITG--SSWEIRGVTPHVEVNAEDALATAIKIV
M1_takRub  RYTSSGEIS-GIPYIVSYFTQAE-PVVHIDSVYDRPSNTTTKLFSLSNLLGERYGITKPLIILTSKNTKGIAEDVAYCLKNLKRATIVGERTAGGSVKLDNFKVGST------DFYITVPTAKSINPVTG--SSWEITGVKPDVEVNAEDALATAIKIV
M1_gasAcu  RYTSSGDIS-GIPYIVSYFTEAG-TPIHIDSIYDRPSNTTTKLFSMSTLLGERYSTSKPLIILTSKNTKGIAEDVAYCLQNLKRATIVGEKTAGGSVKVDKIQVRDT------GFYVTVPTAKSVNPITG--STWEVTGVTPNVEVNAEDALATAIKIV
M1_oryLat  RYTSSGDIT-GIPYIISYLTDAK-SEIHIDTIYDRPLNTTTKLLSMQSTLGQTYGGTKPLLVLTSKNTKDIAEDVAYCLKNLKRATIVGEKTAGGSAKIKKFRVGDT------DFYVTLPTAKSINPITG--SSWEVTGVKPNVEVNAEEALATALKII
M1_danRer  RSTVTGELS-GIPYIVSYFTDPE-PLIHIDSVYDRTADLTIELWSMPTLLGKRYGTSKPLIILTSKDTLGIAEDVAYCLKNLKRATIVGENTAGGTVKMSKMKVGDT------DFYVTVPVAKSINPITG--KSWEINGVAPDVDVAAEDALDAAIAII
M1_petMar  RYNSHGDIT-GLPYLVSCFCEPR-PVVHLDTVYYRPTNESKEIWSLPDLQGARFAKHKDVFVLVSANTEGVAENVAYVLKHLHRATVIGEQTAGGSLEVERFRLGDS------RFFVTVPTARS-EPAD---RSW---GVFPCVSAPSERALDKALEIL
M1x_takRu  RFSTAGGWS-GIPSIVSYFTEPH-SLVHIDTVYDRPSNTTTELWTMSSVRGKTFGGKKDMIVLIGRRTAGAAEAVAYTLKHLNRAIVVGERSAGGSLKVRKFRIAES------DFYITMPVARSVSPITG--KSWEVSGISPTVNVAAREALAKAQTFL
M1x_danRe  RFSTAGELS-GLPYIVSYFSDSD-PLLHIDTIYERPTNITRELWTLPTLLGERFGKRKDLIVLISKRTIGAAEGVAYILKHLKRAVIIGERSAGGSVRVDKLKIGDS------GFYITVPVARSVNPVTG--QSWEVSGVAPSVTVNPKESIAKAKSLI
M2_homSap  RHNPGGPSS-AVPLLLSYFQGPEAGPVHLFTTYDRRTNITQEHFSHMELPGPRYSTQRGVYLLTSHRTATAAEEFAFLMQSLGWATLVGEITAGNLLHTRTVPLLDTPEG---SLALTVPVLTFIDNHG---EAWLGGGVVPDAIVLAEEALDKAQEVL
M2_bosTau  RQNPGGPSS-AVPLLLSYFQSPDASPVRLFSTYDRRTNITREHFSQTELLGRPYGTQRGVYLLTSHRTATAAEELAFLMQSLGWATLVGEITAGSLLHTHTVSLLETPEG---GLALTVPVLTFIDNHG---ECWLGGGVVPDAIVLAEEALDRAQEVL
M2_monDom  RYNPGGPSS-AVPLLLSYFQDPAAGPIRLFTTYDRQTNQTQEHLSRAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNG---NLVLTVPILTFIDNNG---ECWLGGGVVPDAIVLAEEALDKAKEVL
M2_sacHar  RYNPGGPSS-AVPLLLSYFQDPSAGPVRLFATYDRQTNQTQEYRSRAELLGKPYGAERGVYLLTSYHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNG---SLVLTVPTLTFIDNHG---ECWLGGGVVPDAIVLAEEALDKAKEVL
M2_macEug  RYNPGGPSS-AVPLLLSYFQDPAAGPVRLFATYDRQTNQTREYRSQAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGNLMHTRTFSLLQPPDG---SLVLTVPILTFIDNHG---ECWLGGGVVPDAIVLAEEALDKAKEVI
M2_galGal  RYNPGGPSSSAVPMLISYFQDPTAGPVHLFTTYDRRTNHTQEHNSQAELLAQPYGAQRGIYVLTSRHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTCTFPLVQPEQGITRGLTITVPVITFIDNHG---ESWMGGGVVPDAIVLAEDALEKAEEVL
M2_taeGut  RYNLGGPSSSAVPVLLSYFQDPAAGPVHLFTTYDRRTNHTQEHNSQAELLGQSYGAKRGVYLLTSHHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTRTFPLLQPGPGITRGLTITVPVITFIDNHG---ESWMGGGVVPDAIVLAEDALEKAEEVL
M2_anoCar  RYNIGGPSSSAVPVLLSYFQDPSAGPVHFFTTYNRLTNQTQAYSSSAEMVGKPYGARRGVYLLTSHNTATAAEEFAYLMQTLGRATLVGEITAGSLSHTHTFCILELGGGC--GLLINVPVITLIDNHG---EYWLGGGVVPDSIVLADEALEKAREVL
M2_ornAna  RNNPGGPSS-AVPLLLSYFQDPAAGPIRLFTTYNRPADVTREYASRAGALEKPYGARRGVYLLTSHRTATAAEEFAYLMQALGRATLVGEITAGRLLHSRTFPLLRPPWE---GLVLTVPFLTLFDPHG---EGWLGGGVVPDAIVLAEEALEKAGEVL
M2_xenTro  RYNIGG-SSTSIPLLLSYFQEPE-NRIHLFTIYNRQQNSTNEVYSLPKVLGKPYGSKKGVYVLTSHETATAAEEFAYLMQSLSRATIIGEITSGNLMHSKAFPLDGTR------LSVTVPIMNFIDNNG---DYWLGGGVVPDAIVLADEALDKAKEII
M2_xenLae  RYNVGG-SSTAVPLLLSYFLDPE-TKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFDGTQ------LSVTVPIINFIDSNG---DYWLGGGVVPDAIVLADEALDKAKEII
M2_petMar  RYNLGG-SSTAIPIVLSYFQDVA--PVHFYTVYDRLRNVTAEFHTVSNLTSQLYGSKKGVYLLTSQHTATAAEEFTYLMQSLNRATIVGEITSGRLAHSLAFRLSDT------GLYMTVPIVNFIDNND---EYWLGGGVVPDAIVLAENALDAAKEII
M2x_takRu  RHNTGG-SSTSVALLLSYLRDPL-PKRHFFTIYDSVQNTTTEYGSRPHIPGPSYGSERGVYVLTSHYTAGAAEEFAYLIQSLHFGTVVGEITSGTLMHSKTFQVEGT------DIFITVPFINFLDNNG---EYWLGGGVVPDAIVLAEEALEHVNRTA
M2x_danRe  RFNTGG-STEALPILLSYMFDTS-SSTYLFSIYDSIKNTTFDFHTLNNISGPSYGSTKGVYVLTSYYTAEAGEEFAYLMQSLHRGTVIGEITSGMLLHSKTFQIEQT------SLAITVPIINFIDVNG---ECWLGGGVVPDAIVLAEEALERAHEII
M3_homSap  RYNPGSYST-AIPLLCSYFFEAE-PRQHLYSVFDRATSKVTEVWTLPQVAGQRYGSHKDLYILMSHTSGSAAEAFAHTMQDLQRATVIGEPTAGGALSVGIYQVGSS------PLYASMPTQMAMSATTG--KAWDLAGVEPDITVPMSEALSIAQDIV
M3_bosTau  RYNPGSYST-AVPLLCSYFFEAE-PRRHLYSVFDRATSRVTEVWTLPHVTGQRYGSHKDLYVLVSHTSGSAAEAFAHTMQDLQRATIIGEPTAGGALSVGIYQVGSS------ALYASMPTQMAMSASTG--EAWDLAGVEPDITVPMSVALSTARDIV
M3_monDom  RYNPGGYST-AVPLLCSYFFEAE-PRRHLYTIFDRAASQLTEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFVHTMKDQHRATVIGEPTGGGALSVGIYQVENS------PLYASMPTQVAISPVTG--KAWDMAGVEPDVSVLSSEALMTTQGIV
M3_macEug  RYNPGSYST-SVPLLCSYFFEAE-PRKHLYTIFDRAASQATEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFAHAMKDLRRATVIGEPTAGGALSVGIYQVSNS------PLYASMPTQVAISPVTG--KAWDIAGVEPDVSVPAREALITTQGIV
M3_sacHar  RYNPGSYST-TVPLLCSYFFEAE-PRKHLYTVFDRATSQFTEVWTLPQVTGERYGSQKDLYILISHTSGSAAEAFAHIMKDLQRATVIGEPTAGGALSVGIYQVGDS------PLYVSMPTQVALSPVTG--KAWDMAGVEPDVSVLANEALITAQGIV
M3_taeGut  RYNTGGYST-AIPILCSYFFDPE-PRKHLYTVFDRSTSRSTEVWTLPQLAGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVVGEPTVGGSLSVGIYRVGNS------SLYASIPSQVVLSPVTG--KVWSVSGVEPHITIQASEAMAAAQHIA
M3_galGal  RYNTGGYST-AVPILCSYFFEPE-PRQHLYTVFDRSTSRSTEVWTLPKVTGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVIGEPTVGGSLSVGIYRVGNS------SLYRSIPSQVVLSPVTG--KVWSVSGAEPHITIQASEALAAAKHIA
M3_anoCar  RYNTGSYST-AVPMFCSYFFDAE-PQQHLYTIIDRSTSQSTEVWTSSQVSGKRYGSTKDLYILISHASGSAAEAFTRSLKDLHRATVIGEPTVGGSLSASIYNIGST------PLYASIPSQIVLSPVSG--KVWSLSGIQPHVTTQSNEALASAQNII
M3_xenTro  RYNTGGYST-AIPIFCSYFFDPE-PLQHLYTVYDRSTSSGTDIWTLPEVVGERYGSTKDIYILTSHMTGSAAEVFTRSMKELNRATIIGEPTSGVSLSVGMYKVGES------NLYVSIPNQVVISSVTG--KVWSVSGVEPHVIAQASEAMNVAHHII
M3_xenLae  RYNTGGYST-AIPIFCSYFFDPE-PLQHLYTVYDRSTSTGKDIWTLPEVFGERYGSTKDIYILTSHMTGSAAEVFTRSLKDLNRATLIGEPTSGVSLSVGMYKVGDS------NLYVTIPNQVVISSVTG--KVWSVSGVEPHVIIQANEAMNIAHRII
M3_petMar  RYNMGGYST-SIPILCSYFFDAS-PPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDS------RLYVFIPNQAGVSPSGG--RTWSVAGVEPHVQTKASEALQSALRMV
M3x_takRu  RYNAGGSST-AVPLWCSYFVDGE-PLQHLYTVYDRTTKTRVEVMTLPEVSGQRYDPGKDVYILTSHMTGSAAEAFVRAMRDLNRVTIVGEPTAGGSLSSATYQIGES------VLYASIPNQVVTSAATG--KLWSISGVEPDVFAQARDALPVAQRII
M3x_danRr  RYNTGGYST-AIPLLCTYFFDAQ-PLTHIYTLFDRSTATVTKVTTLPDVLGQKYSSQKDVYILTSHITGSAAEAFTRTMKDLKRATVIGEPTIGGALSSGTYQIGNS------ILYASIPNQAVLNAVTG--KPWSISGVEPHIVAQASDALIVAQKII
M4_petMar  RYNMGGYST-SIPILCSYFFDAS-PPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDS------RLYVFIPNQAGVSPSGG--RTWSVAGVEPHVQTKASEALQSALRMV
M4_homSap  MFNIGGPTS-SIPILCSYFFDEG-PPVLLDKIYSRPDDSVSELWTHAQVVGERYGSKKSMVILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDT------NLYLTIPTARSVGASDG--SSWEGVGVTPHVVVPAEEALARAKEML
M4_bosTau  RFNIGGPTS-SISALCSYFFDEG-PPILLDKIYNRPNNSVSELWTLSQLEGERYGSKKSMVILTSTLTAGAAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDT------DLYLTIPTARSVGAADG--SSWEGVGVVPDVAVPAEAALTRAQEML
M4_monDom  RFNIGGPTS-SISALCSYFFDEG-QEVLLDQIYNRPNDSISEIWTQSQVAGERYGSKKSVIILTSSMTAGAAEEFVYVMQRLGRALVIGEVTSGGCQPPQTYHVDDT------DLYITIPTARSVGSGDK--PSWEGVGVAPHVEVPADQALSKAKEMF
M4_macEug  RFNIGGPTS-SISALCSYFFDEG-QKVLLDRIYNRPNDSIVEIWTQPHVTGERYGSKKSVIILTSSTTAGAAEEFVYIMQGLGRALVIGEVTSGGCQPPQTYHVDDT------DLYITIPTAQSVGSGDR--PSWEGIGVTPHVEVPADQALSKAKEMF
M4_sacHar  RFNIGGPTS-SISAMCSYFFDEG-QGVLLDRIYNRPNDSISEIWTQPQVIGERYGSKKTVVILTSSMTAGAAEEFVYIMQRLGRALVIGEVTSGGCQPPQTYHVDDT------DLYITIPTTRSVVSGDK--SSWEGVGVVPHMEVPADQALSKAKEMF
M4_ornAna  R-NIGGPTS-SISALCSYFFDED-HPVLLDKIYNRPNDSISEIWTHSHIAGERYGSRKSVVILTSNMTAGAAEEFVSIMKRLGRALVVGEVTGGGCHPPQTYHVDDT------HLYITIPTSRSVGSEDG--SSWEGVGVTPHLVVPADVALSRAKDLF
M4_xenLae  RFNIGGPTS-SIPIFCSYFFDEG-TPVLLDKIYSRTSNAMTDIWTLPDLVGKTFGSKKPLIILTSSLTEGAAEEFVYIMKRLGRAYVVGEVTSGGCHPPQTYHVDDT------HLYLTIPTSRSASAEPG--ESWEGKGVLPDLEISSETALLKAKEIL
M4_xenTro  RFNIGGPTS-SIPTFCSYFFDEG-TPVLLDKIYSRTTNAITDVWTLPHLVGNAFGSKKPVIILTSSLTEGAAEEFVYIMKRLGRAYVIGEVTSGGCHPPQTYHVDDT------HLYLTIPTSRSASAKPG--ESWEGKGVLPDLEITSETALMKAKEIL
M4_taeGut  RYNIGGSTT-PIAILCSYFFDEG-HPVLLDRVYDRPSDSVKEIWTQPQLKGERYGSQKGLVILTSAVTAGAAEEFVYIMKRLSRALIIGEQTSGGCHSPQTYQVDET------NFYVVIPTSRSVTSADS--TSWEGKGVSPHIETPAETALIKAKEML
M4_galGal  RYNIGGYTN-SIPILCSYFFDEG-HQVLLDKVYDRPSDSVKEIWTQPQLRGERYGSQKGLIILTSAVTAGAAEEFVFIMKRLGRALIIGEQTSGGSHSPQTYQVDDT------NFYIIIPTARSVISAES--ASWEGKGVPPHMETPAVTALIKAKEVL
M4_anoCar  RYNVGGPAC-SVPLLCSYFFDEG-HPILLDKVYNRPNDTTSNIWTVSKLAGKRYGLNKGLIILTSSVTSGAAEEFAHIMKRLGRAFIIGQKTSGGCHPPQTFHVDGT------NLYITTPVSRSVFSVN---DSWEGVGVSPHLDVSTDVALIKAKEML
M4_tetNig  RNNVGGPTT-AIAGFCSYFFDAD-KQNRVGQAVRQASGTTTELLTLSELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQTFRVGET------DVFLLIPTVHSDTGA-G--PAWEGAGIAPHIPASAEAALGTARAIL
M4_takRub  RNNVGGPTT-AIAGFCSYFFDAD-KLIVLDKLHDRPSGTTTELLTLPELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQVFSVGEI------GIFLSIPTVHSDTAA-G--PAWEGTGITPHIPVSAEAALGTAKGIL
M4_gasAcu  RNNIGGPTT-AIAGFCSYFFDSD-KQIVLDRLYDRPSGTTTELRTLPELTGTRYGSKKSLVMLTSRATAGAAEEFVYIMKKLGRAMIVGETTAGTSHPPKTFRVGET------DIFLSIPTVHSDTAA-G--PAWEGAGVAPHIPVPADAALETAKGIF
M4_oryLat  RNNVGGPTT-AIAGFCSYFFDGD-KQILLDKLYDRSTGTTTDLLTLGELTGERYGSKKSLIILASRATAGAAEEFVYIMKRLGRAMIVGETTAGASHPPKVFQVGES------DIFLSIPTVHSDTSA-G--PGWEGAGVAPHIPVAAGAALETAKAIL
M4_danRer  RNNIGGHAS-SIAGFCSYFFDAD-KQIVLDHIYDRPSNTTRDLQTLEQLTGRRYGSKKSVVILTSGVTAGAAEEFVFIMKRLGRAMIIGETTHGGCQPPETFAVGES------DIFLSIPISHS-TAQ-G--PSWEGAGIAPHIPVPAGAALDTAKGML

