PRDM9: meiosis and recombination

Introduction

PRDM9 is a gene on human chromosome 5 with a very peculiar history. Its primary function -- after many false starts -- has only recently become clear: scanning the genome with its terminal zinc finger array to locate and mark recombination hotspots with its histone methylase where its transcription factor domain can direct additional proteins to initiate the double stranded breaks needed for meiosis. Recombination between homologous chromosomes is essential to proper alignment and separation into daughter cells (as well as for juxaposing favorable alleles for adaptive evolution).

Such a mission-critical protein is typically highly conserved. However this is not the case here at all. Indeed, it proves exceedingly difficult to find a comprehensive set of PRDM9 orthologs in sequenced mammalian genomes, with immense confusion in the literature over paralogs, lost copies, pseudogenes, and other composite domain proteins overlapping in domain content but having no immediate homology.

Syntenic relationships help resolve events during mammalian evolution. Here TUBB3+ AFG3L1+ GAS8+ has stably existed since the stem amniote, with the arrangement TUBB3+ AFG3L1+ GAS8+ PRDM7- qTer found in nearly all placental mammals. PRDM9 however is found in many syntentic contexts, depending on clade.

From the perspective of comparative genomics, PRDM7 is the fundamental gene, not the disparate collection of genes lumped under PRDM9. At different times in different placental clades, PRDM7 spun off segmental duplications of itself to other sites in other chromosomes, probably because of its susceptible location at the extreme q arm of an autosomal chromosome. Because PRDM7 has stayed at its site, it is possible to say unambiguously which of two otherwise identical copies is the parent gene.

These paralogous copies -- despite all being called PRDM9 -- are not orthologous outside their clade of origi. Orthology requires by definition vertical descent from a common gene in the last common ancestor of two species. Here certain PRDM9 are descended from a common gene (namely the recent duplicate of PRDM7 in the stem preceding speciation) but others arose different stages in evolution. While an unresolved terminological muddle, these copies are sometimes called in-paralogs within a species and co-orthologous across them. However such terms are topologically unstable (tree size dependent) unlike ortholog.

In euarchontoglires, a segmental duplication of PRDM7 occurred in a stem catarrhine primate and descended through speciation events to contemporary old world monkeys and great apes. This second copy (PRDM9) relocated to and stayed within a cadherin gene complex on a different chromosome. PRDM7 persisted at its original ancestral location but became an overt pseudogene in some lineages (rhesus, gibbon, gorilla, chimp and human) but not others (orangutan). Earlier diverging primates such as lemurs, tarsier and new world monkeys have a single PRMR7 gene adjacent to GAS8.

Rodents and lagomorphs also have no counterpart to PRDM9, though the situation is confused by chromosomal rearrangements (no homolog or even debris adjacent to GAS8 or CDH). The mouse gene is then orthologous to primate PRDM7, not PRDM9. The rat gene occurs in the same syntenic context as mouse; other rodent genomes are too incomplete for synteny to be assessed. Rabbit has two apparent PRDM7, called here PRDM7a and PRDM7b; neither copy is syntenic to mouse/rat or any other mammal. The pika genome is too incomplete to determine whether this duplication predated their divergence.

Although an obvious pseudogene, human PRDM7 is often treated as a functional gene with 'isoforms'. However exon 9 of the reference sequence hg18 contains an internal direct tandem repeat of 88 nucleotides that throws off the reading frame and subsequent splice to exon 10, which itself has a frameshift (GGGG to GGG) in the second of its three zinc fingers. The protein is incorrectly described at NCBI, SwissProt and UCSC -- zinc fingers translated into the wrong reading frame cannot possibly form a meaningful fold. Given the comparative genomics context of duplication followed by subsequent pseudogenization (of either parent or duplicate), this feature is unquestionably a pseudogene whether it is still transcribed or not.

However the confusion doesn't stop there. After separate segmental duplication in afrotheres and pecoran ruminants, still other retention and loss scenarios have played out. Both copies can seemingly functions for long periods, but the parental gene PRDM7 can also be lost completely. In others, pseudogene remnants in various degrees of decay can still be detected, implying that gene loss is fairly recent.

Rapid evolution of this gene subfamily occurs at the amino acid level as well, especially in zinc finger number and substitutions at the four residues recognizing their specific dna trinucleotide. All this may be directly related to the role in meiosis: the process tends to destroy its recombination hotspots by biased gene conversion. Since recombination is essential, new hotspots must emerge. The race is then on for PRDM7 and its spun-off PRDM9s to rapidly evolve and define new histone markup sites.

This rapid evolution may cause breeding incompatibility between populations in the F1 generation (meiosis arrest for lack of cross-overs, notably between chrX and chrY). However it takes very different forms in different lineages. In effect each major clade of placentals is evolving a qualitatively different mating system, with its most extreme form in ruminants with 6 PRDM9 genes. This follows upon the very different structures of sex chromosomes between monotremes, marsupials and placentals.

Comparative genomics: sequence availability

Classification of available placental mammal sequences: 56 genes from 34 species. These genes all have ten identically intronated exons but 72 exons of the 560 expected are missing because many genomes are incomplete. The number of zinc fingers is shown in the second column, phylogenetic clade in the third, and an adjacent gene (synteny) in the fifth.

The number of zinc fingers is quite variable in human and likely so in all species; the table provides that of the individuals selected for genome projects. These zinc finger arrays have been corrected in low coverage genomes for minor frameshifts and premature stop codons arising from nucleotide run length errors (eg, ggggg misread as gggg).

Pseudgenes are sometimes obvious (large deletions, multiple reading frame errors, stop codon in early exons, amino acid substitutions disrespecting the conservation profile) but otherwise can be difficult to distinguish from sequencing error or a bad allele of a usually intact gene in the population. A pseudogene can continue being transcribed for tens of millions of years after losing all functionality at the protein level. However no confusion arises here because PRDM7 nor PRDM9 are represented only by a half dozen transcripts among the tens of million mammalian transcripts at GenBank.

The PRDM7 genes are all orthologous in the classical sense but the PRDM9 genes are not unless syntentic and in the same phylogenetic cluster.

• PRDM7: genes with ancestral location GAS8 synteny
• PRDM9: lineage-specific segmental duplications of PRDM7
• Pseudogenes: multiple disabling frameshifts and stop codons

  >PRDM9_homSap   13  prim  gene  CDH12  Homo         sapiens      (human)         NM_020227
  >PRDM9_panTro   19  prim  gene  CDH12  Pan          troglodytes  (chimp)         GU166820
  >PRDM9_gorGor    -  prim  gene  cdh12  Gorilla      gorilla      (gorilla)       CABD02290264
  >PRDM9_ponAbe   10  prim  gene  CDH12  Pongo        abelii       (orangutan)     XR_093432
  >PRDM9_nomLeu   10  prim  gene  cdh12  Nomascus     leucogenys   (gibbon)        ADFV01015315
  >PRDM9_macMul    9  prim  gene  CDH12  Macaca       mulatta      (rhesus)        XM_001083675
  >PRDM9_papHam   11  prim  gene  cdh12  Papio        hamadryas    (baboon)        genome
  >PRDM7_homSap    3  prim  gene  GAS8+  Homo         sapiens      (human)         genome
  >PRDM7_panTro    2  prim  pseu  GAS8+  Pan          troglodytes  (chimp)         genome
  >PRDM7_gorGor    3  prim  pseu  GAS8+  Gorilla      gorilla      (gorilla)       genome
  >PRDM7_ponAbe    4  prim  gene  GAS8+  Pongo        abelii       (orangutan)     genome
  >PRDM7_nomLeu    5  prim  pseu  gas8+  Nomascus     leucogenys   (gibbon)        ADFV01125891
  >PRDM7_macMul    2  prim  pseu  GAS8+  Macaca       mulatta      (rhesus)        genome
  >PRDM7_papHam    2  prim  pseu  gas8+  Papio        hamadryas    (baboon)        genome
  >PRDM7_calJac   12  prim  gene  GAS8+  Callithrix   jacchus      (marmoset)      XR_090591
  >PRDM7_micMur    8  prim  gene  gas8+  Microcebus   murinus      (lemur)         ABDC01433247
  >PRDM7_otoGar    7  prim  gene  GAS8+  Otolemur     garnettii    (galago)        genome
  >PRDM7_tarSyr    -  prim  pseu  gas8+  Tarsius      syrichta     (tarsier)       ABRT011082008
  >PRDM9_oryCun    8  glir  gene  other  Oryctolagus  cuniculus    (rabbit)        genome
  >PRDM7_oryCun    4  glir  gene  other  Oryctolagus  cuniculus    (rabbit)        genome
  >PRDM7_ochPri    -  glir  gene  noDet  Ochotona     princeps     (pika)          AAYZ01312269
  >PRDM7_ratNor   10  glir  gene  PDCD2  Rattus       norvegicus   (rat)           NM_001108903
  >PRDM7_musMus   12  glir  gene  PDCD2  Mus          musculus     (mouse)         NM_144809
  >PRDM7_musMol   11  glir  gene  noDet  Mus          molossinus   (wild_mouse)    GU216230
  >PRDM7_dipOrd    -  glir  gene  noDet  Dipodomys    ordii        (kangaroo_rat)  genome
  >PRDM7_speTri    -  glir  gene  noDet  Spermophil   tridecemlin  (squirrel)      AAQQ01308561
  >PRDM9a_bosTau   7  laur  gene  noDet  Bos          taurus       (cattle)        NW_003053109
  >PRDM9b_bosTau   5  laur  gene  noDet  Bos          taurus       (cattle)        DAAA02065087
  >PRDM9c_bosTau   -  laur  gene  noDet  Bos          taurus       (cattle)        XM_002699750
  >PRDM9d_bosTau   9  laur  gene  noDet  Bos          taurus       (cattle)        genome
  >PRDM9e_bosTau   9  laur  gene  noDet  Bos          taurus       (cattle)        genome
  >PRDM9e_oviAri   -  laur  pseu  noDet  Ovis         aries        (sheep)         genome
  >PRDM9d_oviAri   -  laur  gene  noDet  Ovis         aries        (sheep)         genome
  >PRDM9c_oviAri   4  laur  pseu  noDet  Ovis         aries        (sheep)         genome
  >PRDM9b_oviAri   2  laur  pseu  noDet  Ovis         aries        (sheep)         genome
  >PRDM9a_oviAri   9  laur  gene  noDet  Ovis         aries        (sheep)         genome
  >PRDM9d_munMun   4  laur  gene  noDet  Muntiacus    muntjak      (muntjac)       AC216498
  >PRDM9c_munMun  15  laur  gene  noDet  Muntiacus    muntjak      (muntjac)       AC154919
  >PRDM9b_munMun  13  laur  gene  noDet  Muntiacus    muntjak      (muntjac)       AC218859
  >PRDM9a_munMun   7  laur  gene  noDet  Muntiacus    muntjak      (muntjac)       AC225653
  >PRDM7_bosTau    -  laur  pseu  GAS8+  Bos          taurus       (cattle)        genome
  >PRDM7_turTru    9  laur  gene  gas8+  Tursiops     truncatus    (dolphin)       ABRN01441536
  >PRDM7_susScr    9  laur  gene  GAS8+  Sus          scrofa       (pig)           FP476134
  >PRDM7_canFam    5  laur  pseu  GAS8+  Canis        familiaris   (dog)           genome
  >PRDM7_felCat   11  laur  gene  GAS8+  Felis        catus        (cat)           genome
  >PRDM7_ailMel    6  laur  gene  GAS8+  Ailuropoda   melanoleuca  (panda)         GL193502
  >PRDM9_pteVam   15  laur  pseu  noDet  Pteropus     vampyrus     (bat)           ABRP01232219
  >PRDM7_pteVam    7  laur  gene  GAS8+  Pteropus     vampyrus     (bat)           ABRP01250178
  >PRDM7_myoLuc    6  laur  gene  gas8+  Myotis       lucifugus    (bat)           AAPE02062260
  >PRDM7_equCab    4  laur  gene  GAS8+  Equus        caballus     (horse)         genome
  >PRDM7_sorAra    8  laur  gene  noDet  Sorex        araneus      (shrew)         AALT01000095
  >PRDM9a_loxAfr  12  afro  gene  noDet  Loxodonta    africana     (elephant)      genome
  >PRDM9b_loxAfr   3  afro  pseu  noDet  Loxodonta    africana     (elephant)      genome
  >PRDM7_loxAfr    5  afro  pseu  GAS8+  Loxodonta    africana     (elephant)      genome
  >PRDM7_echTel    5  afro  pseu  noDet  Echinops     telfairi     (tenrec)        genome
  >PRDM7_proCap   13  afro  gene  noDet  Procavia     capensis     (hyrax)         ABRQ01392668

Comparative genomics of PRDM9 and PRDM7

PRDM9 is one of many human proteins sharing a set of common domains, as well as various multiplicities of the zinc finger domain C2H2. The diagram at left shows an effort at organizing these into phylogenetic tree according to structural considerations of the SET domain these proteins all share.

The traditional SET domain is too small for an enzyme with distinctive substrates so flanking sequence must be added despite its lack of apparent conservation. Using S-adenosyl methionine, PRDM9 places the third methyl group only on the fourth position lysine in mature histone H3 (which is actually position 5 prior to iMet removal: MARTKQTARK...), one of many such epigenetic methylases in the human genome. The histone recognized by such methylases correlates poorly with evolutionary grouping by SET domain (figure).

The upper left corner shows the variability in domain structure. While PRDM9 and PRDM7 share the same domains (an upstream KRAB domain is not shown), of PR-class homologs, PRDM11 shares only the SET domain despite nesting deep within the PRDM9 subtree. PRDM4 has both the SET and C2H2 domains, possibly sharing the early C2H2 domain in an exon beginning with a phase 2 splice acceptor (as shown in reference sequence section). Overall however, PRDM9 and PRDM7 have no full length homologs with matching exon structure. Even the SET domain is intronated differently within PR-class proteins (with the sole exception of PRDM11), suggesting either ancient divergence or unusual evolution. These incongruities may have arisen from domain shuffling, gain and loss.

The human PRDM9 sequence below is annotated in color for domains relative to exon breaks. The protein can be best understood in terms of concatenated domains, not all of which may be present in antecedent and descendant homologs. The first two domains KRAB and SSXRD interact with transcription factors.

Each C2H2 domain -- so named for two cysteines and two histidines liganding to a structural zinc ion -- recognizes a specific trinucleotide (more or less) and so concatenated in a large array recognize specific binding sites along the genome, though tolerance of nucleotide variability and synergistic effects between adjacent units make it difficult to read out these sites precisely, despite immense efforts.

The concatenated C2H2 domains, conserved at the amino acid level so necessarily similar at the dna level, are prone to replication slippage. This process can give rise to point mutations as well as leading to a peaked distribution of repeat number rather than to a single number. Many other unrelated genes with internal repeats (such as the octapeptide region of the prion gene PRNP) are also affected by replication slippage. Such proteins regions are conveniently identified genomewide by mRNA dot plots.

The C2H2 domains generally reside in a long distinctive terminal exon of splicing phase 2 that has been shuffled over mammalian evolutionary time into various contexts. Concepts such as paralogy and orthology need piecewise definitions in these composite proteins. Synteny (gene adjacency) plays a major role in reliably deconstructing events in specific lineages.

Here the unrelated single-copy conserved gene GAS8 plays an important role. PRDM7 occurs immediately distal to it on the negative strand, making the two genes are convergently transcribed). PRDM7 is otherwise the last gene on the q arm of its chromosome in many species which may predispose it to copy number dispersal events. PRDM9 is not consistently located within placental mammals, suggesting independent relocation events.

Both PRDM9 and PRDM7 contain a seldom-mentioned C2H2 domain early in the exon annotated by SwissProt and readily found by the online domain tools regardless of species. This domain conserves the four critical residues needed for zinc binding (and so the associated fold) but lacks the terminal cap TGEKP which otherwise serves to lock down a C2H2 zinc finger after it has scanned along genomic dna to an appropriate trinucleotide. The function of this early domain and the following 112 residues are unknown -- no homologous 3D structure has ever been determined.

The first C2H2 of the main repeat region is proximaly degenerate, beginning in VKY in all species (instead of YCE). The tyrosine cannot plausibly replace the usual cysteine for zinc binding though the other three needed residues are present. This domain ends in a typical cap region TGEKP. Humans are the exception here where the conserved helix-ending proline has been replaced with leucine in the reference human genome with unknown functional consequences.

>PRDM9_homSap Homo sapiens (human) Q9NQV7 10 exons chr5:23,509,579 span 18,301 bp KRAB SSXRD SET C2H2 cap
0 MSPEKSQEESPEEDTERTERKPM 0
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPWMALRVEQRKHQK 0
0 GMPKASFSNESSLKELSRTANLLNASGSEQAQKPVSPSGEASTSGQHSRLKL 1
2 ELRKKETERKMYSLRERKGHAYKEVSEPQDDDYL 1
2 YCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQPENPCPGDQNQEQQYPDPHSRNDKTKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSCRVGKRIMEEESRTGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSVKSDVITHQRTHTGEKL
YVCRECGRGFSWKSHLLIHQRIHTGEKP
YVCRECGRGFSWQSVLLTHQRTHTGEKP
YVCRECGRGFSRQSVLLTHQRRHTGEKP
YVCRECGRGFSRQSVLLTHQRRHTGEKP
YVCRECGRGFSWQSVLLTHQRTHTGEKP
YVCRECGRGFSWQSVLLTHQRTHTGEKP
YVCRECGRGFSNKSHLLRHQRTHTGEKP
YVCRECGRGFRDKSHLLRHQRTHTGEKP
YVCRECGRGFRDKSNLLSHQRTHTGEKP
YVCRECGRGFSNKSHLLRHQRTHTGEKP
YVCRECGRGFRNKSHLLRHQRTHTGEKP
YVCRECGRGFSDRSSLCYHQRTHTGEKP YVCREDE* 0
         -1  23  6           traditional numbering of dna recognizing amino acids
HPCPSCCLAFSSQKFLSQHVERNH     alignment of early C2H2 domain
  *  *            *  *       zinc liganding positions

Only in PRDM11 (and PRDM1 to a lesser extent) is the SET domain intronated like PRDM9 and PRDM7:

>PRDM9_homSap 
2 YCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1

>PRDM11_homSap intronation of SET domain
2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPQGMEVVKDTSGESDVRCVNEVIPKGHIFGPYEGQISTQDKSAGFFSWL 0
0 IVDKNNRYKSIDGSDETKANWMR 2
1 YVVISREEREQNLLAFQHSERIYFRACRDIRPGEWLRVWYSEDYMKRLHSMSQETIHRNLAR 1

>PRDM1_homSap intronation of SET domain
0 AAPKCNSSTVRFQGLAEGTKGTMKMDMEDADMTLWTEAEFEEKCTYIVNDHPWDSGADGGTSVQAEASLPRNLLFKYATNSEE 0
0 VIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWR 0
0 IYSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGELTMMNL 1

>PRDM4_homSap intronation of SET domain
2 WCTLCDRAYPSDCPEHGPVTFVPDTPIESRARLSLPKQLVLRQSIVGAEV 1
2 GVWTGETIPVRTCFGPLIGQQSHSMEVAEWTDKAVNHIWK 0
0 IYHNGVLEFCIITTDENECNWMMFVRKAR 2
1 NREEQNLVAYPHDGKIFFCTSQDIPPENELLFYYSRDYAQQI 1

Divergence of SET domains:

Different segmental duplications relate PRDM9 and PRDM7

In humans, PRDM9 and PRDM7 are related by a 26 kbp segmental duplication that begins about 8 kbp upstream of the start codon and continues through most of the 3' UTR. Since the retroposon patterns are nearly identical, the duplication must be fairly recent. The overall percent identity of non-coding dna is about 93%, again inconsistent with either early (within stem placental or late divergence (post-chimpanzee). The duplication contains a potentially diagnostic 1845 bp retroposon-free region upstream of the first coding exon.

Note PRDM7 is situated at the extreme tip of chromosome 16q, perhaps predisposing it to chromosomal copy number rearrangements. The syntenic context is TUBB3+ DEFB+ AFG3L1+ DBNDD1- GAS8+ PRDM7- qTel, meaning it is transcribed convergently with GAS8, a non-homologous highly conserved single copy gene often detectable even in low coverage genomes in the small contig containing PRDM7. This association has been extremely stable over boreoeutheran placental mammal evolutionary time and so serves to reliably define PRDM7 orthologs and their spin-off copies. Elephants also have a gene pair similar to human PRDM9 and PRDM7. The former is at a syntenically novel site but the latter is an old pseudogene but still detectably adjacent to GAS8 in opposite orientation. It thus follows that 'PRDM9' in elephant is an independent earlier spin-off of its conventional PRDM7 gene. This is consistent with telomeric susceptibility to repeated rearrangements.

Recall here the actual definition of gene orthology: two genes in two species are orthologous if they are vertically descended from the same gene in their last common ancestor. Here the LCA of human and elephant is ur-placental mammal which had PRDM7 but no PRDM9. The two PRDM9 genes are thus not descended from a common ancestral PRDM9 gene but from parallel gene duplications of a common PRDM7 gene at different times in different clades during the course of mammalian speciation. Such genes are called in-paralogs within a given species and co-orthologs across them.

The syntenic context of PRDM9 is quite variable, supporting the scenario of multiple origins. This context can be used to count the number of distinct segmental duplications of PRDM7. For example, in humans, PRDM9 basically lies in a retroposon-rich gene desert but is eventually flanked by two pairs of cadherin genes at the much larger scale of 7 mbp. In rhesus, these same genes are seen (with some minor rearrangements), establishing that this PRDM9 segmental duplication preceded the divergence of old world monkeys.

Marmoset has a seemingly functional PRDM7 in the usual position facing GAS8, still at the extreme end of chromosome 20. The cadherin cluster is intact on chr2:178,954,165-180,696,523. However Blastx of the intervening dna -- which is similar in size to rhesus and human so not suggesting large deletions -- shows not even a suggestion of an old PRDM9 pseudogene. The assembly is gapless here. and Blastx is sensitive enough to detect very old pseudogenes provided they decayed by small indels and nucleotide substitutions. Thus it appears that PRDM7 never duplicated in marmoset -- placing that even in the stem to old world monkeys (or prior to tarsier divergence -- that assembly has poor coverage). Note that the marmoset PRDM7 has a respectable terminal zinc finger array of twelve units, enough to specify 36 bp.

Gene  Strand Protein      Start     Species
CDH18    -   cadherin 18  19981287  homSap  ponAbe  macMul
CDH12    -   cadherin 12  22853731  homSap  ponAbe  macMul  calJac
PRDM9    +   human PRDM9  23528704  homSap  ponAbe  macMul  calJac
CDH10    -   cadherin 10  24644911  homSap  ponAbe  macMul  calJac
CDH9     -   cadherin 9   27038689  homSap  ponAbe  macMul

Lemurs present a new complication. The Otolemur assembly has two distinct and seemingly functional PRDM7 copies (each with seven zinc fingers) containing GAS8 end-sequence in expected opposite orientation. One of the GAS8 copies appears to be a pseudogene. This represents a new type of lineage-specific segmental duplication. There is no sign of PRDM9. The other lemur with an assembly, Microcebus murinus, has but a single copy, again with seven zinc fingers. The only relevant contigs (ABDC01433247 and ABDC01371462) contain no coding syntenic information so this gene cannot be assigned to PRDM7 with certainty.

The tree shrew assembly, like tarsier, has low coverage and only blast matches to zinc finger arrays that cannot be assigned to the PRDM family. This cannot be totally attributed to low coverage because many ordinary genes are satisfactorily represented in these species. Other issues such as telomeric position, gene copy number (mobility), pseudogenization, deletional loss, chimerization, and individual heterozygosity must be affecting recovery of PRDM9 gene models in these species.

Moving on to laurasiatheres, Bos taurus presents a much more complicated situation. First, the GAS8 locus on chr18 contains the first two exons of a PRDM7 pseudogene in expected orientation but distal regions of the gene are completely deleted. The cadherin locus on chr20 is also intact but the 2.6 mbp region between CDH12 and CDH10 contains no indication of PRDM9, consistent with that segmental duplication being primate-specific and PRDM7 being the older parental location. This holds in the Baylor 4.0 assembly carried at UCSC, the Baylor 4.2 assembly, and the alternative assembly of the same data, UMD3.1. The latter two can be queried by the genomic blast server at NCBI.

A third locus on chr 1 hosts an unreviewed GenBank pipline entry called PRDM9, derived as NW_003053109 from the alternative bovine assembly UMD3.1 Staff corrected an unspecified frameshift to fix the reading frame -- a dangerous practise in a gene family so prone to pseudogenization. The gene, called PRDM9a here, resides on the extreme end of chromosome 1 and differs from the Baylor 4.0 assembly at two amino acids outside the zinc finger region. The syntenic context here is novel: EFHB- RAB5A+ PCAF+ ZNF596- PRDM9a- which corresponds overall to human chr 3. The juxtapositioning of two zinc finger proteins on the same strand causes PRDM9 alignments to extend spuriously into the 12 zinc fingers of ZNF596, jumping over its 5 earlier coding exons.

ZNF596 contains a KRAB domain but no SET methylase. Humans encode a best-blast protein of the same assigned name on chr 8 (77% identity). Note the early exons of ZNF596 can be added to end of PRDM9a to form an artificial probe for this association in other species, though the two genes have a 43,400 bp spacer in cow, which is large relative to contig size in low coverage assemblies. The sole fragmentary transcript from yak testis (EF432551) is nearly identical to this PRDM9a, suggesting that the gene -- and perhaps its syntenic location -- became established prior to yak-cow divergence and is still functional. However its array of seven zinc fingers could recognize at most a region of 21 bp.

ZNF596 did not arise from a PRDM9-like gene through loss of the SET domain, though it is one of the better matches within the large zinc finger family. Excluding the zinc finger domain, ZNF343, ZNF133 and ZNF169 provide much higher blastp scores, as they also do just comparing the zinc finger arrays. The juxtaposition of ZNF596 and PRDM9a is likely coincidental rather than a consequence of inhomogeneous recombination between zinc fingers bringing PRDM9 to this site.

The fourth PRDM9 locus of interest, called here PRDM9b, is still not mapped to any bovine chromosome. It resides in contig DAAA02065087 in the UMD3.1 assembly and is temporarily assigned to chr Un.004.649 at Baylor assembly. Here the reading frame in exon two can be restored if a run of 5 A's is corrected to 6 A's. That is done here in the reference sequences because this is typically just sequencing error. The protein has a full set of domains KRAB SSXRD SET C2H2 with a moderate zinc finger array of five. Synteny cannot be determined in chr Un features which can simply pool unrelated unplaceable contigs into a manageable unit. Flanking dna in DAAA02065087map to several places in the cow genome, suggesting this feature has copy number attributes, perhaps of telomeric repeat type. PRDM9b is not a recent feature because it differs at a considerable number of amino acids from other PRDM9 in the cow genome. These substitutions avoid highly conserved residues, not consistent with early pseudogenization. PRDM9b is capable of histone marking but it is not clear whether that has functional significance to meiosis.

Yet another locus in the Baylor 4.0 assembly, called PRDM9c here, could not initially be placed on a cow chromosome. While such features are often assembly artefacts, this one is supported by a transcript from 4-cell embryos (GO353654) consistent with a role in or after meiosis. In UMD3.1, this gene has been placed on chr X. Despite a very large contig, no zinc fingers occur in any reading frame, suggesting that the gene was transferred here without the last exon (or it subsequently got deleted). In any event, the penultimate exon does not have a phase 1 splice donor in expected position and so terminates at the next stop codon downstream. The protein retains the KRAB, SSXRD and SET domains but does not possess the ability to scan or bind dna. It has accrued various amino acid substitutions relative to other bovine that rule out recent establishment.

Finally, two additional genes, denoted PRDM9d and PRDM9e here, are located as a parallel tandem pair in a higher quality region of bovine chr X. These are 96% identical as proteins, consistent with one being derived fairly recently from the other. Synteny here will not be informative until other ruminant genomes become available.

Overall the situation in cow is very different from primates and rodents. Results there about the function of single-copy autosomal PRDM9 gnes in meiosis markup can scarcely be carried over to a species with five seemingly intact genes, three of which are on chr X (which intriguingly has the very limited pseudoautosomal region on chr Y where it can cross over).

The cow situation cannot be limited to the Hereford breed used for the genome project because the PRDM9 are too diverged from one another outside the zinc finger region. Indeed there is some suggestion from non-NCBI sheep genome that it too has many of these copies. However other cetartiodactyl genomes (dolphin, pig and alpaca) and other laurasiatheres (panda, dog, cat, shrew, bats) do not show these copies, suggesting that this complexity could be limited to pecoran ruminants. All-vs-all blastp percent identities are consistent with this, though rates of evolution in this gene family are hardly typical.This cannot be resolved with cow genome alone -- there is no good candidate still present for parent gene to all these copies. These results are summarized in the table below:

Gene   #ZNF  Status  Chr  Synteny  cDNA  Accession    9a_bosTau 9b_bosTau 9e_bosTau 9a_oviAri 9a_turTru 7_ailMel

PRDM7    -   pseudo  18    GAS8     no   none           --        --        --        --        --       --
PRDM9a   7     ok     1    ZNF596   yes  NW_003053109  100%      85%        81%       82%       76%      72%
PRDM9b   5     ok     ?    not det  no   DAAA02065087   81%     100%        78%       79%       72%      68%
PRDM9c   0     ok     X    not det  yes  XM_002699750   80%      80%        82%       83%       74%      73%
PRDM9d   9     ok     X    ---      no   none           80%      78%        96%       93%       73%      67%
PRDM9e   9     ok     X    ---      no   none           81%      78%       100%       93%       73%      68%

The role of CpG mutations

Human PRDM9 has 39 CpG sites in its coding exons, potentially mutational hotspots. After attempted dna repair, these usually resolve to CpA or TpG. If not at a synonymous site, these changes alter the encoded amino acid. Some 28 of the CpG sites are at arginine CGn codons (of which the protein has 90 overall). These always result in a substitution: for G -> A, histidine for CGT and CGC and glutamine for CGG and CGA; for C -> T, cysteine for CGT and CGC and tryptophan and stop codon for CGG and CGA. These changes are in fact seen in many of the reference sequences. The display below shows wildtype human PRDM9 in the top lines and the effects of G -> A and C -> T in the next. The zinc finger array is highlighted. Note that position -1 is sensitive to the CpG hotspot effect, at least in human PRDM9 as it stands. However the rapid evolution reported for the four dna-recognizing residues cannot be primarily attributed to the CpG effect. The terminal partial finger YVCREDE* is commonly altered to Y*CREDE* but this is likely insufficient for loss of function.

PRDM9_homSapWT   MSPEKSQEESPEEDTERTERKPMVKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITIGLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQVKPPWMALRVEQRKHQKGMPKASFSNESSLKELSRTANLLNASGSEQAQKPVSPSGEASTSGQHSRLKLELRKKETERKM
PRDM9_homSapCA   ...................Q.............................H...................Q......Q...................................H...................................................................
PRDM9_homSapTG   ...................W.............................C...................*......*...................................C........V..........................................................

PRDM9_homSapWT   YSLRERKGHAYKEVSEPQDDDYLYCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWLITKGRNCYEYVDGKDKSWANWMRYVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDE
PRDM9_homSapCA   ...Q...........K........................................H.........................................Q....K......................................Q.....................Q...............
PRDM9_homSapTG   ...*............L.......................................C..............................L..........*...........................................W.....................*...............
                                                    
PRDM9_homSapWT   YGQELGIKWGSKWKKELMAGREPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQPENPCPGDQNQEQQYPDPHSRNDKTKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSCRVGKRIMEEESRTGQKVNPGNTGKLFVGVGISRIAK
PRDM9_homSapCA   .S..............................................H.....................................H............................................................................
PRDM9_homSapTG   ................................................C.....................................C............................................................................

........-1..23..6..........   ........-1..23..6..........   ........-1..23..6..........   ........-1..23..6..........
VKYGECGQGSVKSDVITHQRTHTGEKL   YVCRECGRGSRQSVLLTHQRRHTGEKP   YVCRECGRGRDKSHLLRHQRTHTGEKP   
...........................   .......Q..Q................   .......Q.HN................   
...........................   .......W..W................   .......W.C.................   
YVCRECGRGSWKSHLLIHQRIHTGEKP   YVCRECGRGSWQSVLLTHQRTHTGEKP   YVCRECGRGRDKSNLLSHQRTHTGEKP   
.I.....Q...................   .......Q...................   .......Q...................   
.......W...................   .......W...................   .......W...................   
YVCRECGRGSWQSVLLTHQRTHTGEKP   YVCRECGRGSWQSVLLTHQRTHTGEKP   YVCRECGRGSNKSHLLRHQRTHTGEKP   
.......Q...................   .......Q...................   .......Q...................   
.......W...................   .......W...................   .......W...................   
YVCRECGRGSRQSVLLTHQRRHTGEKP   YVCRECGRGSNKSHLLRHQRTHTGEKP   YVCRECGRGRNKSHLLRHQRTHTGEKP   YVCRECGRGSDRSSLCYHQRTHTGEKP   YVCREDE
.......Q..Q................   .......Q...................   .......Q.H.................   .I.....Q..N................   .I.....
.......W..W................   .......W...................   .......W.C.................   .......W...................   .......

Excluding pseudogenes, a weblogo from an alignment of the remaining placental PRDM7 and PRDM9 genes illustrates the location of potential CpG mutations relative to conserved residues. These will be relatively high frequency disease alleles. In the initial KRAB domain, the potentially affected arginines are not especially well-conserved. However, at the first site, neither histidine nor cysteine is part of the reduced alphabet ans so these changes are unlikely to be tolerated. At the second and third sites, glutamine does occur secondarily in some species (cow, sheep and muntjac) and murid rodents, respectively. These changes are thus borderline for adverse effects on functionality.

In terms of potentially protective upstream CpG islands, PRDM9 has none. Three occur somewhat near the start of PRDM7 but do not extend into the coding region and may not be associated at all with this gene. Thus cytidines would be methylated in both coding regions, rendering them susceptible to hotspot mutations. The composite snapshot below from the UCSC human genome browser shows CpG islands relative to the two genes.

Structural considerations in C2H2 zinc fingers

High resolution structures of C2H2 zinc finger domains have been available for decades. As the name suggests, the divalent zinc atom locks the two cysteines and two histidines into a rigid geometry providing a core conformation that a small peptide of 28 residues could not otherwise stably assume. Note in the unbound state, finger tips must retain flexibility while the domain ensemble scans its genome for specific dna sequences appropriate to its function. Each finger binds a trinucleotide -- in effect making a zinc finger the protein counterpart to tRNA anticodon. However overall binding is not a simple read-off code because adjacent fingers alter each other's specificities in subtle ways.

The linker region TGEKP plays a key role when the correct DNA sequence is encountered, snap-locking its finger down onto its target by capping the C-terminus of its alpha helix. A hydrogen bond between the first threonine and middle glutamate is key to this binding-induced conformational shift. From comparative genomics, it appears that a serine in first position can also form this hydrogen bond. The role of the glycine is to stay out of the way; the lysine counterbalances the negative charge of the glutamate; the proline terminates any helical propensity, allowing a fresh start in the adjacent finger.