Evolutionary origin of RBP3 (IRBP)

Lamprey sequence was recovered by a French group in 2008 from unassembled genome project contigs but not explicitly provided in the article nor posted to GenBank. They reported four modules despite uncertainty in whether these all resided in the same gene. Below, a nearly full length gene (exon 3 and 4 are missing) has been independently recovered from the initial lamprey assembly and parsed into its modules using Superfamily HMM. It indeed has four modules classifying to the expected types and ordering, proving the modern version of the gene was fully established prior to the last common ancestor of mammals and lamprey. As the lamprey ancestor already had fully modern ciliary color vision (so need for retinol shuttling), the role of RBP3 (IRBP) in extant species may have already been established 500 myr ago.

It cannot yet be verified that lamprey has the third intron, though otherwise intron positions and phases are identical to other vertebrates. While no full length chondrichthyes sequence is available, close study of the elephantshark contig containing exon 3 establishes that the final intron occurs with the same phase 0 and position seen in later-diverging tetrapods. While intron loss in lamprey is possible, the simpler explanation is intron gain in the stem for reasons provided below. 

Callorhinchus milii contig AAVX01012059 establishes that exon 3 has standard flanking phase 1 introns on both sides: 

VIASTSSLIVDLRYNIGGPTSSIPILCSYFFDDDKTVLLDTVYSRPTDTISEMKAIPQVAGNGSTESSVHSYIGERYGSKKSMVIL
+I  T+SL  D RYNIGGPTSSIPILCSYFFDDDKTVLLDTVYSRPTDTISEMKAIPQVAGNGSTESSVHSYI E     K  +I+
LIIETNSL-RDHRYNIGGPTSSIPILCSYFFDDDKTVLLDTVYSRPTDTISEMKAIPQVAGNGSTESSVHSYICEDLHHCKYGLII

Previous efforts to trace the gene back to earlier deuterostomes (or metazoa) proved futile. That remains the case in March 2009 for tunicate (despite a third assembly and massive transcript set) and much-studied sea urchin, establishing that in all likelihood homologs have been lost. However it is possible but implausible that sequences have diverged to the point of unrecognizability. It is equally implausible that a complex fold matching known bacterial folds arose de novo in Cambrian deuterostomes. This creates the unresolved dilemma of ghost gene retention over an immense time frame in ancestral eyeless species yet loss in almost all extant clades.

With the advent of the second assembly of the cephalochordate Branchiostoma floridae (which has far fewer polymorphism-related assembly stutters than the first release), it is straightforward to recover a homolog in this species (after rubbishing an unmotivated fusion to the adjacent sulfotransferase in a JGI gene model). The smaller gene here consists of a single module that clusters best with M3 and M4. This suggests that the module number expansion -- like so many key events in vertebrate gene evolution -- took place between cephalochordate and agnathan divergences.

The shocking aspect of the Branchiostoma RBP3 (IRBP) gene is its 9 exons. These range in size from 30 to 66 amino acids, quite typical of the average vertebrate gene. Splice junctions are all standard GT-AG. The anomaly here is really in the immense size of the first exon of the vertebrate four-module gene which extends for 1018 residues in human. That can be placed in prospective using the UCSC Table Browser to determine the overall size distribution of the 190,000-odd human coding exons. The average protein has 450 residues and 8-9 exons.

The second anomaly is that the placement and phasing of the Branchiostoma introns do not correspond at all (via blastp registration) to those of module 4, the only vertebrate module with internal exons (3 of them). A great majority of introns are immensely conserved -- from human to cnidarian -- so the notion of massive erasure followed by de novo intronation in either the Branchiostoma or vertebrate gene can be discarded. However some explanation of descent is required because the genes are strongly homologous (chance expectation e-30) though at best 31% identical and gappy in alignment.

The Branchiostoma gene can be assumed orthologous to vertebrate IRBP for lack of a better candidate, but nearby genes in the assembly (EARS2 DNAJC19 UGT2B4 CD79B) bear no obvious synteny to those flanking the human RBP3 gene (RBP3 ZNF488 GDF2 GDF10 ANXA8L1) and only broken chromosomal correspondence is seen in whole genome alignment to human (net track).

It follows that searches for earlier diverging species that still carry a homolog should probably be carried out with a single-domain protein as query. The amphioxus protein is the only one currently available and may be highly diverged from its ancestral form. In any event, it does not expose any cryptic homologs in tunicate or echinoderm, much less lophotrochozoa, arthropods or cnidaria known to have ciliary opsin systems.

Under the twin assumptions of orthology and approximately ancestral intronation pattern in Branchiostoma, how do we get from a one module gene with 8 introns to a four module gene with 3 unrelated introns by lamprey divergence? This in some ways may have been the critical step in the evolution of imaging eyes with their massive requirement for rapid retinol recycling that likely vastly exceeded that of the ancestral cephalochordate (note RPE65 is rate-limiting). IRBP co-evolved its interstitial location and shuttling function with the newly developed supporting role of the retinal pigmented epithelium, which together were essential for effective vertebrate imaging vision.

One hypothetical scenario is formation first of a retroprocessed intronless gene with one module. This may have displaced the nine-exon parental gene because of selection for higher throughput translation. The protein may have been initially a non-cyclic tetramer of discrete subunits. The gene dosage perhaps doubled via a tandem copy, again to meet the need of increased retinol cycling. Next the intervening untranslated region experienced deletions fusing the previously independent modules, leading to a dimer of the internal repeat dimer at the protein level.

The gene complex then doubled again perhaps through recombinational module mismatch, once again to meet the newly evolving need for rapid retinol recycling -- at this point all four modules may have bound retinol. New introns with were gained by an unexplained process that favored the 3' end of the gene. Finally a need for allosteric regulation or interaction with other proteins allowed subfunctionalization of other domains to non-retinol shuttling roles despite the apparent loss of previously selection for efficiency because RPE65 had become rate-limiting.

While this scenario is speculative and non-unique, elements of it are not uncommon in other genes, even in opsins. For example, a retroprocessed fish RHO1 displaced the parental 5-exon gene into the pineal and LWS repeated spawned secondary cone opsin genes that were initially tandem. A great many human proteins have internally repeated domains and some like titin quite large numbers of them. There may not exist sufficient surviving members of the cephalochordate, hagfish and lamprey clades to specifically illuminate what really happened here. The highest priority would be to study localization and function of RBP3_braFlo within that the visual systems of that organism. 

>RBP3_braFlo Branchiostoma floridae Region: 9 exons; 1 domain: 83-381 
0 MTRPSKVDIVFPIKPFTIPTAHEQVKGEGPVDINKNALCKSADEGHTHP 1
2 VSIAMAPTAYIVFVALVPTVLSVDWLDVVMGIGDVMADHYLDQDLRALNDQSLLQRWNRTLVHRFQ 0
0 SWSQDDMSDSLRMEEGLTSELRNITGDETIK 0
0 VWDFGVYENTTQEPVPREFYNFSTFVDNFK 2
1 KNREKHINVTMLEGNVGYVSIRSMSHIVDIILPDPEMTEFFLSKMAALNESK 0
0 AIILDLRYNLGGDREGVVHWASFFFNATPSVPLSDVYYRDGVNQYWTLLE 0
0 VPGGIRFPDMPLYLLTSNRTSREAEEFAYAMQVVNRTTIIGETT 1
2 AGEEFTGMWFPIDQTDVHLLTRTNVVRNPITQDSWSGK 1
2 GVTPDIIVPSEKALTVALRKIQGSEDTKMAASSGNIEPPRWTVYLVFICTSIAILTYPTFM*

RBP3 (IRBP) use in marsupial phylogeny

The first three homology domains and part of the fourth are all encoded by the first large exon of 1090 amino acids. Sequenced fragments of this exon (often starting internally within module M1) has been much used in marsupial phylogeny (along with the first intron of transthyretin). Indeed the 96 marsupial species in 51 genera having partially determined IRBP sequences at GenBank include a Dec 2008 partial sequence for the extinct species Thylacinus cynocephalus, as well as for Sarcophilus harrisii (replaced here by a full length sequence derived from the genome project).

The use of IRBP in phylogenetic trees requires a high level of sequence accuracy, particularly since 'informative' characters are precisely the differences. However the PCR survey sequences exhibit various discrepancies in comparison to very high coverage genomic sequences. Some differences could arise from valid polymorphisms in individual animals used as dna source or represent an acceptable (low) level of PCR sequencing error, but other discrepancies appear to be gross errors in GenBank submissions (all from the same research group).

The Sacrophilus entry AY532685 has 6 amino acids inconsistent with genomic data (too many for polymorphic variation) as well as a gross error affecting a 17 residue block. It seems likely in the rush to obtain enough 'informative' characters, a completely unworkable error rate has been tolerated. All marsupial phylogenetic studies based in part on analysis of IRBP thus come into question.

None of the fragmentary marsupial GenBank entries provide a numbering system relative to a full length marsupial IRBP gene (eg Monodelphis) or its modules; the 4x module repeat structure of the gene is conducive to erroneous module cross-alignment. cDNA sequences typically start at position 73 of M1 (beginning of first hyper-variable indel region) and continue half way through M2 (to position 143), for example EF028750 of Myrmecobius fasciatus (numbat). Thus the region commonly sequenced is poorly coordinated with internal modular structure or existing 3D data.

The closest matches to the thylacine IRBP are shown in the difference alignment of the first 60 residues below. These species all lie with the Dasyuromorphia. The indicated E-->K may be one of several phyloSNPs breaking this group into blue and green subclades. The numbat Myrmecobius fits implausibly (its amino terminal sequence EF028750 needs verification) -- its affinities seem to lie with the Didelphimorphia in view of the shared Q.VV.K motif. Thylacinus is not basal within Dasyuromorphia relative to Myrmecobius using IRBP. This is not a case of mis-comparison of modules. 

  *           *                                     *
STSKAPQHDSKFTNATQEELLALFQQIIKYQVLEGNVGYLRVDYIPGREMIEEVGEFLVN EU091365  0 Thylacinus cynocephalus
.........P..A..................I............................ AY532676  3 Myoictis wallacei
........NP..A............................................... AY532687  3 Neophascogale lorentzii
........NP..A........T...................................... AY532686  4 Phascolosorex dorsalis
.........P..V............................................... AY532670  2 Parantechinus apicalis
....V....P..A..................I.....................L...... AY532675  5 Myoictis melas
.........P..A...................................D........... AY532679  3 Dasyurus hallucatus
...E.....P..A............K........D.............D........... AY532685  6 Sarcophilus harrisii
...E.......RA..........L............................Q..K.... EF028748  6 Sminthopsis crassicaudata
.......R.P.LA.........SL.......................Q....Q....... EF028749  8 Planigale ingrami
..A......P.LA.V.....................................K....... EF028736  6 Antechinus stuartii
..A......P.L..V.....................................K....... EF028743  5 Micromurexia habbema
..A......P.LA.V.....................................K....... EF028744  6 Murexchinus melanurus
..A......P.L..V....V................................K....... EF028746  6 Paramurexia rothschildi
..A......P.LA.V.....................................K....... EF028747  6 Phascogale calura
..A......P.LA.V.....................................K....... EF028745  6 Phascomurexia naso
.SA......P.LA.V.....................................K....... AY532667  7 Murexia longicaudata
......K..PNLA........T.L..R....................Q.VV.K....... EF028750 12 Myrmecobius fasciatus
..PET...VP..A.V........L..M....................Q.VV.K....... AY233765 13 Caluromys philander
..PET...VP.LA.V.......QL..M....................Q.VV.K....... AF257675 15 Caluromysiops irrupta
..PET...VP.LA.V......T.L..M....................Q.VV.K....... AF257688 15 Glironia venusta  
.IPET...VP..A.V.R....T.L..M....................Q.VV.K....... AF257683 16 Didelphis albiventris
.IPE....VP.LA.I......T.L..M....................Q.VV.K....... AF257686 15 Gracilinanus microtarsus
.IPET...VP..A.V......T.L..M....................Q.VV.K....... AF257676 15 Marmosops noctivagus
.IPET...VP.LA.V........L..M....................Q.VV.K....... AY233788 15 Philander opossum
.IPET...VP.LA.I......T.L..M....................Q.VV.K....... AF257689 16 Thylamys pallidior

Using Sarcophilus as probe in a different region, 721-900, we find a very peculiar outcome for numerous GenBank marsupial entries: the 17 residue region orthologous to 38-54 in M2 (VLTEEDLAAKLNAMLQA in M2_sacHar) has been replaced by a non-homologous 17 residue section copied over from 143-158 of M1 (SLVLDLQHSRGGEVSG in M2_myrFas), explaining non-alignment in the latter region (blue shows M2): 

myrFas:    61 DIWKKVMETSSLVLDLQHSRGGEVSGIPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTL 120
              DIWKKVMETSSLVLDLQHSRGGEVSGIPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTL
sacHar:   154 DIWKKVMETSSLVLDLQHSRGGEVSGIPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTL 213

myrFas:   121 PQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKEMRRAIVVGEQTQGGVLDLRKLRIGQ 180
              PQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILK+MRRAIVVGEQTQGG LDLRKLRIGQ
sacHar:   214 PQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKKMRRAIVVGEQTQGGSLDLRKLRIGQ 273

myrFas:   181 SDFFITVPVARSLSPLGGGSQTLEGSGVVPCVGIPAEKALEKTLAILTLRRARPGAIQRL 240
              SDFFITVPVARSLSPLGGGSQT EGSGVVPCVGIPAE+ALEK LAILTLRRARPGAIQRL
sacHar:   274 SDFFITVPVARSLSPLGGGSQTWEGSGVVPCVGIPAEQALEKALAILTLRRARPGAIQRL 333

myrFas:   241 MEILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE 300
              MEILQKYYTLVDRVPALLHHLTAIDYSS L  +   ++   +   VSEDPRLLVRVLR E
sacHar:   334 MEILQKYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAMLQAVSEDPRLLVRVLRPE 393

The source of this error cannot plausibly be explained XY difference, pseudogene, balanced polymorphism, nonhomologous recombination, frameshifts, internal inversion, or systemic experimental error (eg Dasyurus maculatus AY532680 is identical to AY243439 outside the 15 amino acid block). Genomic reads from Sarcophilus, Macropus and Monodelphis show no sign of novel substitution gene despite excellent coverage. All Didelphimorphia and Diprotodontia entries at Genbank are normal; sauropods, platypus and dozens of placentals establish this as ancestral. For some marsupials, independent sequencing finds the normal version of the gene.

These peculiar sequences were all submitted by C. Krajewski on 23-JAN-2004 and utilized in a paper entitled "Molecular systematics of the enigmatic phascolosoricine marsupials of New Guinea" published in the Aust. J. Zool. 52, 389-415 (2004). Two similarly flawed sequences submitted the same day (AY532677, AY532679) were subsequently corrected on 25-SEP-2006 by the same individual resulting in GenBank entries being fixed. However many subsequent studies of IRBP may have used the 17 flawed sequences that were never corrected. The same authors resequenced species such as Pseudantechinus roryi (EU086689) obtaining the correct sequence in this region on 07-AUG-2007 but still did not fix their earlier entry AY532673. 

AY532685 MEILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE Sarcophilus harrisii
AY532684 ....E................................S....................P. Dasyurus geoffroii
AY532681 ....E................................S....................P. Dasyurus albopunctatus
AY532683 ....E................................S....................P. Dasyurus viverrinus
AY532682 ....E........................P.......SE...................P. Dasyurus spartacus
AY532680 ....E..............R.................SR...................P. Dasyurus maculatus
AY532678 ..V..................................S....................P. Dasycercus cristicauda
AY532669 ..V..................................S....................P. Dasykaluta rosamondae
AY532676 ..V..................S...............S....................P. Myoictis wallacei
AY532675 ..V..................S...............S....................P. Myoictis melas
AY532687 ..V........N.L.......................S....................P. Neophascogale lorentzii
AY532671 ..V..................................S....................P. Parantechinus bilarni
AY532670 ..V.................................TS.........RG.........P. Parantechinus apicalis
AY532686 ..V..................................S........P...........p. Phascolosorex dorsalis
AY532674 ..V.......................................................P. Pseudantechinus ningbing
AY532672 ..V..................................S....................P. Pseudantechinus woolleyae
AY532673 ..V........N..R......................S...................SP. Pseudantechinus roryi
454 read MEILQKYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAMLQAVSEDP           Sarcophilus harrisii
EF028739 ............................V.TEEDLAAKLNAMLQA.............P. Antechinus minimus
AY243439 ....E..............R........V.TEEDLAAKLNAMLQA.............P. Dasyurus maculatus
EF028750 ....K................KT.....I.TEEDLAAKLNAILQA.............P. Myrmecobius fasciatus
EF028737 ..V.........................V.TEEDLAAKINAMLQA.............P. Antechinus flavipes
EF028748 ..V.........................V.TEEDLAAKLNA.LQA.............P. Sminthopsis crassicaudata
AY243438 ..V.........................V.TEEDLAAKLNA.LQA.............P. Planigale sp.
EF028749 ..V.........................V.TEEDLAAKLNA.LQA.............P. Planigale ingrami
AY532679 ..V.........................V.TEEDLAAKLNAMLQA............... Dasyurus hallucatus
AF025382 ..V.........................V.TEEDLAAKLNAMLQA.............P. Phascogale tapoatafa
EF028741 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus godmani
AY532666 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus swainsonii
EF028736 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus stuartii
EF028742 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus agilis
EF028738 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus bellus
EF028740 ..V.........................V.TEEDLAAKLNAMLQA.............P. Antechinus leo
EF028747 ..V.........................V.TEEDLAAKLNAMLQA.............P. Phascogale calura
EF028744 ..V.........................V.TEEDLAAKLNAMLQA.............P. Murexchinus melanurus
EF028743 ..V.........................V.TEEDLAAKLNAMLQA.............P. Micromurexia habbema
EU086688 ..V.........................V.TEEDLAAKLNAMLQA.............P. Pseudantechinus macdonnellensis
EU086689 ..V.........................V.TEEDLAAKLNAMLQA.............P. Pseudantechinus roryi
EU086686 ..V.........................V.TEEDLAAKLNAMLQA............SP. Pseudantechinus macdonnellensis
EU086687 ..V.........................V.TEEDLAAKLNAMLQA..........G..P. Pseudantechinus mimulus
AY532667 ..V.........................V.TEEDLAAKLNAMLQA.............P. Murexia longicaudata
EF028746 ..V.........................V.TEEDLAAKLNAMLQA.............P. Paramurexia rothschildi
AY532677 ..V.........................V.TEEDLAAKLNAMLQA.............P. Dasyuroides byrnei
EF028745 ..V..........I..............V.TEEDLAAKLNAMLQA.............P. Phascomurexia naso

Macropus eugenii assembly         
sacHar   MEILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE 
         ME+LQ YYTLVDRVPALLHHLTAIDYSS L  +   ++       VSEDPRLLVRVLR E
macEug   MEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPE  

Monodelphis domestica assembly     TSSLVLDLQHSSGGEISG 
sacHar   MEILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE  
         ME+LQ YYTLVDRVPALLHHLTAIDYSS L  +   ++       VSEDPRLLVRVLR E
monDom   MEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPE  

Ornithorhynchus anatinus assembly
sacHar    EILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE 
          ++L+ YY LVDRVPALL HL A+D SS L  +   SR        SEDPRLLVR L  E
ornAna    DLLRDYYALVDRVPALLRHLAALDLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPE  

Equus caballus assembly
sacHar    EILQKYYTLVDRVPALLHHLTAIDYSSSLVLDLQHSRGGEVSGTVSEDPRLLVRVLRSE  
          E LQ YYTLVDRVPALLHHL ++D+SS +  D   ++       VSEDPRLLV V+RS+
equCab    EALQDYYTLVDRVPALLHHLASMDFSSVVSEDDLVAKLNAGLQAVSEDPRLLVWVVRSK

It emerges from direct tblastn that the Sacrophilus individual sequenced was female. That is, ATRX is well represented but not ATRY (though the situation is somewhat confused due to additional paralogs). Marsupial XY are quite different from placentals:

"Many or most genes on the mammal Y chromosome evolved a testis-specific function after diverging from an X-borne copy with a general function in both sexes. In marsupial but not eutherian mammals, a testis-specific ortholog (ATRY) of the widely expressed X-borne ATRX gene lies on the Y chromosome. Since mutations in human ATRX cause sex reversal, it is possible that one function of ATRY in marsupials is testicular differentiation. We report here the isolation and sequencing of the tammar wallaby (Macropus eugenii) ATRY cDNA, and comparison of its sequence with that of tammar ATRX. The evolution of a testis-specific function for the ATRY protein distinct from the general role of ATRX in both sexes has been accompanied by sequence changes in many protein domains that would alter protein binding partners. A large open reading frame encodes a 1771 amino acid ATRY protein that has diverged extensively from ATRX. The conservation and loss of particular motifs identify those required for testicular function (ATRY) and function in other tissues (ATRX)."

Reference sequences

These are organized both parsed into functional modules (signal peptide and spacer residues are dropped) as determined by global multiple alignment consistency and as intronated genes showing position and phase of intron breaks. Both sets are in phylogenetic order with respect to the canonical deuterostome tree.

RBP3 (IRBP) sequences parsed into structural modules

>M1_homSap
LFQPSLVLDMAKVLLDNYCFPENLLGMQEAIQQAIKSHEILSISDPQTLASVLTAGVQSSLNDPRLVISYEPSTPEPPPQVPALTSLSEEELLAWLQRGLRHEVLEGNVGYLRVDSVPGQEVLSMMGEFLVAHVWGNLMGTSALVLDLRHCTGGQVSGIPYIISYLHPGNTILHVDTIYNRPSNTTTEIWTLPQVLGERYGADKDVVVLTSSQTRGVAEDIAHILKQMRRAIVVGERTGGGALDLRKLRIGESDFFFTVPVSRSLGPLGGGSQTWEGSGVLPCVGTPAEQALEKALAIL
>M1_bosTau
LFQPSLVLEMAQVLLDNYCFPENLMGMQGAIEQAIKSQEILSISDPQTLAHVLTAGVQSSLNDPRLVISYEPSTLEAPPRAPAVTNLTLEEIIAGLQDGLRHEILEGNVGYLRVDDIPGQEVMSKLRSFLVANVWRKLVNTSALVLDLRHCTGGHVSGIPYVISYLHPGSTVSHVDTVYDRPSNTTTEIWTLPEALGEKYSADKDVVVLTSSRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRVGQSDFFLTVPVSRSLGPLGEGSQTWEGSGVLPCVGTPAEQALEKALAVL
>M1_monDom
IFQPSLVRDMAKILLDNYCFPENLMGMQEVIEQAIKSGEILDISDPQMLASVLTAGVQGALNDPRLVISFEPSIPETPQHVPKLANVTQEELLILLQQMIKYQVLEGNVGYLRVDYIPGQEVVEKVGEFLVNNIWKKLMGTSSLVLDLQHSSGGEISGIPFVISYLHQGDILLHVDTVYDRPSNTTTEIWTLPQVLGERYGGEKDMVVLTSHRTVGVAEDIAYILKKLRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALGKALAIL
>M1_macEug
IFQPSLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLASVLTAGVQGSLNDPRLVISYEPSPAEAPQQSPKLTSLTQEELLTLLQQMIKYQVLDGNVGYLRVDYIPGQEVVEKVGEFLVNDIWKKLMGTSSLVLDLQHSTEGEVSGIPFVISYLHEGDILLHVDTVYDRPSNTTTEIWTLPQVLGERYSGEKDLVILTSHRTVGVAEDIAYILKKMRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALEKALAIL
>M1_sacHar
IFQPTLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLANVLTAGVQGSLNDPRLVISYEPSTSEAPQHDPKFANATQEELLALFQKIIKYQVLEDNVGYLRVDYIPGRDMIEEVGEFLVNDIWKKVMETSSLVLDLQHSRGGEVSGIPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTLPQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKKMRRAIVVGEQTQGGSLDLRKLRIGQSDFFITVPVARSLSPLGGGSQTWEGSGVVPCVGIPAEQALEKALAIL
>M1_ornAna
VSQPSMVLDVAKILLDNYCYPENLMGMQEAIEEAIQRGEILDIADPKRLASVLTAGVQGSLNDPRLVISYEPAPVAVSQQPPEPASLPAEQPLERLRPAVGSEVLEGNVGYLRVDRLPGREEIERVGAVLGRDIWEKLLGTSALVLDLRHSTGGHVSGIPFFISYFYPEGPALHVDTVYDRPSNATRQLWTLPRVLGARYAADKDVVVLTSRLTAGVAEDVAYILQQMRRAIVVGERTAGGPLVFRKLRVGLSDFFITVPVACSLGPLGGGGRSWEGSGVLPCVAVPADRALDEALDIL
>M1_galGal
IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPSLHAAPKQEAETYPTREQLLSLIEHVVIYDKLEGNVGYLRIDYIIGQEVVEKVGAFLVDKVWKTLINTSALVIDLRYSTGGQISGIPFIISYLHEADKMLHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITLGEKTAGGSLDIQKLRIGPSNFYMMVPVSRSVSPLSGGGQSWEVSGVMPCVASEAEQALKKSLDIL
>M1_taeGut
IFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPLPHSGPKQEAEGSPTREQLLSLIEHVIMYDKLEGNVGYLRIDYIIGEEVVQKVGAFLVDKVWKTLIETSALVIDLRHSTGGQISGLPFIISYLHEQDKILHVETVYNRPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITVGEKTAGGSLDIQKLRIGPSNFYMMVPVSRSVSPLSGGGQSWEVSGVMPCVATEAEQALQKSLDIL
>M1_anoCar
VLQSTLVLDMAKLLLDNYCLPENLVGMREAIEQAIKNGEVLDISDPKLLATVLTAGVQGALNDPRLVISYEPTAPAAPKQRMETSLTPEQLLSLIQHTVKYEVLDDNVGYLRIDYIMGQDIVQKIGSFLVEKVWKTLLGTSALILDLRYTTGGDVSGIPFIISYLYNGDKVLHVDTVYNRPSNTTVEILTLPKVLGVRYSKDKDVILLISKYTTGVAENVAYILKHMHRTIIVGEKSAGGSLDTQKMQIGNSQFYMTVPLSCSVSPLSGSGQSWEISGVTPCVVISAEQALDKALAIL
>M1_xenLae
LFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAVKGGEILHISDPDTLANVFTSGVQGYLNDPRLVVSYEPNYSGPQTEQSLELTPEQLKFLINHSVKYDILPGNIGYLRIDFIIGQDVVQKVGPHLVNNIWKKLMPTSALILDLRYSTQGEVSGIPFVVSYLCDSEIHIDSIYNRPSNTTTDLWTLPELMGERYGKVKDVVVLTSKYTKGVAEDASYILKHMNRAIVVGEKTAGGSLDTQKIKIGQSDFYITVPVSRSLSPLTGQSWEVSGVSPCVVVNAKDALDKAQAIL
>M1_xenTro
VFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAMKSGEILHISDPETLANVFTSGVQGFLNDPRLVVSYEPNYSGPRKEQSPEPTLEQLKFLLDHSVTYDLLPGNIGYLRIDFIIGQDVVQKVGPLLVNNIWKKLMPSSALILDLRYSTQGKVSGIPFVVSYLTDPQIHIDSIYNRPSNTTTDLWTLSELMGERYGKDKDVVVLTSKYTEGIAEGAAYILKHMSRAIVVGEKTAGGSLDIQKIKIGQSEFYITVPVSRSISPLTGQSWEVAGVFPCVVVNANNALNKAQGIL
>M1_tetNig
AFPPSLIADMAKIVLDNYCSPEKLAGMKEAIKAAGTNTEVLNIPDGESLARVLSAGVQGTVSDPRLMVSFQPNYVPAGPHKMPPLPPEHLVAVLQTSVKLDILEGNTGYLRIDHILGEEVADKVGPALIDLIWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPVVHIDSVYDRPSNTTTKLLSLPNLLGQRYGVSKPLIVLTSKNTKGIAEDVAYCLKNLKRATIVGEKTAGGSLKLDTFKVGDTDFYITVPTAKSINPITGSSWEIRGVTPHVEVNAEDALATAIKIV
>M1_takRub
AFPPSLITDMAKIVLDNYCSPEKLAGMKEAIEAAGTNTEVLNIPDGESLARVLSAGVQGTVSDSRLMVSYQPDYVPAVPPKMPPLPPEHLVAVLQTSIKLDLLEGNTGYLRIDHIIGEDVAEKVGPSLIDLIWNKILPTSALIFDLRYTSSGEISGIPYIVSYFTQAEPVVHIDSVYDRPSNTTTKLFSLSNLLGERYGITKPLIILTSKNTKGIAEDVAYCLKNLKRATIVGERTAGGSVKLDNFKVGSTDFYITVPTAKSINPVTGSSWEITGVKPDVEVNAEDALATAIKIV
>M1_gasAcu
GFAPNVIIDMAKIVIDNYCSPEKLAGMKEAIEAAGSNTEVLSIPDAETLANVLSAGVQTTVSDPRLMISYEPNYVPVVPPKMPPLPPDQVIAVLQTSIKLDILEGNIGYLRIDHILGEDVAEKVGPLLLDLVWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTEAGTPIHIDSIYDRPSNTTTKLFSMSTLLGERYSTSKPLIILTSKNTKGIAEDVAYCLQNLKRATIVGEKTAGGSVKVDKIQVRDTGFYVTVPTAKSVNPITGSTWEVTGVTPNVEVNAEDALATAIKIV
>M1_oryLat
SFPPSLITDLAKIVMDNYCSPEKLSGMKEDIATAGANTDVLNIPDGEALAKVLTDGVQTTVSDPRLRVSYEPNYVPVVPPQLPPEQLIAVLQTSIKLDILEGNIGYLRIDSIIGEEVAEKVGPLLLELVWSKILPTSALIFDLRYTSSGDITGIPYIISYLTDAKSEIHIDTIYDRPLNTTTKLLSMQSTLGQTYGGTKPLLVLTSKNTKDIAEDVAYCLKNLKRATIVGEKTAGGSAKIKKFRVGDTDFYVTLPTAKSINPITGSSWEVTGVKPNVEVNAEEALATALKII
>M1_danRer
NFSPTLIADMAKIFMDNYCSPEKLTGMEEAIDAASSNTEILSISDPTMLANVLTDGVKKTISDSRVKVTYEPDLILAAPPAMPDIPLEHLAAMIKGTVKVEILEGNIGYLKIQHIIGEEMAQKVGPLLLEYIWDKILPTSAMILDFRSTVTGELSGIPYIVSYFTDPEPLIHIDSVYDRTADLTIELWSMPTLLGKRYGTSKPLIILTSKDTLGIAEDVAYCLKNLKRATIVGENTAGGTVKMSKMKVGDTDFYVTVPVAKSINPITGKSWEINGVAPDVDVAAEDALDAAIAII
>M1_petMar
KFDTAVVLHLAKVLLDNYCIPENLVGMDEAIQRAVDNGELLGVSDPESAASALTEGIQAALNDPRIAVSYVPDVDDDGDREEGDAEGWDAGEQHRPTTFEELLATIPQKTSFAVLDGNVGYLRADEIISEATIKKLGPVIVQRIWNRLVDTDTFVLDLRYNSHGDITGLPYLVSCFCEPRPVVHLDTVYYRPTNESKEIWSLPDLQGARFAKHKDVFVLVSANTEGVAENVAYVLKHLHRATVIGEQTAGGSLEVERFRLGDSRFFVTVPTARSQSPLTGRSWELTGVFPCVSAPSERALDKALEIL