While this motif is immensely conserved within C2H2 zinc finger of PDRM9 homologs, exceptions do occur. It is important to understand these because these loss of dna lock-down could loosen or even eliminate trinucleotide binding specificity. Such steps might represent initial stages of pseudogenization. However many exceptions occur within the first or last fingers. It is also common for fragmentary and imperfect motifs to end the protein, sometimes continuing on in another reading frame past the current stop codon.

Note in aligning zinc finger motifs, the breaks should always be put at the end of the linker region. It is completely illogical to break at the first cysteine as some authors do because capping by the linker region is specific to its zinc finger, not the following one.

Predicting dna binding sites of zinc finger domains

Curated reference sequences

The sequences below have been compiled from genome projects -- only rarely do validating transcripts exist at GenBank. Sequences with a single frameshift or other glitch have been edited to allow full length proteins on the theohry that the error either reflects an aberrant atypical individual chosen for sequencing or simple error in low coverage projects within a difficult repeat region. However such sequences may instead reflect early stages of pseudogenization. Many sequences are in fact clearly pseudogenes; here recognizable exons have been collected to allow rough dating of loss of function.

In the case of more intensively studied species such as human and mouse, the number of C2H2 repeats varies widely. Only the most common representative is shown here. This variation likely occurs in all species but the individual animal chosen for sequencing may or may not be typical. Many clades have distinctive patterns of gene amplification and gene loss, making both orthologous and functional comparisons problematic.

Other useful sequences such as the GAS8 synteny neighbor, other zinc finger quasi-homologs having similar exon and domain structures, and bogus orthologs outside of mammals are also included for reference purposes.

Carnivores -- but not bats or horses -- have an intervening cadherin gene before GAS8:

PRDM7_ailMel    1724     1   579   579 100.0%  GL193502.1  +-     628987    644235  15249
CAD1_homSap      185   133   334   882  72.9%  GL193502.1  +-     620344    624223   3880
GAS8_homSap     1110     2   478   478  91.0%  GL193502.1  ++     594843    609901  15059

PRDM7_canFam     681   141   880   884  82.3%     5  ++   66560684  66567275   6592
CAD1_homSap      368   134   521   882  74.7%     5  ++   66571832  66581008   9177
GAS8_homSap     1188     2   478   478  93.4%     5  +-   66587321  66604940  17620

PRDM7_felCat     707   337   572   572 100.0%  Un_ACBE01450414  +-      10493     13105   2613
CAD1_homSap      130   133   223   882  74.7%  Un_ACBE01450414  +-       3902      4280    379

PRDM7_equCab    1294     1   435   435 100.0%     3  +-   36378853  36387224   8372
GAS8_homSap     1176     2   478   478  93.0%     3  ++   36348528  36361906  13379

>PRDM9_homSap Homo sapiens (human) genome Prim gene 13 CDH12 chr5 10 exon size 18,301 bp KRAB SSXRD SET C2H2
0 MSPEKSQEESPEEDTERTERKPM 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPWMALRVEQRKHQK 0
0 GMPKASFSNESSLKELSRTANLLNASGSEQAQKPVSPSGEASTSGQHSRLKL 1
2 ELRKKETERKMYSLRERKGHAYKEVSEPQDDDYL 1
2 YCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQPENPCPGDQNQEQQYPDPHSRNDKTKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSCRVGKRIMEEESRTGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSVKSDVITHQRTHTGEKL
YVCRECGRGFSWKSHLLIHQRIHTGEKP
YVCRECGRGFSWQSVLLTHQRTHTGEKP
YVCRECGRGFSRQSVLLTHQRRHTGEKP
YVCRECGRGFSRQSVLLTHQRRHTGEKP
YVCRECGRGFSWQSVLLTHQRTHTGEKP
YVCRECGRGFSWQSVLLTHQRTHTGEKP
YVCRECGRGFSNKSHLLRHQRTHTGEKP
YVCRECGRGFRDKSHLLRHQRTHTGEKP
YVCRECGRGFRDKSNLLSHQRTHTGEKP
YVCRECGRGFSNKSHLLRHQRTHTGEKP
YVCRECGRGFRNKSHLLRHQRTHTGEKP
YVCRECGRGFSDRSSLCYHQRTHTGEKP
YVCREDE.....................

>PRDM9_panTro Pan troglodytes (chimp) genome Prim gene 19 CDH12 chr5 frag assembly glitch in mid C2H2
0 MSPERSQEESPEGDTERTERKPM 0 
0 VKDAFKDISIYFTKEEWAEMGDWgKTRYRiVKMNYNALITi 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPWMAFRGEQSKHQK 0
0 GMPKASFNNESSLkELSGmPNLLNTSgSEQAQKPVSPPGEASTSGQHSRLKL 1
2 ELRRKETvGKMYSLRERKGHAYKEISEPQDDDYL 1
2 yCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLRVWNEASDPPLGLHSGPYEGQITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDKSwANWMR 2
1 YENCARDDEEQNLVSFQYHRQSFYRTCRVIRPGCELLVWYGDE GQELGIKWGSKWKKELMAGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQPENPCPGDQNQEQQYPDPRSRNDKTKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSCRVGKRIMEEESRTGQKVNPGNTAKLFVGVGISRIAK
VKYGECGQGFSDKSDVITHQRTHTGGKP
YVCRECGRGFSWKSHLLSHQRTHTGEKP
YVCRECGRGFSVKSSLLSHRTTHTGEKP
YVCRECGRGFSVKSSLLSHQRTHTGEKP
YVCRECGRGFSQQSNLLSHQRTHTGEKP
YVCRECGRGFSVKSSLLSHQRTHTGEKP
YVCRECGRGFSVKSSLLSHQRTHTGEKP
YVCRECGRGFSKQSHLLSHQRTHTGEKP
YVCRECGRGFSVQSNLLSHQRTHTGEKL
YVCRECGRGFSQQSHLLRHQRTHTGEKP
YVCRecgrgfsqqshLLSHQRTHTGEKP
YVCRECGRGFSVKSSLLSHQRTHTGEKP
YVCRECGRGFSKQSHLLSHQRTHTGEKP
YVCRECGRGFSQQSHLLSHQRTHTGEKP
YVCRECGRGFSQQSHLLRHQRTHTGEKP
YVCRECGRGFSVKSSLLSHQRTHTGEKP
YVCRECGRGFSVKSSLLSHQRTHTGEKP
YVCRECERGFSQQSHLLRHQRTHTGEKP
YVCRECGRGFSRQSALLIHQRTHTGEKP
VCREDE......................

>PRDM9_gorGor Gorilla gorilla (gorilla) CABD02290264 Prim gene -- cdh12 chr5 several contigs needed, most of ZNF domain missing
0 MSPERSQEESPEEDTERTERKPM 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPCMALRVEQRKHQK 0
0 GMPKASFSNESSLKELSRTANLLNASGSEQAQKPVSPPGEASTSGQHSRLKL 1
2 ELRKKETEGKMYSLRERKGHAYKEVSEPQDDDYL 1
2 yCEMCQNFFIDSCAAHGPPIFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYKGRITEDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARTLLQPENPCPGDQNQEQQYPDPRSRNDKTKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSCRVGKRIMEEESR TGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSVKSDVITHQRTHTGEKP
YVC.........................

>PRDM9_ponAbe Pongo abelii (orangutan) genome Prim gene 10 CDH12 chr5 frameshift extra a penultimate ZNF
0 MSPERSQEESPkGDTERTERKPM 0 
0 VKDAFKDISIYFTKEEWTEMGDWEKTRYRNVKRNYKTLITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPWMAFRGEQSKHQK 0
0 GMPKASFNNESSLKELSGTQNLLNTSGSEQAQKPVSPPGEASTSGQHSTLKI 1
2 ELRRKETEGKTYSLRERKGHAYKEVSEPQDDDYL 1
2 YCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDKEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCAWDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMPGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQPENPCPGDQNHEQQYSDPRSCNDKTKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSCRVGKRIMEEESRTGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSDKSDVITHQRTHTGGRS
YVCRECGRGFSRQSVLLIHQRTHTGEKP
YVCRECGRGFSRRSVLLIHQRTHTGEKP
YVCRECGRGFSQQSVLLIHQRTHTGEKP
YVCRECGRGFSRRSVLLIHQRTHTGEKP
YVCRECGRGFSWKSVLLRHQRTHTGEKP
YVCRECGRGFSQQSVVFIHQRTHTGEKP
YVCRECGRGFSGKSVLFRHQRTHTGEKP
YVCRECGRGFSDKSGVCYHQRTHTRGEA
YVCRECGRGFSVKSNLLSHQRTHTEEKL
YVCREDE.....................

>PRDM9_nomLeu Nomascus leucogenys (gibbon) ADFV01015315 Prim gene 10 cdh12 ADFV01015317 ADFV01015319 no CDH but best blastn favors PRDM9
0 MSPERSQEESPEEDTERTEQKPT 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2  0
0  1
2  1
2              AAHGPPTFIKDSTVGKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1  1
2 EPKAEIHPCPSCCLAFSSQKFLSQHVARHHSSQNFPGPSARKFLQPENPCPGDQNQEQQYSDPRSCNDKTKGQEIKERSKLLNKRTWQREISRAFSSSPKVQMGSCRVGKRIIEESRTGQKVNPGNTGQLFVGVGISRIAE
VKYGECGQGFSVKSDVITHQRTHTGEKL
YLCRECGRGFSVKSSLLSHQRTHTGEKP
YVCRECGRGFSKKSNLLSHQRTHTGEKP
YVCRECGRGFSDKSSLLRHQRTHTGEKP
YVCRECGRGFSQKSSLLSHQRTHTGEKP
YVCRECGRGFSQKSSLLSHQRTHTGEKP
YVCRECGRGFSDKSSLLRHQRTHTGEKP
YVCRECGRGFSQKSSLLSHQRTHTGEKP
YVCRECGRGFSVKSNLLSHQRTHTGEKP
YVCRECGRGFSDKSSLLRHQRTHTGEKP

>PRDM9_macMul Macaca mulatta (rhesus) genome Prim gene 9 CDH12 chr6 exon 4 lost to Ns
0 MSPERSQEESPEEDTERTERKPT 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2  0
0 GMPKASFNNESSLKEVSGMANLLNTSGSEQAQKPVSPPGEARTSGQHSRLKL 1
2 ELRRKETEGKMYSLRERKGHAYKEVSEPQDDDYL 1
2 YCEMCQNFFIDSCAAHGPPTFIKDSAVEKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITQDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSTQNFPGPSARRLFQPENLCSGDQNQEQQYSDPRSCNDKTKGQEIKERSKLLNKRTWPKEISRAFSSPPKGQMGSSRVGERMMEEEYRTGQKVNPENTGKLFVGVGISRIAK
VKYGECGQGFSDKSDVIIHQRTHTGEKP
YLCRECGRGFSQKSSLRRHQRTHTGEKP
YLCRECGRGFRDNSSLRYHQRTHTGEKP
YLCRECGRGFSNNSGLCYHQRTHTGEKP
YLCRECGRGFSDNSSLHRHQRTHTGEKP
YLCRECGRGFSNNSGLRYHQRTHTGEKP
YLCRECGRGFSNNSGLRHHQRTHTGEKP
YLCRECGRGFSQKANLLRHQRTHTGEKP
YLCRECGRGFSQKADLLSHQRTHTGEKP
VCRKDE......................

>PRDM9_papHam Papio hamadryas (baboon) genome Prim gene 11 cdh12 contigs scattered
0  0 
0  1
2  1
2 VKPPWMAFRVEQSKHQK 0
0 EMPKTSFSNESSLKELSGTPNLLSTSGSEQAQKPASPPGEASTSGQHSRLKL 1
2 ELRRKEAEGKMYSLRERKGHAYKEVSELQDDDYL 1
2 ycEMCQNFFIDSCAAHGPPTFVKDSAVNKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDKEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1  1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSTQNFPGPSARRLLQPENLCSGDQNQEQQYSDPCSCNDKTKGQEIKERSKLLNKRTWQKEISRAFSSPPKGQMGSSRVGERMMEEESRTGQKVNPENIGKLFVEVGISRIAK
VKYGECGQGFSGKSDVITHQRTHTEGKP
YLCRECGRGFSQKSNLLRHQRTHTGEKP
YLCRECGRGFRDNSSLRCHQRTHTGEKP
YLCRECGRGFRDNSSLRCHQRTHTGEKP
YLCRECGRGFSDNSSLRYHQRTHTGEKP
YLCRECGRGFRDNSSLRYHQRTHTGEKP
YLCRECGRGFSVKSNLLSHQRTHTGEKP
YVCRECGRGFSDNSSLRCHQRTHTGEKP
YLCRECGRGFSQMSHLRCHQRTHTGEKP
YLCRECGRGFSVKSNLLSHQRTHTGEKP
YVCRECGRGFSRKANLLSHQRTHTGEKP

>PRDM7_homSap Homo sapiens (human) genome Prim gene 3 GAS8+ chr16 TUBB3+ DEFB+ AFG3L1+ DBNDD1- GAS8+ PRDM7- 92% id
0 MSPERSQEESPEGDTERTERKPM 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKMNYNALITV 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPWMAFRGEQSKHQK 0
0 GMPKASFNNESSLRELSGTPNLLNTSDSEQAQKPVSPPGEASTSGQHSRLKL 1
2 ELRRKETEGKMYSLRERKGHAYKEISEPQDDDYL 1
2 YCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDKSSANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQPENPCPGDQNQERQYSDPRCCNDKTKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSSRVGERMMEEESRTGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSDKSDVITHQRTHTGGKP
YVCRECGRgFSRKSDLLSHQRTHTGEKP
YVCRECERGFSRKSVLLIHQRTHRGDAP
VCRKDE......................

>PRDM7_panTro Pan troglodytes (chimp) genome Prim pseu 2 GAS8+ chr16 
0 MSPERSQEESPEEDTERTERKPM 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPLMALRVEQRKHQK 0
0 GMPKASFSNESSLKELSRTANLLNASGSEQAQKPVSPPGEASTSGQHSRLKL 1
2 ELKKKETEGKMYSLRERKGHAYKEVSEPQDDDYL 1
2 YCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYKGRITEDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLQPENP PGDQNQERQYSDPRCCNDKTKGQEVKERSKLLNKWTWQREISRAFSSLPKGQMGSSRVGERMMEEESRTGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSVKSDVITHQRTHTGEKP
YVCRECGQGFSRKSVLLIHQRTHRGEKP
VCRKDE......................

>PRDM7_gorGor Gorilla gorilla (gorilla) genome Prim pseu 3 GAS8+ chr15730 numerous frameshifts in terminal ZNF domain
0 MSPERSQEESPEGDTERTERKPM 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATQPVFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2  0
0 GMPKASFNNESSLKELSGTPNLLNTSGSEQAQKPVSPPGEASTSGQHSRRKL 1
2 ELRRKETEGKMYSLRERKGHAYKEISKPQDDDYL 1
2 yCEMCQNFFIDSCAAHGPPTFVKDSAVDKRHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDKEAANSGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVALQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELTAGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQPENPCPGDQNQERQYSDPRCCNDKTKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSSRVGERMMEEESRTGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSWKSNLLRHQRTHTGGKP
YVCRECGRGFSWKSDLLSHQRTHTGEKP
YVCRECGRGFSWKSNLLSHQRTHTGEKP

>PRDM7_ponAbe Pongo abelii (orangutan) genome Prim gene 4 GAS8+ chr16 
0 MSPERSQEESPEDDTERTERKPT 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPWMALRVEQRKHQK 0
0 GMPKASFNNESSLKELSETANLLNASGSEQAQKPVSPPGEASTSGQHSRLKL 1
2 ELRSKETEGNTYSLRERKGHAYKEISEPQDDDYL 1
2 yCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALTLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITKDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARHLLQAENPCPGDQNQEQQYSDPDCCNDKTKGQEIKERSKLLNKRTWQREISRAFSSSAKGQMGSSRVGERMMEEESGTGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSVKSDVITHQRTHTGEKP
YICRESGRGFTQKSGLLSHQRTHTGEKP
YVCRECGWGFSQKSNLLRHQRTHTGEKP
YVCRECGRGFSRKSVLLIHQRTHTGEKP
VCRKDE......................

>PRDM7_nomLeu Nomascus leucogenys (gibbon) ADFV01125891 Prim pseu 5 gas8+ synteny implied by non-coding
0  0 
0  1
2  1
2 IKSPWMAVRVEQSKHQK 0
0 GMPKASFNNESGLKELSGTQNLLNTSG EQARKPVSPPGEASTSGQHSRQKL 1
2 ELRRKETEGKMYSL ERKGHAYKEVSEPQDDDYL 1
2 yCEMCQNFFTDSCAAHGPPTFVKDSAVDKGHPNHSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKS ANWMK 2
1 YVNCARDHEEQNLVAFQYHRQIFYRTCQVIRPGCEPLVWYGDEYGQELGIKWGSKWKKELTAER 1
2 EPKPEIHPCPSCCLVFTSQKFLSQHVECNHSSQNFPGPSARKLLQRENPCPGDQNQEQQYSDSRSCNDKTKGQEIKERSKL NKRIWQRKISRAFSSLPKGQMGSSRVGERMMEEESRTGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSDKSDVIAHQGTHTGGKS
.ICRECGWGFSQESHLLIHQRTHTGEKL
YVCRECGQGFSQKSDLLSHQRTHTGEKP
YVRRECGRGFSQKSNLLSHQRTHTEEKP
YVCRECGWGFSQKSHLLIHQRTHTGKKP
VCRKDE......................

>PRDM7_macMul Macaca mulatta (rhesus) genome Prim pseu 2 GAS8+ chr20 frameshifts exon 5 and 10, exon 10 a to aa restores frame
0  0 
0  1
2  1
2 VKPPWMAFRVEQSKHQK 0
0 EMPKTSFNNESSLKELSGTPNLLSTSDSE AQKPASPPGEASTSGQHSRLKL 1
2 ELRRKETEGKMYSLRERKRHAYKEASELQHDDYL 1
2 YCEMCQNFFIDSCAAHGPPTFVKDNAVNKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPCEGRITEDKEAANSGYSWL 0
0 ITKGRNCYEYVDGKDKSWAKWMR 2
1  1
2 EPKPEIYPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQSENPCPGDQNQEQQYSDPSSCNDKTKGQEIKERSKLLNKRTWQREILRAFTSPPKGQMGSSRVGERMMEEEFRTGQKANPGNTGKLFVGVEISRIAK
VKYGECGQGFSGKSDVITHQRTHTEGKP
YVCRGCGRRFSQKSSLLRHQRTHTGEKP
VCKKNE......................

>PRDM7_papHam Papio hamadryas (baboon) genome Prim pseu 2 gas8+ contigs scattered
0 MSPERSQEESPEEDTERTEWKPM 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPWMAVRVEQSKHQK 0
0 GMPKASFNNESSLKEVSGMANLLNTSGSEQAQKPVSPPGEARTSGQHSRLKL 1
2 ELRRKETEGKMYSLRERKGHAYKEVSEPQDDDYL 1
2 YCEMCQNFFIDSCAAHGPPTFIKDSAVEKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITQDEEAANNGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 EPKPEIYPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQSENPCPGDQNQEQQYSDPSSCNDKTKGQEIKERSKLLNKRTRQRQILRAFTSPPKGQMGSSRVGERMMKEEFRTGQKANPGNTGKLFVGVEISRIAK
VKYGECGQGFSDKSDVVIHQRTHTREKP
YVYRgCGQGFSIKSNLLRHQRIHTGEKP

>PRDM7_calJac Callithrix jacchus (marmoset) genome Prim gene 12 GAS8+ chr20 one frameshift in repeat area chr20 terminus
0 MSPERSQEESPEGDTGRTEQKPM 0 
0 VKDAFKDISMYFSKEEWAEMGDWEKTRYRNMKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPGMAFRVGQSKHQK 0
0 GMPKASFGNESSLKKLSGTANVLNTSGPEQAQKPVSPPGEASTSGQHSRLKL 1
2 ELRRKDTEEKMYSLRERKGLAYKEVSEPQDDDYL 1
2 yCEICQNFFIDSCAAHGPPTFVKDSAVDKGHPNHAALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRVTEDEEAASSGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 ESKPEIHPCPSCCLAFSSQKFLSHHVERNHSSQNFPGTSTRKLLQPENPCPGKQKEEQQYFDPCNSNDKTKGQETKERSKLLNIRTWQREMARAFSNPPKGQMGSSRVEERMMEEESRTGQKVNPVDTGKLFVGVGISRIAK
AKYGECGQGFSDMSDVTGHQRTHTGEKP
YVCRECGRGFSQKSALLSHQRTHTGEKP
YVCRECGRGFSQKSHLLSHQRTHTGEKP
YVCTECGRGFSQKSVLLSHQRTHTGEKP
YVCTECGRGFSRKSNLLSHQRTHTGEKP
YVCRECGRGFSRKSALLSHQRTHTGEKP
YVCRKCGRGFSQKSNLLSHQGTHTGEKP
YVCTECGRGFSQKSHLLSHQRTHTGEKP
YVCRKCGRGFSQKSNLLSHQRTHTGEKP
YVCRECGRGFSFKSALLRHQRTHTGEKP
YVCRECGRGFSRKSHLLSHQGTHIGEKP
YVCRECGRGFSRKSNLLSHQRIHTGEKP
YVRREDE.....................

>PRDM7_micMur Microcebus murinus (lemur) ABDC01433247 Prim gene 8 gas8+ weak coverage
0 MSPEKSQEESPEEDTERTERKPM 0 
0 vKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKPPWMALRVEQRKHQK 0
0 GMPKASFSNESSLKELSRTANLLNASGSEQAQKPVSPSGEASTSGQHSRLKL 1
2 ELRKKETERKMYSLRERKGHAYKEVSEPQDDDYL 1
2 YCEKCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLKIRPSGIPQAGLGVWNEASELPLGLHFGPYEGQVTEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDDSWANWMR 2
1 YVNCARDEEEQNLVAFQYHRQIFYRTCQVIRPGCELLVWYGDEYGQELGIKWGSKWKEELTIRQ 1
2 EPKPEIHPCPSCSLAFSSQKFLSQHVKHTHSSQISPRTSGRKHLQPENPCPGDQNQEQQHSDPHSCNDKAKDQEVKERPKPFHKKTQQRGISRAFSSPPKGKMGSCREGKRIMEEEPRTGQKVGPGDTDKLCAAGGISRISR
VKYGDSGQSFSDKSNVIIHQRTHTGEKP
YVCRECGRGFSQKSDLLKHQRTHTGEKP
YVCRECGRGFSQKSHLLRHQRTHTGEKP
YVCRECGRGFSQKSDLLIHQRTHTGEKP
YVCRECGRGFSCKSHLLIHQRTHTGEKP
YVCRECGRGFSCKSSLLIHQRTHTGEKP
YVCRGVWGEALAESQTSSYTRGHTQGRS
PVFAGRVSKSLALNYISTATGGHLLTSH
LPTPALGGASKGSLLTLYISQECKETRN

>PRDM7_otoGar Otolemur garnettii (galago) genome Prim gene 7 GAS8+ good coverage
0 MSPEKSQEESPEEDTERTERKPM 0 
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1
2 VKHPWMAFRMEQSKRQK 0
0 ILKKCMLSFNMHLKELSGPASLPNISGSEQHQKHMSSPREASTSGQHSGRKS 1
2 DLRIKEIEVRMYSLRERKGHAYKEVSEPQDDDYL 1
2 yCEKCQNFFIDNCAVHGPPTFVKDTAVEKGHPNRSVLSLPSGLGIRTSGIPQAGFGVWNEASDLQLGLHFGPYEGQVTEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDESQGNWMR 2
1 YVNCARDEEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELTAGQ 1
2 EPKPEIHPCPSCSLAFSTQKFLSQHVERTHPSQISQGTSGRKNLRPQTPCPRDENQEQQHSDPNSRNDKTKGQEVKEMSKTSHKKTQQSRISRIFSCPPKGQMGSSREGERMIEEEPRPDQKVGPGDTEKFCVAIGISGIVK
VKNRECVQSFSNKS
NLRHQRTHTGEKP
YMCRDCGRGFSHKSSLFRHQRTHTGEKP
YVCRDCGRGFSLKANLLTHQRTHTGEKP
YVCRDCGQGFSQKAHLLRHQRTHTGEKP
YMCRDCGQGFSRKAYLLTHQRTHTGEKP
YVCRDCGQGFSQKAHLLTHQRTHTGEKP
YVCRDCGRGFSHKSSLFRHQRTHTGEKP
YICRDCG

>PRDM7_tarSyr Tarsius syrichta (tarsier) ABRT011082008 Prim pseu -- gas8+ double frameshift in exon 5, ABRT010499286
0  0 
0  1
2 GLRAPRPAFMCHRKRAIKPLVDDTEDSDEEWTPRQQ 1
2  0
0 GMPRAPLSIVSSLKELSEMANLLNTSDSEQAWKPVSPSREASTSEQHSRKKL 1
2 EFRKKEIEVNMYSLRERKDCAYKEVNEPQDDDYL 1
2 YCEQCQNFFIDSCATHGIPTFINDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASELPLGLHFGPYEGQITDDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRIIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 1
2 

>PRDM9_oryCun Oryctolagus cuniculus (rabbit) genome Glir gene 8 other Un0161 exon 2 ttt to tt restores frame; ZNF717+ DCAF4+ YAP1+ PRDM9- qTer 
0 MSAAAPAEPSPGADAGQARGKPE 0 
0 VQDAFRDISIYFSKEEWAEMGEWEKIRYRNVKRNYCALVAI 1
2 GLRAPRPAFMCHRRLAVRARADDTEDSDEEWTPRQQ 1
2 VKPPWMAFRTEHSKHQK 0
0 GMPRLPVNNESSLKELSGTANLLKTTGSEEDQKPSFPPKETRTSGQHSTRKL 1
2 GLRRKNIEVKMYSFRKRKSQAYKECSEPQDDDYL 1
2 YCEKCQNFFLDSCAVHGPPIFVKDSAVDKGHPNRSVLSLPPGLRIGPSGIPEAGLGVWNEASDLPLGLHFGPYEGQITEEEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDRSWANWMR 2
1 YVNCARNDEEQNLVAFQYHKQIFYRTCQVIKPGCELLVWYGDEYGQELGIKWGSKWKEELTAGR 1
2 EPKPEIHPCPSCSLAFSSHKFLSQHMERSHSSQIFPGAPARNHLQPANPCPGKEHQKLSDPQSWNDKNEGQDVKEKSRFSSKRTRQKAISRSFSSLPKGQVETSREGERMIEEEPRIGQELNPEDTGKSSVGAGLSRIAG
VKYRDCRQGLSDKSHLINGQRAHTGEKP
YACRECERGFTVKSNLISHQRTHTGEKP
YACRECGRGFTVKSALTTHQRTHTGEKP
YACRECGRGFTVKSHLISHQRTHTGEKP
YACRECGRGFTVKSALITHQRTHTGEKP
YACRECGQGFTVKSNLISHQRTHTGEKP
YACRECGRGFTQKSHLINHLRAHTGEKP
YACRECGRGFTVKSDLISHQRTHTGEKP
YACRVDE.....................

>PRDM7_oryCun Oryctolagus cuniculus (rabbit) genome Glir gene 4 other synteny novel
0  0 
0  1
2 GLRAPRPAFMCHRRLAVRARADDTEDSDEEWTPRQQ 1
2 VKPPWMAFRTEHSKHQK 0
0 GMPRLPVNNESSLKELSGIANLLNTTGSEEDQKPSFPPKETRTSGQHSTRKL 1
2 GLRRKNIEVKMYSFRKRKSQAYKECSEPQDDDYL 1
2 YCEKCQNFFLDSCAVHGPPIFVKDSAVDKGHPNRSVLSLPPGLRIGPSGIPEAGLGVWNEASDLPLGLHFGPYEGQITEEEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDRSWANWMR 2
1 YVNCARNDEEQNLVAFQYHKQIFYRTCQVIKPGCELLVWYGDEYGQELGIKWGSKWKEELTAGR 1
2 EPKPEIHPCPSCSLAFSSHKFLSQHMECSHSSQIFPGAPARNHLQPANPCPGKEHQKLSDPQSWNDKNEGQDVKEKSRFSSKRTRQKAISRSFSSLPKGQVETSREGERMIEEEPRIGQELNPEDTGKSSVGAGLSRIAG
VKYRDCRQGLSDKSHLINGQRAHTGEKP
YACRECGQSFTVKSNLISHQRTHTGEKP
YACRECGRGFTQKSHLIRHQRTHTGEKP
YACRECGQSFTWKSNLISHQRTHTGEKP
YACRVDE.....................

>PRDM7_ochPri Ochotona princeps (pika) AAYZ01312269 Glir gene -- noDet dubious fragment, no orthologous terminal exon
0  0 
0  1
2  1
2  0
0  1
2  1
2 yCEMCQNFFIESCAVHGSPTFVKD     GHPHRSVLSLPSGLRIGPSGIPEAGLGVWNETTDLPLGLHFGPYEGQVTEEEEATNSGYSWL 0
0 ITKGRNRYEYVDGKDPSQANWMR 2
1 YVNCARNDEEQNLVAFQYHRQIFYRTCRAVRQGCELLVWYGDEYGQELGIKWGSKWKEELTAGR 1
2 

>PRDM7_ratNor Rattus norvegicus (rat) P0C6Y7 Glir gene 10 PDCD2 chr1 FM103467 single transcript from body fat
0 MNTNKPEENSTEGDAGKLEWKPK 0 
0 VKDEFKDISIYFSKEEWAEMGEWEKIRYRNVKRNYKMLISI 1
2 GLRAPRPAFMCYQRQAIKPQINDNEDSDEEWTPKQQ 1
2 VSSPWVPFRVKHSKQQK 0
0 ETPRMPLSDKSSVKEVFGIENLLNTSGSEHAQKPVCSPEEGNTSGQHFGKKL 1
2 KLRRKNVEVNRYRLRERKDLAYEEVSEPQDDDYL 1
2 YCEKCQNFFIDSCPNHGPPVFVKDSVVDRGHPNHSVLSLPPGLRIGPSGIPEAGLGVWNEASDLPVGLHFGPYKGQITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGQDESQANWMR 2
1 YVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGRELLVWYGDEYGQELGIKWGSKMKKGFTAGR 1
2 ELRTEIHPCFLCSLAFSSQKFLTQHVEWNHRTEIFPGASARINPKPGDPCPDQLQEHFDSQNKNDKASNEVKRKSKPRHKWTRQRISTAFSSTLKEQMRSEESKRTVEEELRTGQTTNIEDTAKSFIASETS
RIERQCGQCFSDKSNVSEHQRTHTGEKP
YICRECGRGFSQKSDLIKHQRTHTEEKP
YICRECGRGFTQKSDLIKHQRTHTEEKP
YICRECGRGFTQKSDLIKHQRTHTGEKP
YICRECGRGFTQKSDLIKHQRTHTEEKP
YICRECGRGFTQKSSLIRHQRTHTGEKP
YICRECGLGFTQKSNLIRHLRTHTGEKP
YICRECGLGFTRKSNLIQHQRTHTGEKP
YICRECGQGLTWKSSLIQHQRTHTGEKP
YICRECGRGFTWKSSLIQHQRTHTVEK.

>PRDM7_musMus Mus musculus (mouse) Q96EQ9 Glir gene 12 PDCD2 chr17 CN723438 eight transcripts, four from retina
0 MNTNKLEENSPEEDTGKFEWKPK 0 
0 VKDEFKDISIYFSKEEWAEMGEWEKIRYRNVKRNYKMLISI 1
2 GLRAPRPAFMCYQRQAMKPQINDSEDSDEEWTPKQQ 1
2 VSPPWVPFRVKHSKQQK 0
0 ESSRMPFSGESNVKEGSGIENLLNTSGSEHVQKPVSSLEEGNTSGQHSGKKL 1
2 KLRKKNVEVKMYRLRERKGLAYEEVSEPQDDDYL 1
2 YCEKCQNFFIDSCPNHGPPLFVKDSMVDRGHPNHSVLSLPPGLRISPSGIPEAGLGVWNEASDLPVGLHFGPYEGQITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGQDESQANWMR 2
1 YVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKMKKGFTAGR 1
2 ELRTEIHPCLLCSLAFSSQKFLTQHMEWNHRTEIFPGTSARINPKPGDPCSDQLQEQHVDSQNKNDKASNEVKRKSKPRQRISTTFPSTLKEQMRSEESKRTVEELRTGQTTNTEDTVKSFIASEIS
SIERQCGQYFSDKSNVNEHQKTHTGEKP
YVCRECGRGFTQNSHLIQHQRTHTGEKP
YVCRECGRGFTQKSDLIKHQRTHTGEKP
YVCRECGRGFTQKSDLIKHQRTHTGEKP
YVCRECGRGFTQKSVLIKHQRTHTGEKP
YVCRECGRGFTQKSVLIKHQRTHTGEKP
YVCRECGRGFTAKSVLIQHQRTHTGEKP
YVCRECGRGFTAKSNLIQHQRTHTGEKP
YVCRECGRGFTAKSVLIQHQRTHTGEKP
YVCRECGRGFTAKSVLIQHQRTHTGEKP
YVCRECGRGFTQKSNLIKHQRTHTGEKP
YVCRECGWGFTQKSDLIQHQRTHTREK.