>M1x_takRu
FYQHTLVLEMAKLLLENYCIPENLVGMQEAIQRAIKSREILQISDRKTLATVLTVGVQGALNDPRLSVSYEPSFSPLPLQALSSLPVEQQLRLLRNSIKLDILDSDVGYLRIDRIIDEETLLKFGPLLRENVWDKAAQTSSLILDLRFSTAGGWSGIPSIVSYFTEPHSLVHIDTVYDRPSNTTTELWTMSSVRGKTFGGKKDMIVLIGRRTAGAAEAVAYTLKHLNRAIVVGERSAGGSLKVRKFRIAESDFYITMPVARSVSPITGKSWEVSGISPTVNVAAREALAKAQTFL
>M1x_danRe
SFQSALVLDMAKILLDNYCFPENLIGMQEAIQQAINSGEILHISDRKTLASVLTAGVQGALNDPRLTVSYEPNYTLITPPALHSLPTEQLIRLIRSTVKLEVMDNNIGYLRIDRIIGQETVVKLGRLLHNNIWKKVAHTSAMIFDLRFSTAGELSGLPYIVSYFSDSDPLLHIDTIYERPTNITRELWTLPTLLGERFGKRKDLIVLISKRTIGAAEGVAYILKHLKRAVIIGERSAGGSVRVDKLKIGDSGFYITVPVARSVNPVTGQSWEVSGVAPSVTVNPKESIAKAKSLI

>M2_homSap
SALPGVVHCLQEVLKDYYTLVDRVPTLLQHLASMDFSTVVSEEDLVTKLNAGLQAASEDPRLLVRAIGPTETPSWPAPDAAAEDSPGVAPELPEDEAIRQALVDSVFQVSVLPGNVGYLRFDSFADASVLGVLAPYVLRQVWEPLQDTEHLIMDLRHNPGGPSSAVPLLLSYFQGPEAGPVHLFTTYDRRTNITQEHFSHMELPGPRYSTQRGVYLLTSHRTATAAEEFAFLMQSLGWATLVGEITAGNLLHTRTVPLLDTPEGSLALTVPVLTFIDNHGEAWLGGGVVPDAIVLAEEALDKAQEVL
>M2_bosTau
RALPGVIQRLQEALREYYTLVDRVPALLSHLAAMDLSSVVSEDDLVTKLNAGLQAVSEDPRLQVQVVRPKEASSGPEEEAEEPPEAVPEVPEDEAVRRALVDSVFQVSVLPGNVGYLRFDSFADASVLEVLGPYILHQVWEPLQDTEHLIMDLRQNPGGPSSAVPLLLSYFQSPDASPVRLFSTYDRRTNITREHFSQTELLGRPYGTQRGVYLLTSHRTATAAEELAFLMQSLGWATLVGEITAGSLLHTHTVSLLETPEGGLALTVPVLTFIDNHGECWLGGGVVPDAIVLAEEALDRAQEVL
>M2_monDom
RARPGAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATMGSEASEEEDATPAANSLPEDESQRQALVDSVFQVSVLPGNVGYLRFDEFADSSVLGTLAPYVIRQVWEPLQDTNHLIMDLRYNPGGPSSAVPLLLSYFQDPAAGPIRLFTTYDRQTNQTQEHLSRAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGNLVLTVPILTFIDNNGECWLGGGVVPDAIVLAEEALDKAKEVL
>M2_macEug
RARPAAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATAGAESREEAATAAPVPLPDGESQRQALVNSVFQVSVLPGNVGYLRFDEFADSSVLGALAPYVLQQVWEPLQDTDHLIMDLRYNPGGPSSAVPLLLSYFQDPAAGPVRLFATYDRQTNQTREYRSQAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGNLMHTRTFSLLQPPDGSLVLTVPILTFIDNHGECWLGGGVVPDAIVLAEEALDKAKEVI
>M2_sacHar
RARPGAIQRLMEILQKYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAMLQAVSEDPRLLVRVLRPEEATVEAEPGEESATPASVSLPESDAERQALIDSVFQVSVLPGNVGYLRFDEFADNSVLGTLAPYVLRQVWEPLQDTDHLIMDLRYNPGGPSSAVPLLLSYFQDPSAGPVRLFATYDRQTNQTQEYRSRAELLGKPYGAERGVYLLTSYHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGSLVLTVPTLTFIDNHGECWLGGGVVPDAIVLAEEALDKAKEVL 
>M2_ornAna
GAVPGAVAHLADLLRDYYALVDRVPALLRHLAALDLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPEEAERGPPRKEEEQKEEEEEDQPSPGASILPGDGSSLFRVSVLPGNVGYLCFDEFPEASALERLGPLLGRRVWEPLEATDHLMVDLRNNPGGPSSAVPLLLSYFQDPAAGPIRLFTTYNRPADVTREYASRAGALEKPYGARRGVYLLTSHRTATAAEEFAYLMQALGRATLVGEITAGRLLHSRTFPLLRPPWEGLVLTVPFLTLFDPHGEGWLGGGVVPDAIVLAEEALEKAGEVL
>M2_galGal
RAVPGTLSRLTDILKDYYSLVERVPVLLRHLTTSDFSSVQSAEDLATKLNTEMQTLSEDPRLLVRTMMPGEAAAPPAEMPIAMAANLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYIVKKVWEPLQNTENLIMDLRYNPGGPSSSAVPMLISYFQDPTAGPVHLFTTYDRRTNHTQEHNSQAELLAQPYGAQRGIYVLTSRHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTCTFPLVQPEQGITRGLTITVPVITFIDNHGESWMGGGVVPDAIVLAEDALEKAEEVL
>M2_taeGut
RAVPGTISHLKNILKDYYSLVERVPALLRRLTTSDFSSVQSSEDLATKLNTELQALSDDPRLMVRVMMPGEAADSPAEKPVGMAADLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYLVHKVWEPLQNTENLIMDLRYNLGGPSSSAVPVLLSYFQDPAAGPVHLFTTYDRRTNHTQEHNSQAELLGQSYGAKRGVYLLTSHHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTRTFPLLQPGPGITRGLTITVPVITFIDNHGESWMGGGVVPDAIVLAEDALEKAEEVL
>M2_anoCar
KAIPNSMSYLVDIIKNNYSMLEQVPVLLQHLSTFDYSSVLSVKDLASKLNAELQTISEDPRLFLRVPASDEAVTSQTDEKVAMASDLPNNEQLMKALVMTVFKVSVLPGNVGYMRFDEFGDATVLVKLGPYLLQHVWEPLQATDYLIIDLRYNIGGPSSSAVPVLLSYFQDPSAGPVHFFTTYNRLTNQTQAYSSSAEMVGKPYGARRGVYLLTSHNTATAAEEFAYLMQTLGRATLVGEITAGSLSHTHTFCILELGGGCGLLINVPVITLIDNHGEYWLGGGVVPDSIVLADEALEKAREVL
>M2_xenTro
SSITHILLQLSEILVNNYAFSERIPTLLQHLPNLDYSSVISEEDITAKLNYELQSLTEDPRLVLKSKTDSLVMPEDSTQVENLPDDEATLQALVNTVFKVSILPGNIGYLRFDEFADVSVLAKLGPYIVNTVWDPITVTENLIIDLRYNIGGSSTSIPLLLSYFQEPENRIHLFTIYNRQQNSTNEVYSLPKVLGKPYGSKKGVYVLTSHETATAAEEFAYLMQSLSRATIIGEITSGNLMHSKAFPLDGTRLSVTVPIMNFIDNNGDYWLGGGVVPDAIVLADEALDKAKEII
>M2_xenLae
SSVTHVLHQLCDILANNYAFSERIPTLLQHLPNLDYSTVISEEDIAAKLNYELQSLTEDPRLVLKSKTDTLVMPGDSIQAENIPEDEAMLQALVNTVFKVSILPGNIGYLRFDQFADVSVIAKLAPFIVNTVWEPITITENLIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFDGTQLSVTVPIINFIDSNGDYWLGGGVVPDAIVLADEALDKAKEII
>M2_petMar
GVARKAVEAAGELLLSSYTFVERASAIADHLSWSEYGSVVSVEDLTSKLTQDLQSVAEDPRLVVSNREPEWPPLAQPIPPGPPAPLPDDEQMLEAIVDSAFKVEVLEGNIGYLRFDEFGDASAVMKLRKQLVSKVWERIHPTDDVIIDLRYNLGGSSTAIPIVLSYFQDASPPVHFYTVYDRLRNVTAEFHTVSNLTSQLYGSKKGVYLLTSQHTATAAEEFTYLMQSLNRATIVGEITSGRLAHSLAFRLSDTGLYMTVPIVNFIDNNDEYWLGGGVVPDAIVLAENALDAAKEII

>M2x_takRu
SRIPKVLQIVLDIIGRFYAFADRVQALLQQLESADLFSVVSEEDLAARLNHDLQTASEDPRLIIRHKRDNIPRAEEEPELHAANDHDGELVEGFTVQVLPHNTGYLRLDRFVRCSEGDKLEEIVAEKVWGPLKDTQNLIIDLRHNTGGSSTSVALLLSYLRDPLPKRHFFTIYDSVQNTTTEYGSRPHIPGPSYGSERGVYVLTSHYTAGAAEEFAYLIQSLHFGTVVGEITSGTLMHSKTFQVEGTDIFITVPFINFLDNNGEYWLGGGVVPDAIVLAEEALEHVNRTA     
>M2x_danRe
KTIPKAVRRVSDIIKRYYSFKDKIPALLNQLAKADYFTVVSEEDLAGKLNHEMQSVFEDPRLLIKATQVLTDDASSEDRSSSDDLTDPLFKLEMISGNNGYLRFDRFPTPEVLLRLEDHIKKKIWQPVQETENLVIDLRFNTGGSTEALPILLSYMFDTSSSTYLFSIYDSIKNTTFDFHTLNNISGPSYGSTKGVYVLTSYYTAEAGEEFAYLMQSLHRGTVIGEITSGMLLHSKTFQIEQTSLAITVPIINFIDVNGECWLGGGVVPDAIVLAEEALERAHEII

>M3_homSap
QSLGALVEGTGHLLEAHYARPEVVGQTSALLRAKLAQGAYRTAVDLESLASQLTADLQEVSGDHRLLVFHSPGELVVEEAPPPPPAVPSPEELTYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVRLVWQQLVDTAALVIDLRYNPGSYSTAIPLLCSYFFEAEPRQHLYSVFDRATSKVTEVWTLPQVAGQRYGSHKDLYILMSHTSGSAAEAFAHTMQDLQRATVIGEPTAGGALSVGIYQVGSSPLYASMPTQMAMSATTGKAWDLAGVEPDITVPMSEALSIAQDIV
>M3_bosTau
RSLGELVEGTGRLLEAHYARPEVVGQMGALLRAKLAQGAYRTAVDLESLASQLTADLQEMSGDHRLLVFHSPGEMVAEEAPPPPPVVPSPEELSYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVQLVWQKLVDTAALVVDLRYNPGSYSTAVPLLCSYFFEAEPRRHLYSVFDRATSRVTEVWTLPHVTGQRYGSHKDLYVLVSHTSGSAAEAFAHTMQDLQRATIIGEPTAGGALSVGIYQVGSSALYASMPTQMAMSASTGEAWDLAGVEPDITVPMSVALSTARDIV 
>M3_monDom
QRLGALVEGTGHLLEAHYALPEVVGQASALLKAKLEHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPVSEELTPPQKGVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIAPQLVELVWEKLVHTEALVVDLRYNPGGYSTAVPLLCSYFFEAEPRRHLYTIFDRAASQLTEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFVHTMKDQHRATVIGEPTGGGALSVGIYQVENSPLYASMPTQVAISPVTGKAWDMAGVEPDVSVLSSEALMTTQGIV 
>M3_macEug
QRLGALVEDAGHLLEAHYALPEVVGQASALLRARLVHGTYRTAVDFESLASQLTSDLQEVSGDHRVHVFHSPGELIPEELSPPQNVVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIGPQLIELVWEKLVNTEALVVDLRYNPGSYSTSVPLLCSYFFEAEPRKHLYTIFDRAASQATEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFAHAMKDLRRATVIGEPTAGGALSVGIYQVSNSPLYASMPTQVAISPVTGKAWDIAGVEPDVSVPAREALITTQGIV
>M3_sacHar
QRLGALVEGTGHLVEAHYALPEVVGQASAFLRATLAHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPVPEESSPPHKGVPSPEELTYLIEALFKTDVLPQLGYLRFDMMAEVETVRAIGPQLVELVWEKLVNTEALVVDLRYNPGSYSTTVPLLCSYFFEAEPRKHLYTVFDRATSQFTEVWTLPQVTGERYGSQKDLYILISHTSGSAAEAFAHIMKDLQRATVIGEPTAGGALSVGIYQVGDSPLYVSMPTQVALSPVTGKAWDMAGVEPDVSVLANEALITAQGIV
>M3_taeGut
KNMGVLLEGTGQLLEDHYAIPEVAAKASAMLSTKRAQGGYRSAIDSETLASQLTSDLQEASGDHRLHVFHSHVEPTPEEQLPNVIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLLQMVWNKLVDTDAMIIDMRYNTGGYSTAIPILCSYFFDPEPRKHLYTVFDRSTSRSTEVWTLPQLAGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVVGEPTVGGSLSVGIYRVGNSSLYASIPSQVVLSPVTGKVWSVSGVEPHITIQASEAMAAAQHIA 
>M3_galGal
RKMGILLESTGQLLEAHYAIPEVAEKASVMLSTKRVQGGYRSAVDFETLASQLTSDLQEASGDHRLHVFHSHVEPTPEEQLPNMIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLVQMVWNKLVDTDAMIIDMRYNTGGYSTAVPILCSYFFEPEPRQHLYTVFDRSTSRSTEVWTLPKVTGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVIGEPTVGGSLSVGIYRVGNSSLYRSIPSQVVLSPVTGKVWSVSGAEPHITIQASEALAAAKHIA 
>M3_anoCar
KGMGSLIERVGQLLEAHYAIPEMARRVSSMLNSKLAQGGYRTAVDFETLASQLTNDLQETSGDHQLHVFHSHVEPSLEEQSPFKTLTPEELNFIIEALFKVDVLPGNVGYLRFDMMAEFESVKTIEPQILHMVWEKLVETSAMIVDMRYNTGSYSTAVPMFCSYFFDAEPQQHLYTIIDRSTSQSTEVWTSSQVSGKRYGSTKDLYILISHASGSAAEAFTRSLKDLHRATVIGEPTVGGSLSASIYNIGSTPLYASIPSQIVLSPVSGKVWSLSGIQPHVTTQSNEALASAQNII
>M3_xenTro
PSVFALVEGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASQLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIPSAEELNYIIDALFKIEVLQGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSSGTDIWTLPEVVGERYGSTKDIYILTSHMTGSAAEVFTRSMKELNRATIIGEPTSGVSLSVGMYKVGESNLYVSIPNQVVISSVTGKVWSVSGVEPHVIAQASEAMNVAHHII
>M3_xenLae
PSIFPLVKGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASLLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIPSPEELNYIIDALFKIEVLPGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSTGKDIWTLPEVFGERYGSTKDIYILTSHMTGSAAEVFTRSLKDLNRATLIGEPTSGVSLSVGMYKVGDSNLYVTIPNQVVISSVTGKVWSVSGVEPHVIIQANEAMNIAHRII
>M3_petMar
AKMASLLELAGALVEGYYAMLSDGENATAEILLKYREGWYRSVVDYEALASQLTSDLHEIWGDHRLHAFYSDLQIERMDEDKTPSVPSPEELSVLIDTVFKVDILANNVGYLRFDMMTDAEVLKHVGPQLVEKVWNKISSTRSLVIDVRYNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVLGQRYGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDSRLYVFIPNQAGVSPSGGRTWSVAGVEPHVQTKASEALQSALRMV

>M3x_takRu
QGLRSLIGRTGELLEKHYAIQEVAQKVGEVLLSKWAEGLYRSVVDLESLASQLTADLQEASGDHRLHVFRCDVELESLHGVPKIAAVEEAGFVIDALFKSELLPRNVGYLRFDTMADIEAAKGAAPRLVKSVWNKLVDTDSLIIDMRYNAGGSSTAVPLWCSYFVDGEPLQHLYTVYDRTTKTRVEVMTLPEVSGQRYDPGKDVYILTSHMTGSAAEAFVRAMRDLNRVTIVGEPTAGGSLSSATYQIGESVLYASIPNQVVTSAATGKLWSISGVEPDVFAQARDALPVAQRII
>M3x_danRr
KNIQGLVQEAGDLLEKHYSVPEVAAKVSRLLQSKLTEGLYRSVVDYESLASQLTSDLQETSGDQRLHIFYCETEPETLHDTPKIPSPEEAGFIVEALFKVDVMSGNIGYLRFDMMEDIKVLQAINPEFLKVVWNKLVNTDMLIIDVRYNTGGYSTAIPLLCTYFFDAQPLTHIYTLFDRSTATVTKVTTLPDVLGQKYSSQKDVYILTSHITGSAAEAFTRTMKDLKRATVIGEPTIGGALSSGTYQIGNSILYASIPNQAVLNAVTGKPWSISGVEPHIVAQASDALIVAQKII

>M4_homSap
AKVPTVLQTAGKLVADNYASAELGAKMATKLSGLQSRYSRVTSEVALAEILGADLQMLSGDPHLKAAHIPENAKDRIPGIVPMQIPSPEVFEELIKFSFHTNVLEDNIGYLRFDMFGDGELLTQVSRLLVEHIWKKIMHTDAMIIDMRFNIGGPTSSIPILCSYFFDEGPPVLLDKIYSRPDDSVSELWTHAQVVGERYGSKKSMVILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTNLYLTIPTARSVGASDGSSWEGVGVTPHVVVPAEEALARAKEML
>M4_bosTau
AKVPTVLQTAGKLVADNYASPELGVKMAAELSGLQSRYARVTSEAALAELLQADLQVLSGDPHLKTAHIPEDAKDRIPGIVPMQIPSPEVFEDLIKFSFHTNVLEGNVGYLRFDMFGDCELLTQVSELLVEHVWKKIVHTDALIVDMRFNIGGPTSSISALCSYFFDEGPPILLDKIYNRPNNSVSELWTLSQLEGERYGSKKSMVILTSTLTAGAAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTDLYLTIPTARSVGAADGSSWEGVGVVPDVAVPAEAALTRAQEML
>M4_monDom
AKVPTILQTAGKLVADNYASLEVGSRVASKLAKLQTQYRQVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAKDRIPGIVPMQLPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDMRFNIGGPTSSISALCSYFFDEGQEVLLDQIYNRPNDSISEIWTQSQVAGERYGSKKSVIILTSSMTAGAAEEFVYVMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTARSVGSGDKPSWEGVGVAPHVEVPADQALSKAKEMF 
>M4_macEug lower case: sacHar fix
SKVPTILQTAGKLVADNYASPEVGSRVAAKLARLQTQYRQVTSEGELADMLGADLQTLSGDSHLKTAHIPEDSKDRIPGIVPMQlpspeafedlikfsFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDMRFNIGGPTSSISALCSYFFDEGQKVLLDRIYNRPNDSIVEIWTQPHVTGERYGSKKSVIILTSSTTAGAAEEFVYIMQGLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTAQSVGSGDRPSWEGIGVTPHVEVPADQALSKAKEMF
>M4_sacHar
AKVPTILQTAGKLVADNYASPEVGSRVAAKLASLQIQYGKVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAKDRIPGIVPMQLPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLIQVSDLLVEHVWKKVMHTDGMIIDMRFNIGGPTSSISAMCSYFFDEGQGVLLDRIYNRPNDSISEIWTQPQVIGERYGSKKTVVILTSSMTAGAAEEFVYIMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTTRSVVSGDKSSWEGVGVVPHMEVPADQALSKAKEMF
>M4_ornAna
SKVPTVLRTAAKLVADNYAFRETGAGVAAQMGGLQARCGRVTSEGALAEVLGAHLRALSGDPHLQMVYIPEDAKDRIPGVVPMQIPSAETFEDLIKFSFHTSVMEGNIGYLRFDMFGDCELLTQVSELMVEHVWKKIVHTDGLIIDMRNIGGPTSSISALCSYFFDEDHPVLLDKIYNRPNDSISEIWTHSHIAGERYGSRKSVVILTSNMTAGAAEEFVSIMKRLGRALVVGEVTGGGCHPPQTYHVDDTHLYITIPTSRSVGSEDGSSWEGVGVTPHLVVPADVALSRAKDLF 
>M4_taeGut
AQVPQILQTVGKLVADNYAFVNTGTVIASNLTKNIHKDNYKRINTEEDLAGKVTAILQALSDDKHLKLLYIPEHAKDSIPGIMPKQIPPPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDSELLTQLSDLMIEHVWKKIFHTDALIIDLRYNIGGSTTPIAILCSYFFDEGHPVLLDRVYDRPSDSVKEIWTQPQLKGERYGSQKGLVILTSAVTAGAAEEFVYIMKRLSRALIIGEQTSGGCHSPQTYQVDETNFYVVIPTSRSVTSADSTSWEGKGVSPHIETPAETALIKAKEML 
>M4_galGal
TQVPQIVQTVGKLVAENYAFVDIGTDIASNLTKSVNKENYKRINSEKELARKLTAILQALSDDEHLKILYIPEHAKDSIPGILPKQIPSPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDCELLTQVSDLLVEHVWKKIVHTDALIIDMRYNIGGYTNSIPILCSYFFDEGHQVLLDKVYDRPSDSVKEIWTQPQLRGERYGSQKGLIILTSAVTAGAAEEFVFIMKRLGRALIIGEQTSGGSHSPQTYQVDDTNFYIIIPTARSVISAESASWEGKGVPPHMETPAVTALIKAKEVL
>M4_anoCar
TKLPSVLNTIGKLVADNYAFADIGATVAAKFADYAKKGTYRKINSEIELSGKLAADLKALSGDRHLMISHIPERSKGRILGLVPMQQIPPPEILEDLIKFSLHTNVFENNIGYLRFDMFGDCELMSQVSELLVQHVWNKIVNTDALIIDMRYNVGGPACSVPLLCSYFFDEGHPILLDKVYNRPNDTTSNIWTVSKLAGKRYGLNKGLIILTSSVTSGAAEEFAHIMKRLGRAFIIGQKTSGGCHPPQTFHVDGTNLYITTPVSRSVFSVNDSWEGVGVSPHLDVSTDVALIKAKEML
>M4_xenLae
TKIPTVIQTAAKLVADNYAFADTGANVASKFIALVDKIDYKMIKSEVELAEKINDDLQSLSKDFHLKAVYIPENSKDRIPGVVPMQIPSPELFEELIKFSFHTDVFEKNIGYIRFDMFADSDLLNQVSDLLVEHVWKKVVDQDALIIDMRFNIGGPTSSIPIFCSYFFDEGTPVLLDKIYSRTSNAMTDIWTLPDLVGKTFGSKKPLIILTSSLTEGAAEEFVYIMKRLGRAYVVGEVTSGGCHPPQTYHVDDTHLYLTIPTSRSASAEPGESWEGKGVLPDLEISSETALLKAKEIL
>M4_xenTro
TKIPSVIQTAGKLVADNYAFADTGADVASKLIALVDKINYKMIKSEVELAEKLNYDLQSLSKDVHLKAVYIPENSKDRIPGVVPMQIPSPEMFEDLIKFSFHTDVFEKNLGYIRFDMFADSDLLNQVSDLLVEHVWKKVVNQDALIIDMRFNIGGPTSSIPTFCSYFFDEGTPVLLDKIYSRTTNAITDVWTLPHLVGNAFGSKKPVIILTSSLTEGAAEEFVYIMKRLGRAYVIGEVTSGGCHPPQTYHVDDTHLYLTIPTSRSASAKPGESWEGKGVLPDLEITSETALMKAKEIL
>M4_tetNig
AQIPAIIEGTAALVANNYAFEATGADVAKELRELQANGQYSSVVSKESLEAALSADLQRLSGDKSLKTTPNTPVLPPMDYTPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDLRNNVGGPTTAIAGFCSYFFDADKQNRVGQAVRQASGTTTELLTLSELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQTFRVGETDVFLLIPTVHSDTGAGPAWEGAGIAPHIPASAEAALGTARAIL   
>M4_takRub
AQIPAIIEGAATLIAKNYAFEATGADVATKLRELLAKGQYNSVVSSESLEVALSADLQRLSGDKSLKATQNAPVLPPMDYSPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDLRNNVGGPTTAIAGFCSYFFDADKLIVLDKLHDRPSGTTTELLTLPELTGVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQVFSVGEIGIFLSIPTVHSDTAAGPAWEGTGITPHIPVSAEAALGTAKGIL   
>M4_gasAcu
NRVPAIIEGSATLIADNYAFEDIGAAVAEKLKGLLANGEYSKVVSKDSLEMKLSADLRTLSGDKSLKTTSNVPALPPMNYSPEMYIELIKVSFHTDVFEDNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDAMIVDLRNNIGGPTTAIAGFCSYFFDSDKQIVLDRLYDRPSGTTTELRTLPELTGTRYGSKKSLVMLTSRATAGAAEEFVYIMKKLGRAMIVGETTAGTSHPPKTFRVGETDIFLSIPTVHSDTAAGPAWEGAGVAPHIPVPADAALETAKGIF
>M4_oryLat
LQVPAIIEESATLVANNYAFESTAADVAEKLKGHLANGDYNMVVSKESLEAKLSADLQSLSGDKSLTVSSNTGAPPPMEYTPEMYIELIKISFHTDVFENNIGYLRFDMFGDFEEVKAIAQVIVEHVWNKVLHTDAMIIDLRNNVGGPTTAIAGFCSYFFDGDKQILLDKLYDRSTGTTTDLLTLGELTGERYGSKKSLIILASRATAGAAEEFVYIMKRLGRAMIVGETTAGASHPPKVFQVGESDIFLSIPTVHSDTSAGPGWEGAGVAPHIPVAAGAALETAKAIL   
>M4_danRer
AEIPALAQAAATLIADNYAFPSIGEHVAEKLEAVVAGGEYNLISTKEDLEERLSEDLLKLSEDKCLKTTSNIPALPPMNPTPEMFIALIKSSFQTDVFENNIGYLRFDMFGDFEHVATIAQIIVEHVWNKVVDTDALIIDLRNNIGGHASSIAGFCSYFFDADKQIVLDHIYDRPSNTTRDLQTLEQLTGRRYGSKKSVVILTSGVTAGAAEEFVFIMKRLGRAMIIGETTHGGCQPPETFAVGESDIFLSIPISHSTAQGPSWEGAGIAPHIPVPAGAALDTAKGML   
>M4_petMar
ADAPSILRTVGKLVADGYSRAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHLKAVCVPEHATDRMPGIVPMQMPPTESFEDLIKFSFITDVLEGNIGYLRFDLFSDLEALEHVAHLLVEHVWKKICDTEILIIDLR   

>Mn_braFlo RALNDQSL SKAIILD LNEL insertions omitted
VDWLDVVMGIGDVMADHYLDQDLLQRWNRTLVHRFQSWSQDDMSDSLRMEEGLTSELRNITGDETIKVWDFGVYENTTQEPVPREFYNFSTFVDNFKKNINVTMLEGNVGYVSIRSMSHIVDIILPDPEMTEFFLSKMAASKAIILDLRYNLGGDREGVVHWASFFFNATPSVPLSDVYYRDGVNQYWTLLEVPGGIRFPDMPLYLLTSNRTSREAEEFAYAMQVVNRTTIIGETTAGEEFTGMWFPIDQTDVHLLTRTNVVRNPITQDSWSGKGVTPDIIVPSEKALTVALRKI