>PRDM7_musMol Mus molossinus (wild_mouse) GU216230 Glir gene 11 noDet full length deposit
0 MNTNKLEENSPEEDTGKFEWKPK 0 
0 VKDEFKDISIYFSKEEWAEMGEWEKIRYRNVKRNYKMLISI 1
2 GLRAPRPAFMCYQRQAMKPQINDSEDSDEEWTPKQQ 1
2 VSPPWVPFRVKHSKQQK 0
0 ESSRMPFSGESNVKEGSGIENLLNTSGSEHVQKPVSSLEEGNTSGQHSGKKL 1
2 KLRKKNVEVKMYRLRERKGLAYKEVSEPQDDDYL 1
2 YCEKCQNFFIDSCPNHGPPLFVKDSMVDRGHPNHSVLSLPPGLRISPSGIPEAGLGVWNEASDLPVGLHFGPYEGQITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGQDESQANWMR 2
1 YVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKMKKGFTAGR 1
2 ELRTEIHPCLLCSLAFSSQKFLTQHMEWNHRTEIFPGTSARINPKPGDPCSDQLQEQHVDSQNKNDKASNEVKRKSKPRQRISTTFPSTLKEQMRSEESKRTVEELRTGQTTNTEDTVKSFIASEIS
SIERQCGQYFSDKSNVNEHQKTHTGEKP
YVCRECGRGFTAKSNLIQHQRTHTGEKP
YVCRECGRGFTQKSVLIQHQRTHTGEKP
YVCRECGRGFTQKSDLIKHQRTHTGEKP
YVCRECGRGFTAKSNLIQHQRTHTGEKP
YVCRECGRGFTEKSSLIKHQRTHTGEKP
YVCRECGWGFTAKSNLIQHQRTHTGEKP
YVCRECGRGFTQKSSLIKHQRTHTGEKP
YVCRECGRGFTAKSNLIQHQRTHTGEKP
YVCRECGWGFTQKSNLIKHQRTHTGEKP
YVCRECGWGFTQKSDLIQHQRTHTR.EK

>PRDM7_dipOrd Dipodomys ordii (kangaroo_rat) genome Glir gene -- noDet dubious fragment, no orthologous terminal exon
0  0 
0  1
2 GLKAPRPVFMCHRRQAIKPQVDDTDDSDEEWTPGRQ 1
2  0
0  1
2 elRTKEVKMRMYSLRERKSYAYEEISEPQDDDYL 1
2 yCEQCQNFFINSCTVHGPPIFVRDNVVDKGHYDRSVLSLPPGLRIRQSSIPEAGLGVWNEESDLPLGLHFGPYEGQITEDEDAANSGYSWM 0
0 ITKGRNCYVYVDGKDKSQANWMR 2
1 YVNCARYDEEQNLVAFQYHRQIFYRTCRVIKAGCELLVWYGDEYGQELGIKWGSKWKRELTAgr 1
2 

>PRDM7_speTri Spermophil tridecemlin (squirrel) AAQQ01308561 Glir gene -- noDet plus exon by exon traces
0  0 
0  1
2 GFRAPRPAFMCHQRQTIKLQMDDTEDSDEEWTPRQQ 1
2  0
0 LKPEVLLSNESSLKELSGTANLLNTSGSEQVQKPVSPLREASASRQHSRRKL 1
2 ELRTKEVEVKMYSLRERKGHAYKEVSEPQDDDYL 1
2 yCDKCQNFFMDSCPVHGPPTFIKDSVVNKDHSNHSTLSLPLGLRIGPSSIPEAGLGVWNEATDLPLGLHFGPYRGQITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDESQANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELSAGR 1
2 EPKPEIHPCPSCSLAFSSQKFLSQHVDRSHPSQIFPGTSMRKKLIPGDSSPRDQLQEQQHPDPHGWNDKARGQEVQGSLKPTHKGTRQRGISSPPKGQMGRSEESERMMEDDLKADQEINPEDTDKILVGVEMSRI
-

>PRDM9a_bosTau Bos taurus (cattle) NW_003053109 Laur gene 7 noDet chr1 
0 MSQNRSPEERTKGDAGRTEWKLT 0 
0 AKDAFKDISIYFSKEEWAEMGEWEKTGYRNVKRNYEVLIAI 1
2 GLRATQPAFMHHRRQVIKPQGDDTEDSDEEWTPQHQ 1
2 GKPSRKAFRMEHRKHQK 0
0 GKSRGPLSKVSSLKKLQGAAKLLNTSGSKWAQKPANPPRETRTLEQHSRQKV 1
2 ELRRKETDMKRYSLRERKGHVYQEVSEPQDDDYL 1
2 YCQECQNFFIDSCDAHGPPTFVKDSAVEKGHANRSVLTLPPGLSIKLSGIPEAGLGVWNEASHLPLGLHFGPYEGQITDDKEAINSGYSWL 0
0 ITKGRNSYEYVDGKDTSLaNWMR 2
1 YVNCARHYEEQNLVAFQYHGQIFYRTCQVVRPGCELLVWYGDEYGEKLGIKCESRGKSMFAAGr 1
2 ESKPKIHPCASCSLAFSSQKFLSQHVQHNHPSQTLLRPSARDYLQPEDPCPGSQNQQQRYSDPHSPSDKPEGREVKDRPQPLLKSIRLKRISRASSYSPRGQMGASGVHERITEEPSTSQKPNPEDTGKLFMGAGVSGIIK
VKYGECGQGSKDRSSLITNQRTHTGEKP
YVCGECGQSFNQKSTLITHQRTHTGEKP
YVCGECGRSFNQKSTLITHQRTHTGEKP
YVCGECGRSFSQKSTLIKHQRTHTGEKP
YVCGECGQSFNQKSTLITHQRTHTGEKP
YVCGECGQSFNQKSTLITHQRTHTGEKP
YVCGECGRSFSRKSTLITHQRTHRGEKL
CLQGV......................

>PRDM9b_bosTau Bos taurus (cattle) DAAA02065087 Laur gene 5 noDet chrU aaaaa fixed to aaaaaa in exon 2 KRAB SSXRD SET C2H2
0 MSPNRSPENSTEGDAGRTEWKPM 0 
0 AKDAFKDISIYFTKEEWAEMGEWEKIQYRNVKRNYEALIAI 1
2 GFRATQPGFMHHGRQVLKSQVDDTEDSDEEWTPRQQ 1
2 GKPSGMAFRGEPSKHPK 0
0 RLSRGPLNKVSSLKKLPGAAKLLKKSGSKQAQKPVPPPREARTPGKHPRHKV 1
2 ELRRKETEVKRYSVRERKGHVYQEVSEPQDDDYL 1
2 YCEECQNFFIDSCAAHGPPTFVKDSAVEKGHANRSALTLPPGLSIRPSGIPEAGLGVWNEASDLPLGLHFGPYEGQIIYNEEDSNSGYCWL 0
0 VTKGRNSYEYVDGKDTSLANWMR 2
1 YVNCARDDEEQNLVALQYHGQIFYRTCRVVRPGCELLVWYGDEYGEELGIKQDKRGKSKLSAQR 1
2 AKMHPCASCSLAFSSQKFLSQHVQRNHPSQTLLRPSARDHLQPEDPCPGNQNQQQRYSDPHSPSDKPEGRKAKDRPQPLLKSIKLKRISRASSYSPRGQVGRSGVHERITEEPSTSQKLNPEDTGKLFMGAGVSGIIK
VKYRECGQGSKDRSSLITHERTHRAEAL
CLRRVWAKLQSEVPLLVMHQRTHTGEKL
YVCGECGKSFSQKSPLIRHQRTHTGEKP
YVCGECGKSFSQKSPLIRHQRTHTGKKP
YVCRECGRSFSDKSH.HTPEYTHRGEAL
HLRGVWA.....................

>PRDM9c_bosTau Bos taurus (cattle) XM_002699750 Laur gene -- noDet chrX GO353654 4-cell embryo transcript no zinc downstream despite 43k bp
0 MSPNRSPENSTEGDAGRTEWKPM 0 
0 AKDAFKDISIYFTKEEWAEMGEWEKIRYRNVKRNYEALIAI 1
2 GFRATQPGFMHHRRQVLKPQVDDTEDSDEEWTPRQQ 1
2 GKPSGMAFRGERSKHQK 0
0 RLSRGPLNKVSSLKKLPGAAKLLKKSGSKQAQKPVPPPREARTPGKHPRHKV 1
2 ELRRKETKVKRYSVRERKGHVYQEVSEPQDDDYL 1
2 YCEECQNFFIDSCAAHGPPTFVKDSAVEKGHANRSALTLPPGLSIRPSGIPEAGLGVWNEASDLPLGLHFGPYEGQIIYNEEDSHSGYCWL 0
0 VTKGRNSYEYVDGKDTSLANWMR 2
1 YVNCARDDEEQNLVALQYHGQIFYRTCRVVRPGCELLVWYGDEYGEELGIKQDKRGKSKLSAQR 1
2 

>PRDM9d_bosTau Bos taurus (cattle) genome Laur gene 9 noDet chrX proximal tandem
0 MRPNTSPEESTERDAGRTEWKPT 0 
0 AKDAFKDISVYFSKEEWEEMGEWEKIRYRNVKRNYEALIAI 1
2 GFRATRPAFMHHRRQVIKLQADDTEDSDEEWTPRQQ 1
2 GKLSSMAFRVEHNKHQN 0
0 TMSRAPLSKEFSLKELPGAAKLLKTSGSKQAQKLVPPPGKARTPGQHPRQKV 1
2 ELRRKETEVKRYSLRERKGHVYQEVSEPQDDDYL 1
2 YCEECQSFFIDSCAAHGPPIFVKDCAVEKGHANRSALTLPPGLSIRESSIPEAGLGVWNEVSDLPLGLHFGPYEGQITDDEEAANSGYSWL 0
0 ITKRRNCYEYVDGKDTSLANWMR 2
1 YVNCARDDEEQNLVALQYHGQIFYRTCQVVRPGCELLVWYGDEYGQDLGIKRESSRKSELAGPR 1
2 EPKPKIYPCASCCLSFSSQKFLSQHVQRNHPSQILLRPSIGDHLQPEDPCPGSQNQQQRYSDPHSLSDKPEGREPKERPHPLLKGPKLCIRPKRISTASSYPPKGQMGGSEVHERMTEEPSTSQKLNPEDTGKLFMEAGVSGIVR
VNYGDHEQGSKDRSSLITHEKIHTGEKP
YVCKECGKSFNGRSDLTKHKRTHTGEKP
YACGECGRSFSFKKNLITHKRTHTREKP
YVCRECGRSFNEKSRLTIHKRTHTGEKP
YVCGDCGQSFSLKSVLITHQRTHTGEKP
YVCGECGRSFNEKSRLTIHKRTHTGEKP
YVCGDCGQSFSLKSVLITHQRTHTGEKP
YVCGECGQSFNEKSRLTIHKRTHTGEKP
YACGDCGQSFSLKSVLITHQRTHTGEKP
YVCMECE.....................

>PRDM9e_bosTau Bos taurus (cattle) genome Laur gene 9 noDet chrX distal tandem
0 MRPNRSPEESTEGDAGRTEWKPM 0 
0 AKDAFKDISIYFSKEEWEEMGEWEKIRYRNVKRNYEVLITI 1
2 GFRAARPAFMHHRRQVIKPQVNDIKDSDEEWTPRQQ 1
2 GKPFSMAFRVEHSKHQK 0
0 GMSRAPLSKESSLKELPGAAKLLKTSGCKQAQKLVPPPRKARTPEQHPRQKV 1
2 ERRRKETGVKRYSLREREGLVYQEVSEPLDDDYL 1
2 YCEECQSFFIDICAAHRPPTFVKDCAVEKGHANCSALTLPPGLSIRLSGIPEAGLGVWNEASDLPLGLHFGPYEGQITDDKEAAHSRYSWL 0
0 ITKGRNCYEYVDGKDTSLANWMR 2
1 YVNCARDDEEQNLVALQYQGQIFYRTCQVVRPGCELLVWYGDEYGWDLSIKQDSRGKNKLAAGR 1
2 EPKPKIYPCASCCLSFSSQKFLSQHVQRNHPSQILLRPSIGDHLQPEDPCPGSQNEQQRYSDPHSLSDKPEGREPKERPHPLLKGPKLCIRLKRISTASSYPPKGQMGGSEVHERMTEEPSTSQKLNPEDTGKLFMEAGVSGIVR
VKYGEHEQDSKDKSSLITHEKIHTGEKP
YVCTECGKSFNWKSDLTKHKRTHSEEKP
YACGECGRSFSFKKNLIIHQRTHTGEKP
YVCGECGRSFSEKSNLTKHKRTHTGEKP
YACGECGQSFSFKKNLITHQRTHTGEKP
YVCGECGRSFSEKSRLTTHKRTHTGEKP
YVCGDCGQSFSLKSVLITHQRTHTGEKP
YVCRECGRSFSVISNLIRHQRTHTGEKP
YVCRECEQSFREKSNLVRHQRTHTGEKP
YVCMECE.....................

>PRDM9e_oviAri Ovis aries (sheep) genome Laur pseu -- noDet chr 18 cow has PDRM7 pseudogene; sheep GAS8 is on sheep chr14
0  0 
0  1
2 GLRAP PPFMYHRRQVIKPQVDDIEDSDEEWTPRQQ 1
2  0
0  1
2 ELRRKETEMKIYSLQKRKGHMYQEVSDPQDDNYL 1
2 ycEKCQNF INSCAAHGPPTFVKDCVVEKGHASCSALtLSPGLSIRPSGIPEAGLRVWNEASDLPLGLHFGPYKGQITDDEEVANSRYFWL 0
0  2
1 YVNCAQDDEEQNLVAFQYHRQIFS TCWVVRPGCELLVWYRDEYGQELSIK GSRHKSELTVRR 1
2 

>PRDM9d_oviAri Ovis aries (sheep) genome Laur gene -- noDet chr1 near end chr1
0  0 
0  1
2 GLRATRLAFMHHCRQVIKPQVDDIEDSDEEWTPRQQ 1
2  0
0  1
2  1
2  0
0 ITKGRNCYEYVDGKDTSLANWMR 2
1 YVNCARDDEEQNLVALQYQGQIFYRTCQVVRPGCELLVWYGDEYGQDLGIKRDSSGKSELAAGR 1
2 

>PRDM9c_oviAri Ovis aries (sheep) genome Laur pseu 4 noDet chr5 middle of 108,514,869 bp
0  0 
0  1
2 GLRATRLAFMHHCRQVIKPQVDDIEDSDEEWTPRQQ 1
2  0
0 GMSKALVSNKSSLKEMPGASKLLKTRGPKQAQIPVPAPREPSTSEQHPRQKV 1
2  1
2                HGLPTLVKDCAVEKGHANHSALSLSPGSSIRPSGIPEAGLGVWNKVSDLLLGLHFGSYVGQITDDEEAAKSGYSWL 0
0  2
1 YVNGAQD KEQNLVAFLTHRQIFY TCRVVRPGCELLVWYRDTYSQELSIKCGSRWKSELTASR 1
2 PMCSCSLAFSSQKFLSQHVKCNHPSQILLKTSARDRLQPEDPCPGNPNQQQQYSDLHSWSDKPESRESKEKPQPLLKSIRLRRISRASSYSSRGQMGGFRVHKRMREEPSTGKEVSPEDAGKLFMGEGVSRIMR
VKYGDCG
GSKDRSSLMTHQRTHTGENP
YVCREYE.SFSEKSSLIKHQRTHTGEKP
YVCRECWQSFGRKSTLITHQRMHTREKP
CVCRECGRSFSKKSTLITHQRTHTGQKP

>PRDM9b_oviAri Ovis aries (sheep) genome Laur pseu 2 noDet chrX not tandem: 62 mbp separation
0 MSPNRSPENSTEGDAGRTEWKPM 0 
0 AKDAFKDISIYFTKEEWAEMGEWEKIRYRNVKRNYEALIAI 1
2 GFRATQPAFMHHHRQVIKPQVDDTEDSEEEWTPRQQ 1
2 GKPSGMAFRGERSKHQK 0
0 RLSRGPLNKVSSLKKLPGAAKLLKKTGSKQAQKPVPPPREARTPGQHPRHKV 1
2 ELRRKETEVKRYSLRERKGHVYQEVSELQDDDYL 1
2 yCEECQNFFIDSCAAHGPPTFVKDSAVEKGHANRSALTLPPGLSIRPSGIPEAGLGVWNEASDLPLGLHFGPYEGQVIYNEEASHSGYSWL 0
0 VTKGRNSYEYVDGKDTSLANWMR 2
1 YVNCARDDEEQNLVALQYHGQIFYRTCQVVRPGCELLVWYGDEYGEELGIKQDSRGKSKLSAQR 1
2 ELKPKIHPCASCSPAFSSQKFLSQYVQPNHPSQILLRPSARDHLQPEDPCPGNQNEQQ YSDPHSPSDKPEGCKAKERPPWLLKSMSVRISMASSYSPKGQMRGSETHYRMTEEPSTSQKLNPEDIGKLFMGTGVSGIIK
IKYEECGQVSKDRSSLITHEGTHTREQS
YVCRECGQSFSVKSSLIRLQRTHTGEKP
Y...........................

>PRDM9a_oviAri Ovis aries (sheep) genome Laur gene 9 noDet chrX not tandem
0 MSPNRSPENSTEGDAGRTEWKPM 0 
0 AKDAFKDISIYFTKEEWAEMGEWEKIRYRNVKRNYEALIAI 1
2 GFRATQPAFMHHHRQVIKPQVDDTEDSEEEWTPRQQ 1
2 GKPSGMAFRGERSKHQK 0
0 GMSRGPLSKVSSLKKLPGTTKLLKTSGSKQAQKPVPSSREARTSG HTRQKV 1
2 ELGRKETDMKRYSLRERKGHVYQEVSEPQDDDYL 1
2 yCQECQNFFINSCDAHGPPTFVKDSAVEKGHANRSALTLPPGLSIRLSGIPEAGLGVWNEASHLPLGLHFGPYEGQITDDKEAVNSGYSWL 0
0  2
1 YVNCARHYEEQNLVAFQYHGQIFYRTCQVVRPGCELLVWYGDEYGEKLGIRCESRGKSMLAAGR 1
2 EPKPKIHPCASCSLSFSSQKFLSQHVQRSHPSQILLRPSPRDHLQPEDPCPGKQNQQQRYSDPHSPSDKPEGQEPKERPHPLLKGPKLCIRLKRISTASSYTPKGQMGGSEVHEKMTEEPSTSQKLNPENTGKLFMEAGVSGIVR
VKYGEHEQGSKDKSSLITHERIHTGEKP
YVCKECGKSFNGRSNLTRHKRTHTGEKP
YVCRECGQSFSLKSILITHQRTHTGEKP
YVCGECGQSFSEKSNLTRHKRTHTGEKP
YVCRECGQSFSLKSILITHQRTHTGEKP
YVCRECGRSFSVKSNLTRHKMTHTGEKP
YVCGECGQSFSQKPHLIKHQRTHTGEKP
YVCRECGRSFSAMSNLIRHQRTHTGEKP
YVCRECGRSFSAMSNLIRHQRTHTGEKP
YVCREC......................