RBP3 (IRBP) sequences from human to amphioxus

>RPB3_homSap human
0 MMREWVLLMSVLLCGLAGPTHLFQPSLVLDMAKVLLDNYCFPENLLGMQEAIQQAIKSHEILSISDPQTLASVLTAGVQSSLNDPRLVISYEPSTPEPPPQV
PALTSLSEEELLAWLQRGLRHEVLEGNVGYLRVDSVPGQEVLSMMGEFLVAHVWGNLMGTSALVLDLRHCTGGQVSGIPYIISYLHPGNTILHVDTIYNRPSNTTTEIWTLPQVLG
ERYGADKDVVVLTSSQTRGVAEDIAHILKQMRRAIVVGERTGGGALDLRKLRIGESDFFFTVPVSRSLGPLGGGSQTWEGSGVLPCVGTPAEQALEKALAILTLRSALPGVVHCLQ
EVLKDYYTLVDRVPTLLQHLASMDFSTVVSEEDLVTKLNAGLQAASEDPRLLVRAIGPTETPSWPAPDAAAEDSPGVAPELPEDEAIRQALVDSVFQVSVLPGNVGYLRFDSFADA
SVLGVLAPYVLRQVWEPLQDTEHLIMDLRHNPGGPSSAVPLLLSYFQGPEAGPVHLFTTYDRRTNITQEHFSHMELPGPRYSTQRGVYLLTSHRTATAAEEFAFLMQSLGWATLVG
EITAGNLLHTRTVPLLDTPEGSLALTVPVLTFIDNHGEAWLGGGVVPDAIVLAEEALDKAQEVLEFHQSLGALVEGTGHLLEAHYARPEVVGQTSALLRAKLAQGAYRTAVDLESL
ASQLTADLQEVSGDHRLLVFHSPGELVVEEAPPPPPAVPSPEELTYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVRLVWQQLVDTAALVIDLRYNPGSYSTAIPLLCS
YFFEAEPRQHLYSVFDRATSKVTEVWTLPQVAGQRYGSHKDLYILMSHTSGSAAEAFAHTMQDLQRATVIGEPTAGGALSVGIYQVGSSPLYASMPTQMAMSATTGKAWDLAGVEP
DITVPMSEALSIAQDIVALRAKVPTVLQTAGKLVADNYASAELGAKMATKLSGLQSRYSRVTSEVALAEILGADLQMLSGDPHLKAAHIPENAKDRIPGIVPMQ 0
0 IPSPEVFEELIKFSFHTNVLEDNIGYLRFDMFGDGELLTQVSRLLVEHIWKKIMHTDAMIIDMR 2
1 FNIGGPTSSIPILCSYFFDEGPPVLLDKIYSRPDDSVSELWTHAQVV 1
2 GERYGSKKSMVILTSSVTAGTAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTNLYLTIPTARSVGASDGSSWEGVGVTPHVVVPAEEALARAKEMLQHNQLRVKRSPGLQDHL* 0
 
>RBP3_bosTau cow run-on terminal exon
0 MVRKWALLLPMLLCGLTGPAHLFQPSLVLEMAQVLLDNYCFPENLMGMQGAIEQAIKSQEILSISDPQTLAHVLTAGVQSSLNDPRLVISYEPSTLEAPP
RAPAVTNLTLEEIIAGLQDGLRHEILEGNVGYLRVDDIPGQEVMSKLRSFLVANVWRKLVNTSALVLDLRHCTGGHVSGIPYVISYLHPGSTVSHVDTVY
DRPSNTTTEIWTLPEALGEKYSADKDVVVLTSSRTGGVAEDIAYILKQMRRAIVVGERTVGGALNLQKLRVGQSDFFLTVPVSRSLGPLGEGSQTWEGSG
VLPCVGTPAEQALEKALAVLMLRRALPGVIQRLQEALREYYTLVDRVPALLSHLAAMDLSSVVSEDDLVTKLNAGLQAVSEDPRLQVQVVRPKEASSGPE
EEAEEPPEAVPEVPEDEAVRRALVDSVFQVSVLPGNVGYLRFDSFADASVLEVLGPYILHQVWEPLQDTEHLIMDLRQNPGGPSSAVPLLLSYFQSPDAS
PVRLFSTYDRRTNITREHFSQTELLGRPYGTQRGVYLLTSHRTATAAEELAFLMQSLGWATLVGEITAGSLLHTHTVSLLETPEGGLALTVPVLTFIDNH
GECWLGGGVVPDAIVLAEEALDRAQEVLEFHRSLGELVEGTGRLLEAHYARPEVVGQMGALLRAKLAQGAYRTAVDLESLASQLTADLQEMSGDHRLLVF
HSPGEMVAEEAPPPPPVVPSPEELSYLIEALFKTEVLPGQLGYLRFDAMAELETVKAVGPQLVQLVWQKLVDTAALVVDLRYNPGSYSTAVPLLCSYFFE
AEPRRHLYSVFDRATSRVTEVWTLPHVTGQRYGSHKDLYVLVSHTSGSAAEAFAHTMQDLQRATIIGEPTAGGALSVGIYQVGSSALYASMPTQMAMSAS
TGEAWDLAGVEPDITVPMSVALSTARDIVTLRAKVPTVLQTAGKLVADNYASPELGVKMAAELSGLQSRYARVTSEAALAELLQADLQVLSGDPHLKTAH
IPEDAKDRIPGIVPMQ 0
0 IPSPEVFEDLIKFSFHTNVLEGNVGYLRFDMFGDCELLTQVSELLVEHVWKKIVHTDALIVDMR 2
1 FNIGGPTSSISALCSYFFDEGPPILLDKIYNRPNDSVSELWTLSQLE 1
2 GERYGSKKSMVILTSTLTAGAAEEFTYIMKRLGRALVIGEVTSGGCQPPQTYHVDDTDLYLTIPTARSVGAADGSSWEGVGVVPDVAVPAEAALTRAQEMLQHTPLRARRSPRLHGRRKGHHRQSQGRAGSLGRNQGVgRPEVLTEAPSGQKRGLLQCG* 0

>RBP3_monDom opossum
0 MTSQCLLLFSALLFSLAHAEQIFQPSLVRDMAKILLDNYCFPENLMGMQEVIEQAIKSGEILDISDPQMLASVLTAGVQGALNDPRLVISFEPSIPETPQ
HVPKLANVTQEELLILLQQMIKYQVLEGNVGYLRVDYIPGQEVVEKVGEFLVNNIWKKLMGTSSLVLDLQHSSGGEISGIPFVISYLHQGDILLHVDTVY
DRPSNTTTEIWTLPQVLGERYGGEKDMVVLTSHRTVGVAEDIAYILKKLRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSG
VLPCVGIPAEQALGKALAILTLRRARPGAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATMGSEASEEEDATPAANS
LPEDESQRQALVDSVFQVSVLPGNVGYLRFDEFADSSVLGTLAPYVIRQVWEPLQDTNHLIMDLRYNPGGPSSAVPLLLSYFQDPAAGP
IRLFTTYDRQTNQTQEHLSRAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGNLVLTVPILTFIDNNG
ECWLGGGVVPDAIVLAEEALDKAKEVLEFHQRLGALVEGTGHLLEAHYALPEVVGQASALLKAKLEHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFH
SPGEPVSEELTPPQKGVPSPEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIAPQLVELVWEKLVHTEALVVDLRYNPGGYSTAVPLLCSYFFEA
EPRRHLYTIFDRAASQLTEVWTLPQVAGERYGSQKDLYILISHTSGSAAEAFVHTMKDQHRATVIGEPTGGGALSVGIYQVENSPLYASMPTQVAISPVT
GKAWDMAGVEPDVSVLSSEALMTTQGIVALRAKVPTILQTAGKLVADNYASLEVGSRVASKLAKLQTQYRQVTSEGELADMLGADLQTLSGDRHLKTAHI
PEDAKDRIPGIVPMQ 0
0 LPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDMR 2
1 FNIGGPTSSISALCSYFFDEGQEVLLDQIYNRPNDSISEIWTQSQVA 1
2 GERYGSKKSVIILTSSMTAGAAEEFVYVMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTARSVGSGDKPSWEGVGVAPHVEVPADQALSKAKEMFNHHLQRAK* 0

>RBP3_sacHar Sarcophilus harrisii
0 MTSQCLLLFSALLFSLAHGEEIFQPTLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLANVLTAGVQGSLNDPRLVISYEPSTSEAPQ
HDPKFANATQEELLALFQKIIKYQVLEDNVGYLRVDYIPGRDMIEEVGEFLVNDIWKKVMETSSLVLDLQHSR
GGEVSGIPFVISYLHQGDILLHVDTIYDRPSNTTTEIWTLPQVLGERYSGEKDIVVLTSHHTVGVAEDIAYILKKMRRAIVVGEQTQGGSLDLRKLRIGQSDFFITVPVARSLSPLGGGSQTWEGSG
VVPCVGIPAEQALEKALAILTLRRARPGAIQRLMEILQKYYTLVDRVPALLHHLTAIDYSSVLTEEDLAAKLNAMLQAVSEDPRLLVRVLRPEEATVEAEPGEESATPASVSLPESDAERQALI
DSVFQVSVLPGNVGYLRFDEFADNSVLGTLAPYVLRQVWEPLQDTDHLIMDLRYNPGGPSSAVPLLLSYFQDPSAGPVRLFATYDRQTNQ
TQEYRSRAELLGKPYGAERGVYLLTSYHTATAAEEFAFLMQSLGRATLVGEITAGSLMHTRTFPLLQPPNGSLVLTVPTLTFIDNHGECWLGGGVVPDAIVLAEEALDKAKEVLEFHQRL
GALVEGTGHLVEAHYALPEVVGQASAFLRATLAHGTYRTAVDFESLASQLTSDLQEVSGDHRLHVFHSPGEPVPEESSPPHKGVPSPEELTYLIEALFKTDVLP
QLGYLRFDMMAEVETVRAIGPQLVELVWEKLVNTEALVVDLRYNPGSYSTTVPLLCSYFFEAEPRKHLYTVFDRATSQFTEVWTLPQVTGERYGSQKDLYILISHTSGSA
AEAFAHIMKDLQRATVIGEPTAGGALSVGIYQVGDSPLYVSMPTQVALSPVTGKAWDMAGVEPDVSVLANEALITAQGIVALRAKVPTILQTAGKLVADNYA
SPEVGSRVAAKLASLQIQYGKVTSEGELADMLGADLQTLSGDRHLKTAHIPEDAKDRIPGIVPMQ 0
0 LPSPEAFEDLIKFSFHTNVFEGNIGYLRFDMFGDCELLIQVSDLLVEHVWKKVMHTDGMIIDMR 2
1 FNIGGPTSSISAMCSYFFDEGQGVLLDRIYNRPNDSISEIWTQPQVI 1
2 GERYGSKKTVVILTSSMTAGAAEEFVYIMQRLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTTRSVVSGDKSSWEGVGVVPHMEVPADQALSKAKEMFTHQLQKTK* 0

>RBP3_macEug wallaby 3 alleles to FJ603206 Macropus eugenii frag exon 2 lower case: sacHar fix
0 MTSQCLLLFSALLLSLAHAEQIFQPSLVLDMAKILLDNYCFPENLMGMQEAIEQAIKSGEILDISDPQMLASVLTAGVQGSLNDPRLVISYEPSPAEAPQQSPKLTSLTQEELLTLLQQM
IKYQVLDGNVGYLRVDYIPGQEVVEKVGEFLVNDIWKKLMGTSSLVLDLQHSTEGEVSGIPFVISYLHEGDILLHVDTVYDRPSNTTTEIWTLPQVLGERYSGEKDLVILTSHRTVGVAE
DIAYILKKMRRAIVVGEQTLGGALDLRKLRIGQSDFFITVPVSRSLSPLGGGSQTWEGSGVLPCVGIPAEQALEKALAILTLRRARPAAIQRLMEVLQNYYTLVDRVPALLHHLTAIDYS
SVLTEEDLAAKLNAGLQAVSEDPRLLVRVLRPEEATAGAESREEAATAAPVPLPDGESQRQALVNSVFQVSVLPGNVGYLRFDEFADSSVLGALAPYVLQQVWEPLQDTDHLIMDLRYNP
GGPSSAVPLLLSYFQDPAAGPVRLFATYDRQTNQTREYRSQAELLGKPYGAQRGVYLLTSHHTATAAEEFAFLMQSLGRATLVGEITAGNLMHTRTFSLLQPPDGSLVLTVPILTFIDNH
GECWLGGGVVPDAIVLAEEALDKAKEVIEFHQRLGALVEDAGHLLEAHYALPEVVGQASALLRARLVHGTYRTAVDFESLASQLTSDLQEVSGDHRVHVFHSPGELIPEELSPPQNVVPS
PEELTYLIEALFKTEVLPGQLGYLRFDMMAEAETVRAIGPQLIELVWEKLVNTEALVVDLRYNPGSYSTSVPLLCSYFFEAEPRKHLYTIFDRAASQATEVWTLPQVAGERYGSQKDLYI
LISHTSGSAAEAFAHAMKDLRRATVIGEPTAGGALSVGIYQVSNSPLYASMPTQVAISPVTGKAWDIAGVEPDVSVPAREALITTQGIVTLRSKVPTILQTAGKLVADNYASPEVGSRVA
AKLARLQTQYRQVTSEGELADMLGADLQTLSGDSHLKTAHIPEDSKDRIPGIVPMQ 0
0 lpspeafedlikfsFHTNVFEGNIGYLRFDMFGDCELLTQVSDLLVEHVWKKVVHTDGMIIDMR 2
1 FNIGGPTSSISALCSYFFDEGQKVLLDRIYNRPNDSIVEIWTQPHVT 1
2 GERYGSKKSVIILTSSTTAGAAEEFVYIMQGLGRALVIGEVTSGGCQPPQTYHVDDTDLYITIPTAQSVGSGDRPSWEGIGVTPHVEVPADQALSKAKEMFIHHLQRAD* 0

>RBP3_ornAna platypus genome rife with frameshifts, dels, misassembly frag
0 MGVCLPLLLVAQFSLTGHVEPVSQPSMVLDVAKILLDNYCYPENLMGMQEAIEEAIQRGEILDIADPKRLASVLTAGVQGSLNDPRLVISYEPAPVAVSQ
QPPEPASLPAEQPLERLRPAVGSEVLEGNVGYLRVDRLPGREEIERVGAVLGRDIWEKLLGTSALVLDLRHSTGGHVSGIPFFISYFYPEGPALHVDTVY
DRPSNATRQLWTLPRVLGARYAADKDVVVLTSRLTAGVAEDVAYILQQMRRAIVVGERTAGGPLVFRKLRVGLSDFFITVPVACSLGPLGGGGRSWEGSG
VLPCVAVPADRALDEALDILALRGAVPGAVAHLADLLRDYYALVDRVPALLRHLAALDLSSVLSEEDLTSRLNAGLQAASEDPRLLVRRLEPEEAERGPP
RKEEEQKEEEEEDQPSPGASILPGDGSSLFRVSVLPGNVGYLCFDEFPEASALERLGPLLGRRVWEPLEATDHLMVDLRNNPGGPSSAVPLLLSYF
QDPAAGPIRLFTTYNRPADVTREYASRAGALEKPYGARRGVYLLTSHRTATAAEEFAYLMQALGRATLVGEITAGRLLHSRTFPLLRPPWEGLVLTVPFL
TLFDPHGEGWLGGGVVPDAIVLAEEALEKAGEVLAFHQTLEALVETTGHLLEAHYCFPAGARRAGAQPWPVAGVEPDVMAQAAEALAVAQGIAALRSKVP
TVLRTAAKLVADNYAFRETGAGVAAQMGGLQARCGRVTSEGALAEVLGAHLRALSGDPHLQMVYIPEDAKDRIPGVVPMQ 0 
0 IPSAETFEDLIKFSFHTSVMEGNIGYLRFDMFGDCELLTQVSELMVEHVWKKIVHTDGLIIDMR 2
1 NIGGPTSSISALCSYFFDEDHPVLLDKIYNRPNDSISEIWTHSHIA 1
2 GERYGSRKSVVILTSNMTAGAAEEFVSIMKRLGRALVVGEVTGGGCHPPQTYHVDDTHLYITIPTSRSVGSEDGSSWEGVGVTPHLVVPADVALSRAKDLFRAHLEHRD* 0