>PRDM9d_munMun Muntiacus muntjak (muntjac) AC216498 Laur gene 4 noDet frameshift exon 9 no syntenic loci; identities: 92%b 89%a 90%c
0 MRPNRSQEESTEGNAGRTERKPT 0 
0 GKDAFKDISVYFSKEEWEEMGEWEKIRYRNMKRNYEALIAI 1
2 GFRATQPTFMHHRRQVIKSQVDDTEDSDEEWTPRQQ 1
2 GKPSSMAFRVEHSKNQK 0
0 RMSRAPLSNESGLKELPGAAKSLKTSDSKQARNPVPHHRKARTPGQLPRQKV 1
2 ELRRKETGVKRYSLRERKGHVYQEVSEPQDDDYL 1
2 YCEECQNFFINSCAAHGPpTFVKDCAVEKGHANRSALTLPHGLSIRLSGIPDAGLGVWNKVSDLALGLHFGPYKGQITDNEEAANSGYAWL 0
0 ITKGRNCYEYVDGKDTSWANWMR 2
1 YVNCARDDEEQNLVAFQYHGQIFYRTCQVVRPGCELLVWYGDEYGQDFGIKRNSRGKSELAAGR 1
2 EPKPKIHPCASCSLTFSSQKFLSQHIQCSHPPQTLLRPSERDLLQPEDPCPGNQNQQQRYSDPHSPSDKPEGHEAKDRPQPLLKSIRLKRISRASSCSPRGQMGGSGVHERMTEEPSTSQKLNPGDTGTLLTGAGVSGIMK
VKYGECGQGSKDRSSLSTHERTHTGEKP
YVCRECGQSFSGKPVLIRHQRTHTGEKP
YVCMECGRSFSAKSVLMTHHRTHTGEKP
YICRECGQSFSQKIHLIRHQRIHTGE.P
SVFRECE.....................

>PRDM9c_munMun Muntiacus muntjak (muntjac) AC154919 Laur gene 15 noDet no syntenic loci AC204173 99% identical
0 MRPNRSPEESTEGDAGRTEQKPT 0 
0 AKDAFKDISVYFSKEEWEEMGDWEKIRYRNMKRNYEVLIAI 1
2 GFRATRPDFMHHRRQVIKPQVDDTEDSDEEWAPRQQ 1
2 GKPSSVAFRVEHSKHQK 0
0 RMSRAPLSNESGLKELPGAAKPLKTSGSKQAQNPVPHHRKARTPGQLPRQKV 1
2 ELRRKETGVKRYSLRERKGHVYQEVSKPQDDDYL 1
2 YCEKCQNFFIDSCAAHGPPTFVKDCAVEKGHANRSLLTLPPGLSIRLSGIPDAGLGVWNEASDLPLGLHFGPYEGQITDDEEAANSGYAWL 0
0 ITKGRDCYQYVDGKDTSWANWMR 2
1 YVNCARDDEEQNLVAFQYHGQIFYQTCQVVRPGCELLVWCGDEYGQDLGIKRNSRGKSELVAGR 1
2 EPKPKIHPCASCSLAFSSQKFLSQHIQRSHPSQTLLRPSERDLLQPEDPCPGNQNQRFSDPHRPSDRPQPLLKSIRLKRISRASSYSPRGQMGGSGVHELMTEEPSTSHKLNPEDTGTLLMGAGVSGIMR
VTYGECGQGSKDRSSLTTHERTYTGEKP
YVCGECGRSFCQKAHLITHQRTHTGEKP
YVCRECGQSFSRNSLLIRHQRIHTGEKP
YVCGECGRSFRDKSNLISHRRTHTGEKP
YVCGECGQSFSDKSNLIRHQRTHAGEKP
YVCGECGRSFNRKSHLITHQRTHTGEKP
YACRECGQSFSQKSILITHQRTHTGEKP
YACRECG.SFSQKSILITHQRTHTGEKP
YVCGECGRSFSQKSLLITHQRTHTGEKP
YVCMECGRSFSQKTHLITHQRTHTGEKP
YVCGECGRSFSQKSLLITHQRTHTGEKP
YVCGECGRSFSQKSLLITHQRTHTGEKP
YICMECGRSFSQKTHLITHQRTHTGEKP
YVCGKCGQSFSDKSNLISHKRTHTGEKP
YVCRECGRSFNRKSLLITHQRTHT.E.P
YVCRECE.....................

>PRDM9b_munMun Muntiacus muntjak (muntjac) AC218859 Laur gene 13 noDet no syntenic loci
0 MRPNTSPEESTEGDAGRTERKPT 0 
0 AKDAFKDISVYFSKEEWEEMGDWEKSRYRNMKRNYEVLIAI 1
2 GFRATRPDFMHHRRQVIKPQVDDTEDSDEEWAPRQQ 1
2 GKPSSMAFRVEHSKHQK 0
0 RMSRAPLSNESGLKELPGAAKPLKTSGSKQAQNPVPHHRKARTPGQLPRQKV 1
2 ELRRKETGVKRYSLRERKGHVYQEVSKPQDDDYL 1
2 YCEECQNFFIDSCAAHGPPTFVKDCAVEKGHANRSALTLPPGLSIRLSGIPDAGLGVWNETSDLPLGLHFGPYEGQITDDEEAANSGYAWL 0
0 ITKGRNCYQYVDGKDTSWANWMR 2
1 YVNCARDDEEQNLVAFQYHGQIFYRTCQVIRPGCELLVWYGDEYGQDLGIKRNSRGKSELATGR 1
2 EPKPKIHPCASCSLAFSSQKFLSQHIQRSHPSQTLLRPSERDLLQPEDPCPGSQNQRYSDPHSPSDKPEGQEAKDRPQQLLKSIRLKRISRASSYSPGGQMGGSGVHERMTEEPSTSQKLNPEDTGTLLTGAGVSGIMR
VTYGECWKGSKDRSSLTTHERTHTGEKP
YVCGECGQSFHHGSVLIRHQRTHTGEKP
YVCGECGRSFSQKSVLIRHQRTHTGEKP
YVCGECGRSFSQKSVLIRHQRTHTGEKP
YVCGECGRSFSQKAHLITHQRTHTGEKP
YVCGECGRSFSQKTHLISHKRTHTGEKP
YVCGECGRSFCQKSALIRHQRAHTGEKP
YVCGECGRSFIQKSDFIRHQRTHTGEKP
YVCRECGQSYSDKTVLITHERTHTGEKP
YVCGECGRSYSDKTVLITHERTHTGEKP
YVCGECGRSFLWKSALIRHQRTHTGEKP
YACGDCGRSFNQKSNFIRHQRTHTGEKP
YVCGECWRSFSQKSSSSDTRGHTQGRRP
VCRECG..SFSQKSHLISHQRTHTEEKP
YVCRECE.....................

>PRDM9a_munMun Muntiacus muntjak (muntjac) AC225653 Laur gene 7 noDet unordered contigs htgs; no synteny tag stop instead of aag K
0 MRPNRSPEESTEGDAGRTEQKPT 0 
0 AKDAFKDISVYFSKEEWEEMGEWEKIRYRNVKRNYEALIAI 1
2 GFRATRPDFMHHCRQVIKPQVDDTEDSDEEWTPRQQ 1
2 GKPSSMAFRVKHSKHQK 0
0 GMSRAPLIKESSLKELLGAAKLMKTSGSKQAQNPVPHPRKARTPGQHPRQKV 1
2 ELTRKETGVKRYSLRERKGHVYQEVSEPQDDDYL 1
2 YCEECQNFFIDSCAAHGLPTFVKDCAVEKGHANRSALTLPPGLSIRLSGIPDAGLGVWNEESDLPLGLHFGPYEGQITDDEEAANSGYAWL 0
0 ITKGRNCYQYVDGKDTSWANWMR 2
1 YVNCARDDEEQNLVAFQYHGQIFYRTCQVIRPGCELLVWYGDEYGQDLGIKRNSRGKSELAAGR 1
2 EPKPKIHPCASCSLAFTSQKFLSQHIQRSHPAQTLLRPSERNLLQPEHPCPGSQNQRYSDPHSLSDKPEGQEAKDRPQPLLKSIRLKRISRASSYSPGGQMGGSGVHERMKDEPSTSQKLNPEDTGTLLTGAGVSGIMR
VTYGECGKGSKDRSSLTTHERTHTGEKP
YACRECGRSFRQKSDFITHQRTHTGEKP
YVCGQCGRSFGRKFALIRHQRIHTGEKP
YVCRECGQSFSQKTHLSSHQRTHTGEKP
YVCGECGRSFSQKSVLIRHQRTHTGEKP
YVCQECGRSFSDKSNLISHKRTHMGEKP
YVCRECGRSFIRKSVLIRHQRTHTGE.P
YVCRECE.....................

>PRDM7_bosTau Bos taurus (cattle) genome Laur pseu -- GAS8+ missing C2H2
0 MSPNRSPEESIEGDTGRTEWKPT 0 
0 AKDAFKDISIYFCKEEWAQMG WEKIRYRNVKRNYEALITL 1
2  1
2  0
0  1
2  1
2  0
0  2
1  1
2 

>PRDM7_turTru Tursiops truncatus (dolphin) ABRN01441536 Laur gene 9 gas8+ no useful synteny
0 MSTDRWPEDSTEGDAGRTAWKPT 0 
0 VKDAFKDISIYFSKEEWTEMGEWEKIRYRNVKKNYEALVTL 1
2 GLRAPRPAFMCHRRQAIKAQVGDPEDSDEEWTPRQQ 1
2 VKPSWVAFRVEHSKHQK 0
0 AVPPVPLSNESSLKKLPGAAQLQKASGPAQAQSPAPPPGAASTSAWHTRQKL 1
2 ERRAKQIEVKMYSLRERKGHVYQEVSEPQDDDYL 1
2 yCEKCQNFFIDSCAAHGAPTFVKDSAVEKGHPNRSALTLPPGLSIRPSGIPEAGLGVWNEASDLPLGLHFGPYEGQITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDTSWANWMR 2
1 YVNCARDEEEQNLVAFQYHRQIFYRTCRVVRPGCELLVWYGDEYSQELGIPWGSGWKSQLVaGR 1
2 DPKPKIQPCGSCSLAFSSQKILSQHVECSHPSQVLPRTSARDRVQPEDPCPGYQNRQQQYSDPHSWSNKPECQEVKERSKPLLKRIRLGRISRAFSSSPKGQMGSSRAHERMMEAGPSTGQKVNPEATGKLLIGAGVSRVVK
VKYRSSGQGSKDRSSLTKHQRTHTGEKP
YVCGECGRDFSLKSDLIRHQRTHTGEKP
YVCGECGRDFSLKSGLISHQRTHTGEKP
YVCGECGRDFSQKSGLIRHQRTHTGEKP
YVCGECGRDFSLKSGLISHQRTHTGEKP
YVCGECGRDFSQKSGLIRHQRTHTGEKP
YVCGECGRDFSLKSGLITHQRTHTGEKP
YVCGECGRDFSQKSNLITHQRTHTGEKP
YVCGECGRDFSRKSSYI...........

>PRDM7_susScr Sus scrofa (pig) FP476134 Laur gene 9 GAS8+ unordered HTGS not wgs misassembly or inversion; not in genome browser
0 MRPDRRPEESPDPAAGSTERKAA 0 
0 ATDAFKDISIYFSKEEWTEMGEWEKIRYRNVKRNYEALTTI 1
2 GLRAPRPAFMCHRRQAIKPQVDDTEDSDEEWTPRQQ 1
2 VKPCRVAFRVEHNKHQK 0
0 SDSRVPLSNKSSLKELLTTAEVPETSGSEQAQEPVSPPGEASTSRRRSGQEL 1
2 ARRRKDTEARMYSLRERKGHAYQEVGEPQDDDYL 1
2 yCEKCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALTLPPGLRIRPSGIPEAGLGVWNEAHDLPLGLHFGPYEGQVTEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDKSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVVRPGCELLVWYGDEYGQELGIKWGSKWKKELTAGI 1
2 EPKPKIHPCPSCSLAFSSQRFLSQHVERSHPSQSLPRASARRGLQPEGPCPDNQQQQQPYPDPHSWDGTSESQDVKEGSKPFLERRRLRKTSRASSYAPEGQMRSSRVRERMTEEEPSAGQKVNPEDTGTLFTVAGES
GILRVENRGYGPDSGLTRHPRTHTGEKP
HVCSECGRGFSVKSHLIRHQRTHTGEKP
YVCRECGRGFSVKSHLIRHQRTHTGEKP
YVCRECGRGFSVKSSLITHQRTHTGEKP
YVCRECGRGFSVKSHLIRHQRTHTGEKP
YVCRECGRGFSEKSSLVTHQRTHTGEKP
FVCRECGRGFSVKSSLVTHQRTHTGEKP
YVCRECGRGFSVKSNFITHQRTHTGEKP
YVCRECGRGFSEKSSLVTHQRTHTGEKP
YVCREGE.....................

>PRDM7_canFam Canis familiaris (dog) genome Laur pseu 5 GAS8+ frameshift fixed to 6 ZNF; synteny MNS1 K1F1B intervening CDH3 oddity
0  0 
0  1
2  1
2 VKPSWVAFRMEQSKHQK 0
0 GIPRVPLSNKSSLKELSETAKLLNTSSPEQGQKSVSLPGKASTSGHHTRQKL 1
2 ELRRKDVEVKMYSLQERKGLAYQEVSEPQDDDYL 1
2 yCEK QTFFIDSCTVHGPPTFVKDSEVDKGQPNHSALTLPPGLRIRTSSIPQAGLGVWN ASDLPLGLHFGPYKGQITEDEEAANSGYSCL 0
0 ITKGRNCYEYVDGKDkSWANWMR 2
1 YMNCARDDEEQS LVAFQYHRQIFYRTPGHQASCELLVWYGDEYSQELGIKWGSKWKSELTAGK 1
2 EPNPEIHPCPSCSL AFSSQKFLSQHLEHNHPSQILPRISVREHFRPKDPCPGCQNQQQQQHSDPQRWNDRAKGQEGKERFKPLPKSIRQRRISRAFSTPCKGQTTCEGIVKEEPSAGSQKLNPEDTGKLFKGVGMTRIIR
VKYRGCGRGFNDRSHLSRHQRTHTGENP
YVCRECGRGFIHRTNLIIHQRTHTGEKP
YVCRECGtGFIQRSNLSIHQRTHTGEKP
YVCRECGRGFTQRSTLNEHQRTHTEEKP
YVCRECGRSFTRRSTLITHQRTHTGEKP
YVCRECGRSFT.................
KRSTWDPWVAQRFGACLWP.........

>PRDM7_felCat Felis catus (cat) genome Laur gene 11 GAS8+ two contigs GAS8 implied by downstream CAD1
0 mSPLRFPEQSAERGSRKARWKPT 0 
0 AKDAFKDISIYFSKEEWTEMGDWEKIRYRNVKRNYEALMTI 1
2 gLRAPRPAFMCHRRQAIKPQVDVTEDSDEEWTPRQQ 1
2 VKPSWVASRVDQNKQHK 0
0 GTHRVPLSKESSLKDFSETAKLLNTSGSEQGQKPVSLPGEASTSGHHSRRKL 1
2 frRRKEIGVKMYSLRERKGFAYQEVSEPQDDDYL 1
2 yCEKCQNFFIDSCAVHGPPTFVKDNAVGKGHPNRSALTLPPGLRIRPSSIPEAGLGVWNEASDLPLGTHFGPYEGQITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDNSWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKSELSTGK 1
2 EPQPDIHRCPSCSLAFSSQKFLSQHVECKHSSQSLPQISARKHFQPENPCPGDQNQQQQQHSDPHSWNDKAKCQEVKERSRPLLKSIKQRRISRAFSTPCKGQMGSSRVCEGMVEEGPSMGQNLNSEDTGKLFMGVGMSRIVR
IKNRGCEQGFNDRSHFSRHQRTHKEEKP
SVCNEFRRDFSHKSALITHQRTHTGEKP
YVCRECGRGFTQRSNLFRHQRTHTGEKP
YVCRECGRGFTQRSDLFTHQRTHTGEKP
YVCRECGRGFTRRSNLFTHQRTHTGEKP
YVCRECGRGFTRRSHLFTHQRTHTGEKP
YVCRECGRGFTQRSNLFTHQRTHTGEKP
YVCRECGRGFTQRSDLFRHQRTHTGEKP
YVCRECGRGFTQRSHLFTHQRTHTGEKP
YVCRECGRGFTQRSNLFRHQRTHTGEKP
YVCRECGRGFTWRSNLFTHQRTHTGEKP
YVCRKDGQGFTNKLHL.SYQRT......
NVATTHSIPQL.................

>PRDM7_ailMel Ailuropoda melanoleuca (panda) GL193502 Laur gene 6 GAS8+ first three exons from different contig
0 MSLNTSPEETPERDSGRTGWKPT 0 
0 AKDAFKDISIYFSKEEWTEMGDWEKIRYRNVKRNYEALITI 1
2 GLRAPRPAFMCHRRQAIKPQVDDTEDSDEEWTPRRQ 1
2 VRPSWVAFRMEQSKHQR 0
0 GIPRAPLRNESSLKELSETAKLLNTSGSELGQKPVSLPGEASTSGHDSLQKL 1
2 GFRRKDVEVKMYSLRERKSLAYQEVSEPQDDDYL 1
2 yCEKCQNFFIDSCAVHGPPTFVKDSAVDKGQPNRSALTLPPGLRIRPSGIPQAGLGVWNEASDLPLGLHFGPYEGQITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDNSWANWMR 2
1 YVNCARDEEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKSELAAGK 1
2 EPKPEIHPCPSCSLAFSSQKFLSQHLEHNHPSQILSRKSASEHFQQEDPCPGHQNQQQQQHSDPHRWNDKAKGQEVKERFKPLLKSIRQRRISRAFSSPCKGQTRSSTVCEGMVEEEPSAGQKLNPEETGKLFMGVGMSGIIR
VKYRGCGRDFSDRSHQSGHQRRHQ
KKP
SVCKKVKREFSHKSVLITHQRTHTGEKP
YVCRECGRGFTQRSNLIRHQRTHTGEKP
YVCRECGRGFTQRSNLIRHQRTHTGEKP
YVCRECGRGFTQRSSLIRHQRTHTGEKP
YVCRECGRGFTLRPNLIGHQRTHTEALP
INYISTTKEQM.................

>PRDM9_pteVam Pteropus vampyrus (bat) ABRP01232219 Laur pseu 15 noDet frameshift ttt to tttt fixed in last zinc finger; no blastx synteny
0  0 
0  1
2  1
2 vQPSWVAFGVEQSKHQK 0
0 AMPRVPLSNESSLKELSVIANPLKASGSEQNQQPVFPPGKASASRQHSRRKL 1
2 eLRRKGVEVKMDSLRERMGRVYQEVSEPQDDDYL 1
2 yCEKCQNFFIDSCAAHGSPIFVKDSEVDIGHPNHSALTLPPGLRIGPSGIPEAGLGVWNEASNLPLGLLFGPYEGQVTEDEEAANSKYSwM 0
0 spKGETAEYV DGKDESRANWMR 2
1 YVNCARDDEDQNLVAFQFRRQIFYRTCRVIMPGCELLVWYGDEYGQGLGIKWGSKWKREFTAGR 1
2 EPKPEIHPCPSCSLAFSSRKFLSQHMKRSHPSQSLPGISARKHLQSKEPHPEDQSQQQQQQQHTDPCSWNDKAEGQEVKERSKPMLERNGQRKISRAFSKPPKGQMGSPRECERMMEAEPSTSQKVNPENTGKSSVGVGASRIVR
VKYGGCGHGFDDGSHFIRHQRTHSGEKP
FVCRECERGFNEKSSLTMHQRTHSGEKP
FVCREC.EGFSVKSSLIRHQRTYSGEKP
FVCRECEQGFNEKSSLTMHQRTHSGEKP
FFCRECEGFSVK.SSLIRHQRTHSGQKP
FVCRECKRGFTQKSHLITHQRTHSGEKP
FCRECER.GFTQKSHLIKHQRTHSGEKP
FVCRECA.....................

>PRDM7_pteVam Pteropus vampyrus (bat) ABRP01250178 Laur gene 7 GAS8+ 4 distal exons of GAS8+-; unique F sweep in zinc finger; 15 ZNF dotplot no CAD1
0 MRPDRSPEEAPEGDTRRTGCKPK 0 
0 AKDAFKDISIYFSKEEWTEMGDWEKIRYRNVKRNYDALQAI 1
2 GLRAPRPAFMCRRRQAIKPQVDDSEDSDEEWTPRQQ 1
2  0
0 AMPRVPLSNEPSLKELSVIANLLKASGSEQDQKPVFPPGKASASRQHSRQKL 1
2 GLRRKGVEVKMYSLRERTGRVYQEVSEPQDDDYL 1
2 yCEKCQNFFIDSCAAHGSPIFVKDSEVDIRHPNRSALTLPPGLRIGPSGIPEAGLGVWNEASDLPLGLLFGPYEGQVTEDEEAANSGYSWL 0
0 QGKGRNCYEYVDGKDESRANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKRELTAGR 1
2 EPKPAIHPCPSCSLAFSGQKFLSQHMKRSHPSQSLPGISARKHLQSKEPHPEDQSQQQHNDPRSWNDKAEGQEVKERSKPLLERNRQRKIFRAFSKPPKGQMGSPREYERMMEAEPSTSQKVNPENTGKSSVGVGASRIVI
VKYGGCEHGFDDGSHLIMHQRTHSGEKP
FVCRECERGFSKKSNLITHQRTHSGEKP
FVCRECERGFTRKSSLITHQRTHSGEKP
FVCRECERGFTQKSHLITHQRTHSGEKP
FVCRECERGFSEKSSLIKHQRTHSGEKP
FVCRECERGFTRKSSLITHQRTHSGEKP
FVCRECERGFTQKSSLIKHQRTHSGEKP
FVCRECERGFTQKSSLIKHQRTHSGEKP
FVCRECERGFTQKSSLIKHQRTHSGEKP
FVCRECERGFTQKSSLITHQRTHSGEKP
FVCRECERGFTQKSHLITHQRTHSGEKP
FVCRECERGFSKKSNLITHQRTHSGEKP
FVCRECERGFTRKSLLITHQRTHSGEKP
FVFRECERGFTQKSSLITHQRTHSGEKP
FVCRECERGFTRKSYLITHQRTHSGEKP
FVGRECE.....................

>PRDM7_myoLuc Myotis lucifugus (bat) AAPE02062260 Laur gene 6 gas8+ TGA stop codon; CpG hotspot for R CGA; SXXRD implies missing KRAB no CAD1
0  0 
0  1
2  1
2  0
0 AKSRAPLSNESSLKELSGTANLLTTSGSEQTQKTVPPPGEASTSGQHPRSKL 1
2 dLRRKEIEVKMYSLRERKCRVYQEISEPQDDDYL 1
2 YCEKCQNFFIDSCAVHGPPTFVKDSAVDKGHANRSALTLPPGLRIGPSGIPEAGLGVWNEECDLPVGLHYGPYEGQITEDEAIANSGYSWL 0
0 ITKGRNCYEYVDGKDTSQANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVVRKGCELLVWYGEEYGQELGIKWGSKWKTEPVAGR 1
2 EPKPEIHPCPSCSVAFSSQTFLSQHGKRNHPSEILPGAPAGNHLQSEEPGPERQNQQQQQQTGPHGWNDKAEGQEVKGRSKPLLKRIRQRGTSRASFKPPNRHMGSSSERERIREEEPSTGQNVNHKNTGKLFVGVKRSKSVT
IKHGGCGQGFNDGSHIDTHQRTHSGEKP
YICRECGGFTHKSDL.IRHQRTHSQENP
YVCRECGRGFRDRSTLITHQRTHSGEKP
YVCRECGRGLTEKSTLITHQRTHSGEKP
YVCRECGRGFTRKSTLITHQRTHSGEKP

YVCRECGRGSRVKSNLIRHQRTHSGEK
SGVCIEGE....................

>PRDM7_equCab Equus caballus (horse) genome Laur gene 4 GAS8+ missing front exons, pre-terminal stop GAS8+- flanked right by EMR2-
0  0 
0  1
2  1
2 VKPSWVAFRVEQSKQQK 0
0 RMRTAPLSNESRLKELSGTAKLLKTSSSEQVQKPVSPLGEASSSEQHSRRKL 1
2 ELRRKEVGVKMYSLRERKGHAYQEVSEPQDDDYL 1
2 yCENCQNFFIDSCAAHGPPIFVKDSAVDKGHPNRSALTLPLGLRIRPSGIPEAGLGVWNEASDLPLGLHFGPYEGQITEDEEAANSGYSWL 0
0 ITKGRNCYEYVDGKDISWANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVVRPGCELLVWYGDEYGQELGIKWGSKWKRELTAGR 1
2 EPKLEIHPCPSCSLAFSSQKFLSQHVERNHPSQILPGTSARNHLQPEDPSPGDQNQQQQHSDPHSWKDKAHSQEVKERSKPLLKKIRQRRIPRAFSYPPKGQMENFRMRERIMEEKPSIGRKVNPEDTGKLFLEMRMSRNVR
VQYGGCGRGFNDRASLIKHQRTHTGEKP
YVCRECEQGFTQKSSLIAHQRTHTGEKP
YVCRECEQGFSEKSHLIRHQRTHTGEKP
YVCRECEQGFSVKSNLIRHQRTHTGEKL
.FCREGK.....................

>PRDM7_sorAra Sorex araneus (shrew) AALT01000095 Laur gene 8 noDet no useful synteny; upstream spectrin, IgG; GAS8 contig has no sign of pseudogene
0 MSLNRPAEMNTQGKARKLMLKPM 0 
0 SKDAFKDISMYFSKEEWAEMGDWEKIRHRNVKRNYEELISI 1
2 GLRAARPAFMSHRRQAIKTQLDDTEESDEEWTPNQQ 1
2 VKSLRVAFRAEQSKHQK 0
0 GRSRTPISNESSSKELSGTRTLLNTKCTKQAQKPLFPPGEASTSGHYSKPKL 1
2 ELRRKEPEVKMYSLRERKGRAYQEVSEPQDDDYL 1
2 YCENCQNFFINKCSAHGSPIFVKDNAVAKGHSNRSALTLPHGLRIGPSGIPEAGLGIWNEASDLPLGLHFGPYEGQITNDEEAANSGYSWL 0
0 ITKGRNCYEYVDGVDESLANWMR 2
1 YVNCARDYEEQNLVAFQYHRQIFYRTCRIIKPGCELLVWYGDEYGQELGIKWGSKWKSELTADK 1
2 EPKPEIYPCPCCSLAFSNQKFLSRHVEHSHPSLILPGTSARTHPKSVNFCPGDQNQWQQHSDACNDKPDEPWNDKLENHKSKGRSKPLPKRMGQKRISTAFPNLRSSKMGSSNKHETIMDKINTGQKENPKDTYRVFAGIGMPRIIR
DKHVTLRRSFTNRSSPLTHQRTHTGEKP
YVCRECGRGFSQKSHLLTHQRTHTGEKP
YVCRECGRGFTDRSSLLTHQRTHTGEKP
YVCRECGRGFSLKSSLLRHQRTHTGEKP
YVCRECGRGFSLKSSLLTHQRTHTGEKP
YVCRECGRGFTDRSSLLTHQRTHTGEKP
YVCRECGRGFSLKSSLLTHQRTHTGEKP
YVCRECGRGFSRKSSLLRHQRTHTGEKP
YVCES.......................

>PRDM9a_loxAfr Loxodonta africana (elephant) genome Afro gene 12 noDet chr 153 novel synteny THEG+ MIER2+ PPAP2C PRDM9- ZNF699-
0 MSPARAAKKNPRGDVGSAGRTPT 0 
0 aKDTFRDISIYFSKEEWAEMGEWEKFRYRNVKRNYEALVTI 1
2 GLRAPRPAFMCHRRQAIKAQVDNTEDSDEEWTPRQQ 1
2 VKPPSVASRAEQSRHQK 0
0 GTPKALLGNESSLKEVSGTAILLNTTGSEQAQKPVSSPGEASTSDQPSRWKL 1
2 EPRRNEVEVKMYNLRERKGLEYQEVSEPQDDDYL 1
2 yCEKCQNFFIDTCAVHGAPMFVKDSPVDRGHPNHSALTLPPGLRIGPSSIPKAGLGVWNEASELPLGLHFGPYEGQVTEDKEAANSGYSWL 0
0 ITKGKNCYEYVDGKDESWANWMR 2
1 YVNCARDEEEQNLVAFQYHRQIFYRTCRTIQPDCELLVWYGDEYGQELGIKWGSRWKKELTSGR 1
2 EPKPEIHPCPSCRLAFSSQKFLSQHMKHSHPSPPFPGTPERKYLQPEDPRPGGRRQQRSEQHMWSDKAEDPEAGDGSRLVFERTRRGCISKACSSLPKGQIGSSREGNRMMETKPSPGQKANPEDAEKLFLGVGTSRIAK
VRCGECGQGFSQKSVLIRHQKTHSGEKP
YVCGECGRGFSVKSVLIKHQRTHSGEKP
YVCGECGRGFSVKSVLITHQRTHSGEKP
YVCGECGRGFSVKSVLITHQRTHSGEKP
YVCGECGRGFSQKSDLIKHQRTHSGEKP
YSCRECGRGFSRKSVLITHQRTHSGEKP
YVCGECGRGFSQKSNLITHQRTHSGEKP
YVCGECGRGFSRKSVLITHQRTHSGEKP
YVCGECGRGFSQKSNLITHQRTHSGEKP
YVCGECGRGFSQKSDLITHQRTHSGEKP
YVCRECGRGFSRKSNLITHQRTHSGEKP
YVCRECRRGFSVKSALI...........
GHGRRKCSKSAEPLHFPRVSRDQK....

>PRDM9b_loxAfr Loxodonta africana (elephant) genome Afro pseu 3 noDet approx seq after frameshift correction
0  0 
0  1
2  1
2  0
0 GTPKVLLSNESSLKEVSGTAILLSTMGSEQAQKPVSSPGEASTSDQPSRRKQ 1
2 EPRRKEVEVNMYSLRERKGLVYQEVGEPQDDDYL 1
2 yCEKCQNFFIHTCAVHGAPMFVKDSHVDRGHLNHSALTLPPGLRIGPSSIPEAGLRVR EVSEQLLGLHIGPYEGQVTEDkEAAHSGYSWL 0
0 ITKGRNCYKYVDGKDDPWANRMR 2
1 YVNCIQD KEQNLVAFQYHRQIFHWTCCTIRPGCELLVWYGDNYSQELGIKWGSR KKEL     1
2 EPKPEIHPCPSCPLAISSQKFLDQHTKHSHPSPPFPGTPERKHLQPEDPHPGGRRQQHSEQHLNDKAEDPETGDGSKPVFERARLVGGGAGGVSKVCSSLPKGQMGSSREGNRMMETEGQKVNPEDTEKLFLGVGISRLAK
VRCGEYGQGFSQKSVLIRHQRTYSGEEH
YVCGECGRGFSWKSQLTRHQRSHSWEKP
YVCRECGGFSVKSTLI............
GTGEGNAATIHLHLPS............

>PRDM7_loxAfr Loxodonta africana (elephant) genome Afro pseu 5 GAS8+ scaffold_57 several frameshifts; ZNF540 opposite strand upstream of N-terminus
0  0 
0  1
2 GLRASHPAFTCHCMQAIKAQMDDTEDSNEEQTPRQq 1
2 VRPSWVAFRMEQSKHQR 0
0 GMLRVPRSNESSLKNLSGTSIMLSRAGSEQAQKLVLPPGKASTSDEHSRQKP 1
2 EHRRKGVEVKMYSF ERKGLVYQEIS PQDDDYL 1
2 YCEKCQNFFIDTCESHGVPTFVKNSTTDSGHPNHLALTPSSGLRTRPSSIPKAWLRLWNKAFELLLGLPFSPCEGQVIEDEAVDNSGYSWL 0
0  2
1 YVNGTQDEKEQNLVFFQYHRQIFYQTCYAVWPGCQLLVWYRDECGQELGIKWDNRGKKEFe    1
2 EPKPEAHPCPSCPLAFSSEKFLSQHMKHNHPSQSSPETPERKHLQPEDPHPGHQNQQQQQHSDPHRWNDKAEGQQTGDRSKPMFENIRQEVTSRAFSSLPKGQMVCSREGNRMMETEPSPGLKVNPEVTGKLFLGVESSRIAK
VKYRGCGRDFSDRSHQSGHQRRHQ
KKP
SVCKKVKREFSHKSVLITHQRTHSGEKS
YVCKESGRGFSAKSNLIRPRRTHTGEKP
YVCGERGG.FSVSGLII.HQRAHSPEKP
YVCREGRRGFGDKSSFIKHQRATLGEKS
YVCKESGRGFS.................
AKSNLIRPRRKKCRHDTTPHPQL.....

>PRDM7_echTel Echinops telfairi (tenrec) genome Afro pseu 5 noDet 2 frameshifts plus stop codon
0  0 
0  1
2 GLRAPRPAFMCHHRPAAKGQVEDSEDSDEEWTPRQR 1
2  0
0 GMPGVSLRNESNLKVLSGTAILLTAAEPEQPH PGSPPGEATTSHEHLRQKV 1
2 epELRRRAVMMNSLRERKNLMYQEVSTPCDDNCL 1
2 YGERCHNFFIDTHIAHGATTFVKDS    PMDRSNCSILPPGLRIGPSGIPEAGLGVWNEASELPLGLHFVPYEGQVTKDEAATNSGYSWM 0
0 ITKGRNCYEYVDGKDKSWANwMr 2
1  1
2 EPKPEVNPCPSCPLALSSQQLKHSHPFQSLPGTPAEKHLQAEDFHPRGQKLHHFEHHIRNERAEGLETGDGSKPMLERTRLGKMSKTTYNSPKGQTRSSGETNRIREADLNPGQGVNAEDTRNLFLGIGISRIAK
VRCRECGHGFSVKSSLITHQRIHTGEKP
YVCSECGQGFSQKSVLIRHQRIHTGEKP
YICRECDRGFSRKSHLIKHQRTHSGEKP
YVCRECGQGFSQKSVLITHHRTHSGEKP
YVCRECGRGFSQKSDLIKHERTHS....