>RBP3_taeGut Taeniopygia guttata
0 MIRTHFLLLSALIMCSIPAEEIFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPLPHSGPK
QEAEGSPTREQLLSLIEHVIMYDKLEGNVGYLRIDYIIGEEVVQKVGAFLVDKVWKTLIETSALVIDLRHSTGGQISGLPFIISYLHEQDKILHVETVYN
RPSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITVGEKTAGGSLDIQKLRIGPSNFYMMVPVSRSVSPLSGGGQSWEVSGV
MPCVATEAEQALQKSLDILAVRRAVPGTISHLKNILKDYYSLVERVPALLRRLTTSDFSSVQSSEDLATKLNTELQALSDDPRLMVRVMMPGEAADSPAE
KPVGMAADLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYLVHKVWEPLQNTENLIMDLRYNLGGPSSSAVPVLLSYFQDPAAGPVH
LFTTYDRRTNHTQEHNSQAELLGQSYGAKRGVYLLTSHHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTRTFPLLQPGPGITRGLTITVPVITFIDNH
GESWMGGGVVPDAIVLAEDALEKAEEVLAFHKNMGVLLEGTGQLLEDHYAIPEVAAKASAMLSTKRAQGGYRSAIDSETLASQLTSDLQEASGDHRLHVF
HSHVEPTPEEQLPNVIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLLQMVWNKLVDTDAMIIDMRYNTGGYSTAIPILCSYFFDPE
PRKHLYTVFDRSTSRSTEVWTLPQLAGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVVGEPTVGGSLSVGIYRVGNSSLYASIPSQVVLSPVTG
KVWSVSGVEPHITIQASEAMAAAQHIANLRAQVPQILQTVGKLVADNYAFVNTGTVIASNLTKNIHKDNYKRINTEEDLAGKVTAILQALSDDKHLKLLY
IPEHAKDSIPGIMPK 0
0 QIPPPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDSELLTQLSDLMIEHVWKKIFHTDALIIDLR 2
1 YNIGGSTTPIAILCSYFFDEGHPVLLDRVYDRPSDSVKEIWTQPQLK 1
2 GERYGSQKGLVILTSAVTAGAAEEFVYIMKRLSRALIIGEQTSGGCHSPQTYQVDETNFYVVIPTSRSVTSADSTSWEGKGVSPHIETPAETALIKAKEMLNAHLHSSR* 0

>RBP3_galGal Gallus gallus 1236 aa N-terminal 21 aa signal peptide 5 glyc (3 unique) two W per repeat
0 MRTYFFLFSVLIVCSISAEEIFQPTLVLDMAKVLLDNYCYPENLVGMQEAIEQAIKSGEILDISDPKMLANVLTAGVQGALNDPRLVISYEPSLHAAPKQ
EAETYPTREQLLSLIEHVVIYDKLEGNVGYLRIDYIIGQEVVEKVGAFLVDKVWKTLINTSALVIDLRYSTGGQISGIPFIISYLHEADKMLHVETVYNR
PSNTTTEIWTLPKVLGERYSKDKDVIVLISHHTTGVAEDVAYILKHMNRAITLGEKTAGGSLDIQKLRIGPSNFYMMVPVSRSVSPLSGGGQSWEVSGVM
PCVASEAEQALKKSLDILAVRRAVPGTLSRLTDILKDYYSLVERVPVLLRHLTTSDFSSVQSAEDLATKLNTEMQTLSEDPRLLVRTMMPGEAAAPPAEM
PIAMAANLPDNEQLLHALVDTVFKVSVLPGNVGYMRFDEFADASVLVKLGPYIVKKVWEPLQNTENLIMDLRYNPGGPSSSAVPMLISYFQDPTAGPVHL
FTTYDRRTNHTQEHNSQAELLAQPYGAQRGIYVLTSRHTATAAEEFAYLMQSLGRATLIGEITAGSLSHTCTFPLVQPEQGITRGLTITVPVITFIDNHG
ESWMGGGVVPDAIVLAEDALEKAEEVLTFHRKMGILLESTGQLLEAHYAIPEVAEKASVMLSTKRVQGGYRSAVDFETLASQLTSDLQEASGDHRLHVFH
SHVEPTPEEQLPNMIPSPEELSYIIEALFKIEVLPGNLGYLRFDMMAEAETVKAIGPQLVQMVWNKLVDTDAMIIDMRYNTGGYSTAVPILCSYFFEPEP
RQHLYTVFDRSTSRSTEVWTLPKVTGKRYGSLKDIYILTSHMSGSAAEAFTRSMKDLHRATVIGEPTVGGSLSVGIYRVGNSSLYRSIPSQVVLSPVTGK
VWSVSGAEPHITIQASEALAAAKHIASLRTQVPQIVQTVGKLVAENYAFVDIGTDIASNLTKSVNKENYKRINSEKELARKLTAILQALSDDEHLKILYI
PEHAKDSIPGILPK 0
0 QIPSPEVFEDLIKFSFHTNVFENNIGYLRFDMFGDCELLTQVSDLLVEHVWKKIVHTDALIIDMR 2
1 YNIGGYTNSIPILCSYFFDEGHQVLLDKVYDRPSDSVKEIWTQPQLR 1
2 GERYGSQKGLIILTSAVTAGAAEEFVFIMKRLGRALIIGEQTSGGSHSPQTYQVDDTNFYIIIPTARSVISAESASWEGKGVPPHMETPAVTALIKAKEVLSAHLHSSR* 0

>RBP3_anoCar lizard
0 MLRKCLWLSIVLVCCSSYADSVLQSTLVLDMAKLLLDNYCLPENLVGMREAIEQAIKNGEVLDISDPKLLATVLTAGVQGALNDPRLVISYEPTAPAAPK
QRMETSLTPEQLLSLIQHTVKYEVLDDNVGYLRIDYIMGQDIVQKIGSFLVEKVWKTLLGTSALILDLRYTTGGDVSGIPFIISYLYNGDKVLHVDTVYN
RPSNTTVEILTLPKVLGVRYSKDKDVILLISKYTTGVAENVAYILKHMHRTIIVGEKSAGGSLDTQKMQIGNSQFYMTVPLSCSVSPLSGSGQSWEISGV
TPCVVISAEQALDKALAILSLRKAIPNSMSYLVDIIKNNYSMLEQVPVLLQHLSTFDYSSVLSVKDLASKLNAELQTISEDPRLFLRVPASDEAVTSQTD
EKVAMASDLPNNEQLMKALVMTVFKVSVLPGNVGYMRFDEFGDATVLVKLGPYLLQHVWEPLQATDYLIIDLRYNIGGPSSSAVPVLLSYFQDPSAGPVH
FFTTYNRLTNQTQAYSSSAEMVGKPYGARRGVYLLTSHNTATAAEEFAYLMQTLGRATLVGEITAGSLSHTHTFCILELGGGCGLLINVPVITLIDNHGE
YWLGGGVVPDSIVLADEALEKAREVLEFHKGMGSLIERVGQLLEAHYAIPEMARRVSSMLNSKLAQGGYRTAVDFETLASQLTNDLQETSGDHQLHVFHS
HVEPSLEEQSPFKTLTPEELNFIIEALFKVDVLPGNVGYLRFDMMAEFESVKTIEPQILHMVWEKLVETSAMIVDMRYNTGSYSTAVPMFCSYFFDAEPQ
QHLYTIIDRSTSQSTEVWTSSQVSGKRYGSTKDLYILISHASGSAAEAFTRSLKDLHRATVIGEPTVGGSLSASIYNIGSTPLYASIPSQIVLSPVSGKV
WSLSGIQPHVTTQSNEALASAQNIILFRTKLPSVLNTIGKLVADNYAFADIGATVAAKFADYAKKGTYRKINSEIELSGKLAADLKALSGDRHLMISHIP
ERSKGRILGLVPM 0
0 QIPPPEILEDLIKFSLHTNVFENNIGYLRFDMFGDCELMSQVSELLVQHVWNKIVNTDALIIDMR 2
1 YNVGGPACSVPLLCSYFFDEGHPILLDKVYNRPNDTTSNIWTVSKLA 1
2 GKRYGLNKGLIILTSSVTSGAAEEFAHIMKRLGRAFIIGQKTSGGCHPPQTFHVDGTNLYITTPVSRSVFSVNDSWEGVGVSPHLDVSTDVALIKAKEMLKAHLH* 0

>RBP3_xenLae Xenopus laevis
0 MPPLFQALTTALFFCGIASNPLFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAVKGGEILHISDPDTLANVFTSGVQGYLNDPRLVVSYEPNYSGPQT
EQSLELTPEQLKFLINHSVKYDILPGNIGYLRIDFIIGQDVVQKVGPHLVNNIWKKLMPTSALILDLRYSTQGEVSGIPFVVSYLCDSEIHIDSIYNRPS
NTTTDLWTLPELMGERYGKVKDVVVLTSKYTKGVAEDASYILKHMNRAIVVGEKTAGGSLDTQKIKIGQSDFYITVPVSRSLSPLTGQSWEVSGVSPCVV
VNAKDALDKAQAILAVRSSVTHVLHQLCDILANNYAFSERIPTLLQHLPNLDYSTVISEEDIAAKLNYELQSLTEDPRLVLKSKTDTLVMPGDSIQAENI
PEDEAMLQALVNTVFKVSILPGNIGYLRFDQFADVSVIAKLAPFIVNTVWEPITITENLIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNS
TDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFDGTQLSVTVPIINFIDSNGDYWLGGGVVPDAIVLA
DEALDKAKEIIAFHPSIFPLVKGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASLLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIP
SPEELNYIIDALFKIEVLPGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSTGK
DIWTLPEVFGERYGSTKDIYILTSHMTGSAAEVFTRSLKDLNRATLIGEPTSGVSLSVGMYKVGDSNLYVTIPNQVVISSVTGKVWSVSGVEPHVIIQAN
EAMNIAHRIIKLRTKIPTVIQTAAKLVADNYAFADTGANVASKFIALVDKIDYKMIKSEVELAEKINDDLQSLSKDFHLKAVYIPENSKDRIPGVVPM 0
0 QIPSPELFEELIKFSFHTDVFEKNIGYIRFDMFADSDLLNQVSDLLVEHVWKKVVDQDALIIDMR 2
1 FNIGGPTSSIPIFCSYFFDEGTPVLLDKIYSRTSNAMTDIWTLPDLV 1
2 GKTFGSKKPLIILTSSLTEGAAEEFVYIMKRLGRAYVVGEVTSGGCHPPQTYHVDDTHLYLTIPTSRSASAEPGESWEGKGVLPDLEISSETALLKAKEILESQLEGRR* 0

>RBP3_xenTro Xenopus tropicalis 89% xenLae
0 MSPLFKALTTVLFFCIVASNPVFQPSLVMDMAKVLLDNYCFPENLVGMQETIEQAMKSGEILHISDPETLANVFTSGVQGFLNDPRLVVSYEPNYSGPRK
EQSPEPTLEQLKFLLDHSVTYDLLPGNIGYLRIDFIIGQDVVQKVGPLLVNNIWKKLMPSSALILDLRYSTQGKVSGIPFVVSYLTDPQIHIDSIYNRPS
NTTTDLWTLSELMGERYGKDKDVVVLTSKYTEGIAEGAAYILKHMSRAIVVGEKTAGGSLDIQKIKIGQSEFYITVPVSRSISPLTGQSWEVAGVFPCVV
VNANNALNKAQGILAVRSSITHILLQLSEILVNNYAFSERIPTLLQHLPNLDYSSVISEEDITAKLNYELQSLTEDPRLVLKSKTDSLVMPEDSTQVENL
PDDEATLQALVNTVFKVSILPGNIGYLRFDEFADVSVLAKLGPYIVNTVWDPITVTENLIIDLRYNIGGSSTSIPLLLSYFQEPENRIHLFTIYNRQQNS
TNEVYSLPKVLGKPYGSKKGVYVLTSHETATAAEEFAYLMQSLSRATIIGEITSGNLMHSKAFPLDGTRLSVTVPIMNFIDNNGDYWLGGGVVPDAIVLA
DEALDKAKEIIAFHPSVFALVEGTGHLLEVHYAIPEVAYKVSSVLQNKWSEGGYRSVVDLESLASQLTSEMQENSGDHRLHVFYSDTEPEILEDQPPKIP
SAEELNYIIDALFKIEVLQGNVGYLRFDMMADTEIIKAIGPQLVSLVWNKLVETNSLIIDMRYNTGGYSTAIPIFCSYFFDPEPLQHLYTVYDRSTSSGT
DIWTLPEVVGERYGSTKDIYILTSHMTGSAAEVFTRSMKELNRATIIGEPTSGVSLSVGMYKVGESNLYVSIPNQVVISSVTGKVWSVSGVEPHVIAQAS
EAMNVAHHIIKLRTKIPSVIQTAGKLVADNYAFADTGADVASKLIALVDKINYKMIKSEVELAEKLNYDLQSLSKDVHLKAVYIPENSKDRIPGVVPMQ 0
0 IPSPEMFEDLIKFSFHTDVFEKNLGYIRFDMFADSDLLNQVSDLLVEHVWKKVVNQDALIIDMr 2
1 FNIGGPTSSIPTFCSYFFDEGTPVLLDKIYSRTTNAITDVWTLPHLV 1
2 GNAFGSKKPVIILTSSLTEGAAEEFVYIMKRLGRAYVIGEVTSGGCHPPQTYHVDDTHLYLTIPTSRSASAKPGESWEGKGVLPDLEITSETALMKAKEILVSQLEGR* 0

>RBP3_tetNig frameshifts in genome two domains: 23-324,326-612 no upstream dup
0 MAKALFTVASLLLLANGFFVGAAFPPSLIADMAKIVLDNYCSPEKLAGMKEAIKAAGTNTEVLNIPDGESLARVLSAGVQGTVSDPRLMVSFQPNYVPAG
PHKMPPLPPEHLVAVLQTSVKLDILEGNTGYLRIDHILGEEVADKVGPALIDLIWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTQAEPVVHIDSVYD
RPSNTTTKLLSLPNLLGQRYGVSKPLIVLTSKNTKGIAEDVAYCLKNLKRATIVGEKTAGGSLKLDTFKVGDTDFYITVPTAKSINPITGSSWEIRGVTP
HVEVNAEDALATAIKIVNLRAQIPAIIEGTAALVANNYAFEATGADVAKELRELQANGQYSSVVSKESLEAALSADLQRLSGDKSLKTTPNTPVLPPM 0
0 DYTPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDLr 2
1 NNVGGPTTAIAGFCSYFFDADKQNRVGQAVRQASGTTTELLTLSELT 1
2 GVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQTFRVGETDVFLLIPTVHSDTGAGPAWEGAGIAPHIPASAEAALGTARAILNKHFAGQK* 0

>RBP3_takRub fugu two domains:  23-324,326-612 plus upstream dup
0 MAKALFLVASLLLLANDVLVRAAFPPSLITDMAKIVLDNYCSPEKLAGMKEAIEAAGTNTEVLNIPDGESLARVLSAGVQGTVSDSRLMVSYQPDYVPAV
PPKMPPLPPEHLVAVLQTSIKLDLLEGNTGYLRIDHIIGEDVAEKVGPSLIDLIWNKILPTSALIFDLRYTSSGEISGIPYIVSYFTQAEPVVHIDSVYD
RPSNTTTKLFSLSNLLGERYGITKPLIILTSKNTKGIAEDVAYCLKNLKRATIVGERTAGGSVKLDNFKVGSTDFYITVPTAKSINPVTGSSWEITGVKP
DVEVNAEDALATAIKIVSLRAQIPAIIEGAATLIAKNYAFEATGADVATKLRELLAKGQYNSVVSSESLEVALSADLQRLSGDKSLKATQNAPVLPPM 0
0 DYSPEMYIELIKVSFHTDVFENNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDALILDLR 2
1 NNVGGPTTAIAGFCSYFFDADKLIVLDKLHDRPSGTTTELLTLPELT 1
2 GVRYGSKKSLIILTSGATAGAAEEFVYIMKKLGRAMIVGETTAGASHPPQVFSVGEIGIFLSIPTVHSDTAAGPAWEGTGITPHIPVSAEAALGTAKGILNKHFGGQK* 0

>RBP3_gasAcu sticklebck two domains: 27-317,323-612 no upstream dup
0 MAKLIFLVAPLLVLGNIAFIHAGFAPNVIIDMAKIVIDNYCSPEKLAGMKEAIEAAGSNTEVLSIPDAETLANVLSAGVQTTVSDPRLMISYEPNYVPVV
PPKMPPLPPDQVIAVLQTSIKLDILEGNIGYLRIDHILGEDVAEKVGPLLLDLVWNKILPTSALIFDLRYTSSGDISGIPYIVSYFTEAGTPIHIDSIYD
RPSNTTTKLFSMSTLLGERYSTSKPLIILTSKNTKGIAEDVAYCLQNLKRATIVGEKTAGGSVKVDKIQVRDTGFYVTVPTAKSVNPITGSTWEVTGVTP
NVEVNAEDALATAIKIVTLLNRVPAIIEGSATLIADNYAFEDIGAAVAEKLKGLLANGEYSKVVSKDSLEMKLSADLRTLSGDKSLKTTSNVPALPPM 0
0 NYSPEMYIELIKVSFHTDVFEDNIGYLRFDMFGDFEEVKAIAQIIVEHVWNKVVNTDAMIVDLR 2
1 NNIGGPTTAIAGFCSYFFDSDKQIVLDRLYDRPSGTTTELRTLPELT 1
2 GTRYGSKKSLVMLTSRATAGAAEEFVYIMKKLGRAMIVGETTAGTSHPPKTFRVGETDIFLSIPTVHSDTAAGPAWEGAGVAPHIPVPADAALETAKGIFKKHFAGQK* 0
 
>RBP3_oryLat medaka two domains: 28-314,320-605  no upstream dup
0 MAKTLFLVASLLVLGNVVFLHASFPPSLITDLAKIVMDNYCSPEKLSGMKEDIATAGANTDVLNIPDGEALAKVLTDGVQTTVSDPRLRVSYEPNYVPVV
PPQLPPEQLIAVLQTSIKLDILEGNIGYLRIDSIIGEEVAEKVGPLLLELVWSKILPTSALIFDLRYTSSGDITGIPYIISYLTDAKSEIHIDTIYDRPL
NTTTKLLSMQSTLGQTYGGTKPLLVLTSKNTKDIAEDVAYCLKNLKRATIVGEKTAGGSAKIKKFRVGDTDFYVTLPTAKSINPITGSSWEVTGVKPNVE
VNAEEALATALKIINLRLQVPAIIEESATLVANNYAFESTAADVAEKLKGHLANGDYNMVVSKESLEAKLSADLQSLSGDKSLTVSSNTGAPPPM 0
0 EYTPEMYIELIKISFHTDVFENNIGYLRFDMFGDFEEVKAIAQVIVEHVWNKVLHTDAMIIDLR 2
1 NNVGGPTTAIAGFCSYFFDGDKQILLDKLYDRSTGTTTDLLTLGELT 1
2 GERYGSKKSLIILASRATAGAAEEFVYIMKRLGRAMIVGETTAGASHPPKVFQVGESDIFLSIPTVHSDTSAGPGWEGAGVAPHIPVAAGAALETAKAILNKHIGGQQHAAS* 0

>RBP3_danRer zebrafish upstream frag as well two domains: 22-322,324-609
0 MAQALVLLVSLLFFSNVAHCNFSPTLIADMAKIFMDNYCSPEKLTGMEEAIDAASSNTEILSISDPTMLANVLTDGVKKTISDSRVKVTYEPDLILAAPP
AMPDIPLEHLAAMIKGTVKVEILEGNIGYLKIQHIIGEEMAQKVGPLLLEYIWDKILPTSAMILDFRSTVTGELSGIPYIVSYFTDPEPLIHIDSVYDRT
ADLTIELWSMPTLLGKRYGTSKPLIILTSKDTLGIAEDVAYCLKNLKRATIVGENTAGGTVKMSKMKVGDTDFYVTVPVAKSINPITGKSWEINGVAPDV
DVAAEDALDAAIAIIKLRAEIPALAQAAATLIADNYAFPSIGEHVAEKLEAVVAGGEYNLISTKEDLEERLSEDLLKLSEDKCLKTTSNIPALPPM 0
0 NPTPEMFIALIKSSFQTDVFENNIGYLRFDMFGDFEHVATIAQIIVEHVWNKVVDTDALIIDLr 2
1 NNIGGHASSIAGFCSYFFDADKQIVLDHIYDRPSNTTRDLQTLEQLT 1
2 GRRYGSKKSVVILTSGVTAGAAEEFVFIMKRLGRAMIIGETTHGGCQPPETFAVGESDIFLSIPISHSTAQGPSWEGAGIAPHIPVPAGAALDTAKGMLNKHFSGQK* 0

>RBP3x_takRub fugu single upstream exon 42% frameshift no transcripts three domains: 23-323,325-615,618-907
MAPRTPVLLLVLLFCALPVRSFYQHTLVLEMAKLLLENYCIPENLVGMQEAIQRAIKSREILQISDRKTLATVLTVGVQGALNDPRLSVSYEPSFSPLPLQALSSLPVEQQLRLLRN
SIKLDILDSDVGYLRIDRIIDEETLLKFGPLLRENVWDKAAQTSSLILDLRFSTAGGWSGIPSIVSYFTEPHSLVHIDTVYDRPSNTTTELWTMSSVRGK
TFGGKKDMIVLIGRRTAGAAEAVAYTLKHLNRAIVVGERSAGGSLKVRKFRIAESDFYITMPVARSVSPITGKSWEVSGISPTVNVAAREALAKAQTFLA
VRSRIPKVLQIVLDIIGRFYAFADRVQALLQQLESADLFSVVSEEDLAARLNHDLQTASEDPRLIIRHKRDNIPRAEEEPELHAANDHDGELVEGFTVQV
LPHNTGYLRLDRFVRCSEGDKLEEIVAEKVWGPLKDTQNLIIDLRHNTGGSSTSVALLLSYLRDPLPKRHFFTIYDSVQNTTTEYGSRPHIPGPSYGSER
GVYVLTSHYTAGAAEEFAYLIQSLHFGTVVGEITSGTLMHSKTFQVEGTDIFITVPFINFLDNNGEYWLGGGVVPDAIVLAEEALEHVNRTATFHQGLRSLIGRTGELLEKHYAIQEVAQKVGEV
LLSKWAEGLYRSVVDLESLASQLTADLQEASGDHRLHVFRCDVELESLHGVPKIAAVEEAGFVIDALFKSELLPRNVGYLRFDTMADIEAAKGAAPRLVKSVWNKLVDTDSLIIDMRYNA
GGSSTAVPLWCSYFVDGEPLQHLYTVYDRTTKTRVEVMTLPEVSGQRYDPGKDVYILTSHMTGSAAEAFVRAMRDLNRVTIVGEPTAGGSLSSATYQIGESVLYASIPNQVVTSAATGKL
WSISGVEPDVFAQARDALPVAQRIISARLLKREKGR* 0

>RBP3x_danRer zebrafish single upstream exon 55%/41% transcript DN857398 3 domains: 21-321,324-609,612-901 expressed: inner nuclear layer and ganglion cell layer
MAGVFVFILVTYRVLLVNASFQSALVLDMAKILLDNYCFPENLIGMQEAIQQAINSGEILHISDRKTLASVLTAGVQGALNDPRLTVSYEPNYTLITPPA
LHSLPTEQLIRLIRSTVKLEVMDNNIGYLRIDRIIGQETVVKLGRLLHNNIWKKVAHTSAMIFDLRFSTAGELSGLPYIVSYFSDSDPLLHIDTIYERPT
NITRELWTLPTLLGERFGKRKDLIVLISKRTIGAAEGVAYILKHLKRAVIIGERSAGGSVRVDKLKIGDSGFYITVPVARSVNPVTGQSWEVSGVAPSVT
VNPKESIAKAKSLISVRKTIPKAVRRVSDIIKRYYSFKDKIPALLNQLAKADYFTVVSEEDLAGKLNHEMQSVFEDPRLLIKATQVLTDDASSEDRSSSD
DLTDPLFKLEMISGNNGYLRFDRFPTPEVLLRLEDHIKKKIWQPVQETENLVIDLRFNTGGSTEALPILLSYMFDTSSSTYLFSIYDSIKNTTFDFHTLN
NISGPSYGSTKGVYVLTSYYTAEAGEEFAYLMQSLHRGTVIGEITSGMLLHSKTFQIEQTSLAITVPIINFIDVNGECWLGGGVVPDAIVLAEEALERAH
EIIAFHKNIQGLVQEAGDLLEKHYSVPEVAAKVSRLLQSKLTEGLYRSVVDYESLASQLTSDLQETSGDQRLHIFYCETEPETLHDTPKIPSPEEAGFIV
EALFKVDVMSGNIGYLRFDMMEDIKVLQAINPEFLKVVWNKLVNTDMLIIDVRYNTGGYSTAIPLLCTYFFDAQPLTHIYTLFDRSTATVTKVTTLPDVL
GQKYSSQKDVYILTSHITGSAAEAFTRTMKDLKRATVIGEPTIGGALSSGTYQIGNSILYASIPNQAVLNAVTGKPWSISGVEPHIVAQASDALIVAQKI
IATKQQKKNSGK* 0

>RBP3x_salSal Salmo salar transcript frag DY725143
EETAAKLGPLLRENIWTKVTHASSLIFDLRYSTAGELSGVPFIISYFSDPEPLIHIDTVFDRPSNTTKELWTMSSIMGERYGKRKDLIVLTSKRTMGAAEAIAYTLKHLNRAIIVGERSA
GGSVKVQKIRIGDSGFYITVPVARSVNPITGQSWEVSGVSPSVNINAKEAVANAKNLLAVRSAIPNAVQSVSDIIRQYYSFTDRVPALLQHLESTDFFSVISEEDLANKFNNELQSVSEDPRLMIKL

>RBP3_calMil elephantfish frag 2 domains 6-243,334-531
PPVTRESSPTSDKLPEDPTFLQALVDTVFKVSVLPDNTGYFRFDEFPEISVMSKLVQYIIEKVWLPVKDTDRLIVDLRHNVGGHSSVVPLLLSYFYDPEP
PVGLFTVYNRLTNTTSHTTLPGVGQHVYGSRKDIYVLTSHRTATAAEELAYLLQSLNRATIVGEITSGSLLHSRSFQIPSTHLVITIPFINFMDNHGECW
LGGGVVPDSIVLAEDTLERTKEIIGFHAQVAELVESTGKLLAVHYAIPEVAAEVSAVLSAKLTQGLYRSVVDWESLASRLTVDLQETSVWSVSGAEPHVI
VQANEAMTVALGIINLRAKIPSIFQAAGKLVADNYAFAQTGAGVAETIADLIEGTGYGMINTEGKLAEVLSDTLQQLSGDKHLKAVHIPGDSKHQTPGIAMIQ 0
0 QMPPPEILEDLVKFSYQTKVLENNVGYLRFDMFGDNEMITQVSELMAKHVWNVIASTSSLIVDLR 2
1 YNIGGPTSSIPILCSYFFDDDKTVLLDTVYSRPTDTISEMKAIPQVAGNGSTESSVHSYI 1
2  * 0

>RBP3_petMar lamprey fragment exon3/4 missing, fixed genomic frameshift; four domains: 34-312,327-615,625-914,916-1217
0 MAGSREQRTAFSTRLLLLLLLPLATCPSQAPYKFDTAVVLHLAKVLLDNYCIPENLVGMDEAIQRAVDNGELLGVSDPESAASALTEGIQAALNDPRIAVSYVPDVDDDGDREEGDAEGW
DAGEQHRPTTFEELLATIPQKTSFAVLDGNVGYLRADEIISEATIKKLGPVIVQRIWNRLVDTDTFVLDLRYNSHGDITGLPYLVSCFCEPRPVVHLDTVYYRPTNESKEIWSLPDLQGA
RFAKHKDVFVLVSANTEGVAENVAYVLKHLHRATVIGEQTAGGSLEVERFRLGDSRFFVTVPTARSQSPLTGRSWELTGVFPCVSAPSERALDKALEILNARGVARKAVEAAGELLLSSY
TFVERASAIADHLSWSEYGSVVSVEDLTSKLTQDLQSVAEDPRLVVSNREPEWPPLAQPIPPGPPAPLPDDEQMLEAIVDSAFKVEVLEGNIGYLRFDEFGDASAVMKLRKQLVSKVWER
IHPTDDVIIDLRYNLGGSSTAIPIVLSYFQDASPPVHFYTVYDRLRNVTAEFHTVSNLTSQLYGSKKGVYLLTSQHTATAAEEFTYLMQSLNRATIVGEITSGRLAHSLAFRLSDTGLYMT
VPIVNFIDNNDEYWLGGGVVPDAIVLAENALDAAKEIIEFHAKMASLLELAGALVEGYYAMLSDGENATAEILLKYREGWYRSVVDYEALASQLTSDLHEIWGDHRLHAFYSDLQIERMD
EDKTPSVPSPEELSVLIDTVFKVDILANNVGYLRFDMMTDAEVLKHVGPQLVEKVWNKISSTRSLVIDVRYNMGGYSTSIPILCSYFFDASPPRHLYTVFDRPSRSSTQVFTVPRVLGQR
YGASKDVYILTSHMTGSAGEILTRVMSDLKRATVIGEPTAGGSLSTGTYRIGDSRLYVFIPNQAGVSPSGGRTWSVAGVEPHVQTKASEALQSALRMVALRADAPSILRTVGKLVADGYS
RAEAALGVPSKLAALLEAGEYGALRSEEELAFKLTVHLQLITGDRHLKAVCVPEHATDRMPGIVPMQ 0
0 MPPTESFEDLIKFSFITDVLEGNIGYLRFDLFSDLEALEHVAHLLVEHVWKKICDTEILIIDLR 2

>RBP3_braFlo Branchiostoma floridae Region: 9 exons 1 domain: 83-381 ClpP/crotonase e-38 419-630; misfused to PAPS sulfotransferase
0 MTRPSKVDIVFPIKPFTIPTAHEQVKGEGPVDINKNALCKSADEGHTHP 1
2 VSIAMAPTAYIVFVALVPTVLSVDWLDVVMGIGDVMADHYLDQDLRALNDQSLLQRWNRTLVHRFQ 0
0 SWSQDDMSDSLRMEEGLTSELRNITGDETIK 0
0 VWDFGVYENTTQEPVPREFYNFSTFVDNFK 2
1 KNREKHINVTMLEGNVGYVSIRSMSHIVDIILPDPEMTEFFLSKMAALNESK 0
0 AIILDLRYNLGGDREGVVHWASFFFNATPSVPLSDVYYRDGVNQYWTLLE 0
0 VPGGIRFPDMPLYLLTSNRTSREAEEFAYAMQVVNRTTIIGETT 1
2 AGEEFTGMWFPIDQTDVHLLTRTNVVRNPITQDSWSGK 1
2 GVTPDIIVPSEKALTVALRKIQGSEDTKMAASSGNIEPPRWTVYLVFICTSIAILTYPTFM* 0

See also: Curated Sequences | RPE65 | Transducins | Usher: USH2A | Usher: CDH23 | LOXHD1 | Update Blog

Retrieved from "https://genomewiki.ucsc.edu/index.php?title=Opsin_evolution:_RBP3_(IRBP)&oldid=9783"