>PRDM7a_proCap Procavia capensis (hyrax) ABRQ01227339 Afro pseu 17 noDet frameshift and two stop codons in exon 10 
0  0 
0 AKDAFRDISIYFSKEEWAEMGEWEKSRYRNVKRNYEALVAI 1
2 GLRAPRPAFMCHRRQAIKAQVDNTEDSDEEWTPRQQ 1
2 AKPRSVASREELRKPQK 0
0 GTPKALLGNESSLKEVSGTAILLNTTGSEQAQKPVSSPGEASTSDQPSRWKL 1
2 EPRRKEAEVKRYNLREGTNPAYQEVGDTQDDDYL 1
2 yCEKYQKFCTDVCPAHGALAFLKDLSVERGHPKHSALTLPPGLRIGASGIPEAGLGVWSEASELPPGLHFGPCERQVTKDNEAANRGYLWP 0
0 ITKGRSCSLYMDRKDESRANWMR 2
1 YVRHAGDKEEQNLVAFQYHRQIFYRTCRPVQPGCELLVWPGAEDGQELGLQRGSRWKKELASQT 1
2 EARPEIHPCPSCPLAFSTPKFLSHHVKHSHPCQPFPGTLARRPLQPEDPHPGDRRQQHSEQPNWNDKAEGPEIGHVSRPVFEKTRQEGFSEARSSLPKGQMGRSREAERTTETQNSPGQKVNPEDTEILFLRGGISEIAK
VKCGECGQGFSRKSHLIRHQRTHSGMKP
YVCRECRRGFGVKSLLTRHQRTCSGMKP
YVCRECGQGFRWKSHLIRHQRTHSGEKP
FVCSECGRGFSVRSHLFTHQRTHSGEKP
YVCKECGRGFSVKSYLTTHQRTHTGEKP
YVCKECGRGFSWKSHLITHQRTHSGEKP
YVCRQCGRGFSVQSHLIIHQRTHSGDKP
YICRECGRDFTEKSSLIRHRRTHSGEKP
YVCRDCG*GFTRKSLLITHQRTHSGEKP
YVYRECGRGFSCKSYLISHQKTHLGEKP
YVCSDCGRGFSVKSQLVSHKRTHSGEKP
FVCREC*RGFSVKSSLISHQRTHSGEKP
FVCRECGRGFSVKSSLIKHQRTHSGEKP
YVCKECGRGFSQKSSLITHQRTHSGEKP
YVCRECGRGFGLKSYLITHQRTHTGEKP
YICRECG*GFSVKSSLITDQRTHTGEKP
YVCRECGRAFSKKSSLISHHRTHPAEAV 
YVHRECG.....................

>PRDM7b_proCap Procavia capensis (hyrax) ABRQ01392668 Afro pseu 13 noDet CpG stop in ZNF1, 4aa insert exon 4, frameshift exon 5 c to cc, 4aa del exon 9 etc
0  0 
0 AKEYFRDISMFFS*ERWVEMSESEKFCYRNMKRNCETTGAG 1
2 GIRVFHPAFMIHPRKTIKAQMDDSEDSDEDWTARQQ 1
2 AKPPSVASREELRKPQK 0
0 GPSRAPLRIKSSLKRVSEPAIVWSTADSEQAQERVQKPVLSRREASASDQPLRRKV 1
2 EPRRHEAEDKRYSLRGGTGPACQEVGEPQDDDYL 1
2 yCEECRNFFIDTCVAHGTPVFIKDISVERGHPNRLALTLPTGLRIGPSSIPDAGLGVWNEASELPPGLHFGPCEGQVTEDEEAANSGYSWL 0
0 VTKGRSCFEYVDGKNEALANWMR 2
1 YVRRARDTEERNLVAFQYHRQIFYRTCCTVRPGCELLVWRGAEDSQALG----SRRTMELTSQK 1
2 EARPEIHPCPSCPLAFSTQKFLSYHVNHSHSSEPFPGTHARRHLPREDPRPGYERDQRSEQHNWNDSTGGPERDVSRP VIERTWEGEISEACSSLPRGHMGRSREGERMAETQSSPGLKVTLAK
VRWDEYGQGFGPKSHHITQQTKHSGKKP
CVCKECG*GFRVKSLLKSHQMTHSGEKP
YVCRECGRGFSVKSTLITHQRTHSGEKP
YVCRECGRGFSVKSFLISHQRTHSGEKP
YVCRECGRGFSWKSGLITHQRTHTGEKR
YVCRECGHGFNRPSRLIRHQRTHSGEQP
YVCRECGHGFNRRSQLIRHQRTHTGEQP
YVCRECGQGFSGKSGLNRHQRTHSGEKP
YVYKECGRGFSVKSTLIKHQRGHSGEKP
YVCKECGRGFSRNSGLITHQRTHSGEQP
YVCRECGRGFNQKSGVISHQRIHSGEKP
FVCGECGRRFSWQSNLITHQRTHSGEKP
FVCRECGRGFSAKTSLINHQRIH*GKKP YVCRDGG*

>PRDM7_dasNov Dasypus novemcinctus (armadillo) AAGV020462211 9 xena pseu TRAPP 0  0
0 AQDAFRDISTYFSREEWAEMGRWEKLRYRNVKRNYEALLAI 1
2 GLRAPRPAFMCHRKQSIKPQVDDAEDSDEEWTPRQQ 1
2  0
0  1
2 EPRRKGIDVKMYSLRERKGLAYEEVSEPQDDDYL 1
2 yCEKCQNFFIDSCTVHGPPIFVKDSAVDKGHPNRSALTLPSGLRIGPSGIPEAGLGIWNEASDLPLGLHFGPYEGQVTEDEEAANSGYSWL 0
0 ITKGRNYYEYEDGKDKSWANWMR 2
1 YVNCAWDDKEQNLVAFQYHRQIFYRTCRTIRPGCELLVWYGDEYGQELGIKWGSKWKKEFMTGT 1
2 ELKPEIHPCPSCPLAFSSEKFLSQHVRRHHPSQSFPAACAREHFQPQNPRPRGEEQQQHSDQCGWKDKAEGQETENRPKPLFERIKPMGSPRAFYNPPRGQMRSSREGKRMMEIQPSQDQKMNSE RGQLFLGVGIFKTEV
IKFGENRQDFSDKSDHTSHQRTHTGEKP
YVCRECGRGFSNNSHLTRHQRTHTGVKP
YVCRECGQGFSVKPALTKHQRTHTVEKP
yVCSECG GFSVKSTLITHQRTHTGEKP
CVCRECGRGFNNKPDLTKHQRTHTGEKS
YVCRECG GFSVKSTLIIHQRTHTGEKP
YVCRECGRGFSEKSNLTVHQRTHTGEKP
YVCRECGRGFSEKSNLTVHQRTHTGEKP
YVCRECGRSFSVKSTLITHQRTHTVEKP
YVCMKSEVVVSNKSHLNSHRRMKCGHRT PPPPQL

>PRDM7_choHof Choloepus hoffmanni (sloth) ABVD01893961 2 xena gene noDet 0  0
0  1
2  1
2  0
0  1
2  1
2 ycekcQNFFFENCAAHGPPTLLKDSAVGQGRPKHSALVLPPGLRLGPSGIPEAGLGVWNEASDLPLGLHFGPYEGQVTEDEEATNSGYSWL 0
0 ITKGRNCYEYVDGKDKSCANWMR 2
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRAIRPGCELLVWYGDEYGQELGIKWGSKWKKELTAEK 1
2 GLKPEIHPCPSCPLAFSTEKFLSQHVQRNHPSQIFPVTYARKHLQPQDPRPGDQQQPQPHSDQCHCSDKAEDQETEKRSKPLFESTKQMGISRAYSSPPEGQMRSSREDKRTMEIEPSQDQKMNPEETRLFVGVGILKTAR
IKCGEYGQGFSVKPNLTTHQRTHTEEKP
YVCRECGRGFGQKPNLSRHQRTHTGEKP
YVCRECGRGFG.................

Other sequences of interest

The additional sequences below are not part of the curated placental mammal homolog set. The neanderthal genome is very far from having 1x sequencing coverage so the PRDM9 sequence below is simply derived from the human reference sequence using non-synonymous SNPs reported in the corresponding UCSC browser track. The changes in the zinc finger domain may be enough to create somewhat of a species barrier.

Terminal sequences for 9 species of murid rodents have limited value for comparative genomics because they do not even cover the entire terminal exon and their syntenic contexts (and thus homological relationships) were not established. The single individual sequenced may not be representative of the overall population in the zinc finger region (based on the extensive diversity observed in human), diminishing their utility for predicting species barriers. These genes are most likely PRDM7 orthologs only secondarily related to the catarrhine primate PRDM9 set, ie descended from the unique locus present in stem euarchontoglires.

Although three marsupial genomes have been assembled, none contains an altogether persuasive full-length ortholog of the placental mammal PRDM7/PRDM9. The best available candidates are collected below but none of these provides a full set of expected domains (KRAB SSXRD SET C2H2) nor exhibit placental synteny. This could be attributed either to incomplete sequencing coverage, rapid divergence of early exons to the point of unrecognizability by bioinformatic techniques, absence of domains due to rapid evolution of the gene by domain shuffling and chromosomal rearrangement, gene loss in the marsupial clade, or gene creation from ZNF and PRDM shuffling in the placental clade.

The platypus genome provides a somewhat better antecedent -- indeed a tandem pair -- but here too no KRAB domain is evident. The distinctive phase 2 terminal exon exists but lacks the early ZNF. Transcripts could finalize the gene model but these are all but non-existent in monotremes (and marsupials). The two platypus genes may simply be closely related ZNF genes, descended from an ancestral ZNF gene that contributed to the placental mammal PRDM7 region. However the ZNF family has expanded greatly in some lineages and correspondence between specific genes across mammalian branches is problematic, a situation reminiscent of olfactory genes.

Because birds, lizard and frog utterly lack relevent homologs, the zebrafish gene put forward as an ortholog to placental mammal PRDM9 is implausible. It lacks counterparts in other species of fish with determined genomes and most likely represents an independent gene shuffle that resulted in a similar concatenation of domains (parallel evolution). It lacks a KRSB domain and the ZNF region is highly chaotic. An even more preposterous candidate for PRDM9 orthology in the mollusc Lottia likely has the same origin. There is no basis for believing parallel-evolved genes in these species function in meiosis or illuminate the mammalian situation in any way.

Finally, certain closely related placental ZNF and PRDM genes may have some connection to the origin of PRDM7 and PRDM9. Overall nomenclature is very unsatisfactory in both gene families, as can be seen from lack of correspondence in intronation (which is exceedingly well conserved in metazoa). HKR1, a conventional ZNF family member, is egregiously misnamed. The methylase component is exceedingly old with clear antecedents in bacteria. Multiple gene copies in genome of the early stem eukaryote were subsequently intronated differently and incorporated into various larger proteins. PRDM7 may best be viewed as a ZNF gene with an intercalated SET domain.

>PRDM9_homNea Homo neanderthalus (neanderthal) gene genome CDH12- CDH10- chr5 C2H2 variants R HDL S R
0 MSPEKSQEESPEEDTERTERKPM 0  
0 VKDAFKDISIYFTKEEWAEMGDWEKTRYRNVKRNYNALITI 1 
2 GLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQ 1 
2 VKPPWMALRVEQRKHQK 1  
0 GMPKASFSNESSLKELSRTANLLNASGSEQAQKPVSPSGEASTSGQHSRLKL 1 
2 ELRKKETERKMYSLRERKGHAYKEVSEPQDDDYL 1 
2 YCEMCQNFFIDSCAAHGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPYEGRITEDEEAANNGYSWL 0 
0 ITKGRNCYEYVDGKDKSWANWMR 1  
1 YVNCARDDEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGR 2 
2 EPKPEIHPCPSCCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQPENPCPGDQNQEQQYPDPHSRNDKTKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSCRVGKRIMEEESRTGQKVNPGNTGKLFVGVGISRIAK
VKYGECGQGFSVKSDVITHQRTHTGEKL  
YVCRECGRGFSWKSHLLIHQRIHTGEKP  
YVCRECGRGFSWQSVLLTHQRTHTGEKP  
YVCRECGRGFSRQSVLLTHQRRHTGEKP  
YVCRECGRGFSRQSVLLTHQRRHTGEKP  
YVCRECGRGFSWQSVLLTHQRTHTGEKP  
YVCRECGRGFSWQSVLLTHQRTHTGEKP  
YVCRECGRGFSNKSHLLRHQRTHTGEKP  
YVCRECGRGFRDKSHLLRHQRTHTGEKP  
YVCRECGRGFRDKSNLLSHQRTHTGEKP  
YVCRECGRGFSNKSHLLRHQRTHTGEKP  
YVCRECGRGFRNKSHLLRHQRTHTGEKP  
YVCRECGRGFSDRSSLCYHQRTHTGEKP 

>PRDM7_musCas Mus musculus castaneus ADA68112 terminal fragment 
 ESKRTVEELRTGQTTNTEDTVKSFIASEIS
SIERQCGQYFSDKSNVNEHQKTHTGEKP
YVCRECGRGFTAKSNLIQHQRTHTGEKP
YVCRECGRGFTQKSVLIQHQRTHTGEKP
YVCRECGRGFTQKSDLIKHQRTHTGEKP
YVCRECGRGFTARSNLIQHQRTHTGEKP
YVCRECGRGFTQKSDLIKHQRTHTGEKP
YVCRECGRGFTAKSNLIQHQRTHTGEKP
YVCRECGRGFTEKSSLIKHQRTHTGEKP
YVCRECGWGFTAKSNLIQHQRTHTGEKP
YVCRECGRGFTQKSSLIKHQRTHTGEKP
YVCRECGRGFTAKSNLIQHQRTHTGEKP
YVCRECGWGFTQKSNLIKHQRTHTGEKP
YVCRECGWGFTQKSDLIQHQRTHTREK*

>PRDM7_musSpi Mus spicilegus 281398541 terminal fragment 
 ESKRTVEELRTGQTTNTEDTVKSFIASEIS
SIERQCGQYFSDKSNVNEHQKTHTGEKP
YVCRECGRGFTQKSNLIQHQRTHTGEKP
YVCRECGRGFTQKSNLIQHQRTHTGEKP
YVCRECGRGFTAKSDLIKHQRTHTGEKP
YVCRECGRGFTVKSHLTQHQRTHTGEKP
YVCRECGRGFTQKSDLIKHQRTHTGEKP
YVCRECGRGFTAKSHLTQHQRTHTGEKP
YVCRECGRGFTQKSNLIQHQRTHTGEKP
YVCRECGRGFTAKSNLIKHQRTHTGEKP
YVCRECGRGFTQNSHLTQHQRTHTGEKS
YVCRECGWGFKQKSDLIQHQRTHTREK*

>PRDM7_micAgr Microtus agrestis ADA68122 terminal fragment
ESKKTMEEELRTEQKTNTEDAVRSFIGSEIS
RVGGERGQCFSDKSNVNEHQRTHTGEKP
YVCRECGRGFTRKSNLNVHQRTHTGEKP
YVCRECGRGFTRKALLISHQRTHTGEKP
YVCRECGRGFTQKALLISHQRTHTGEKP
YVCRECGRGFTQKSYLILHQRTHTGEKP
YVCRECGRGFTGKSNLNVHQRTHTGEKP
YVCRECGRGFTQKSYLILHQRTHTGEKP
YVCRECGRGFTGKSLLIRHQRTHTGEKP
YVCRECGRGFTQKSYPILHQRTHTGEK*

>PRDM7_arvTer Arvicola terrestris ADA68121 terminal fragment
ESKKTMEEELRTDQKTNTEDAIKSFIGSEVS
RVEGECGQCFNDKSNVNERQRTHTGEKP
YVCRECGRGFTRKSVLILHQRTHTGEKP
YVCRECGRGFTQKSVLINHQRTHTGEKP
YVCRECGRGFTQKSHLIFHQRTHTGEKP
YVCRECGRGFTQKSHLILHQRTHTGEKP
YVCRECGRGFTWKSVLILHQRTHTGERP
YVCRECGRGFTRKSHLILHQRTHTGEKP
YVCRECGRGFTQKSHLILHQRTHTGEKP
YVCRECGRGFTRKSVLILHQRTHTGEKP
YVCRECGRGFTRKSVLINHQRTHTGEK*

>PRDM7_perPol Peromyscus polionotus ADA68120 terminal fragment
ESKKTMEEALRTGQKTNTKDTVKSLIGSEFS
RIETECGQRFSDKSNVNESQRTHSEEKP
YVCRECGQGFIQKSVLICHQRTHTGEKP
YVCRECGQGFTWKSHLIRHQRTHTGEKP
YVCRECGKGFIRKSHLICHQRTHTGEKP
YVCRECGQGFIQKSHLICHQRTHTGEKP
YVCRECGQGFTQKSVLICHQRTHTGEKP
YVCRECGQGFIRKSYLICHQRTHTGEKP
YVCRECGKGFTWKSVLIRHQRTHTVEK*

>PRDM7_perMan Peromyscus maniculatus ADA68119 terminal fragment
ESKKTMEEELRTGQKTNTKDTVKSLIGSEIS
RTETECGQHFSDKSNANESQRTHSEEKP
YVCRECGQGFTWKSVLIRHQRTHTGEKP
YVCRECGQGFTWKSVLICHQRTHTGEKP
YVCRECGQGFTWKSVLICHQRTHTGEKP
YVCRECGQGFIQKSHLIRHQRTHTGEKP
YVCRECGQGFIRKSHLICHQRTHTGEKP
YVCRECGQGFAQKSVLIYHQRTHTGEKP
YVCRECGQGFTRKSHLICHQRTHTGEKP
YVCRECGQGFAQKSVLICHQRTHTGEKP
YVCRECGQGFTWKSVLICHQRTHTGEKP
YVCRECGQGFIQKSHLIRHQRTHTGEKP
YVCRECGQGFIQKSHLIRHQRTHTGEK*

>PRDM7_perLeu Peromyscus leucopus ADA68118 terminal fragment
ESKKTMEEALRTGQKTNTKDTVKSLIGSEIS
RIETECGQRFSDKSNANESQRTHSEEKP
YVCRECGQGFTRKSYLICHQRTHTGEKP
YVCRECGQGFIQKSVLIRHQRTHTGEKP
YVCRECGQGFTRKSYLICHQRTHTGEKP
YVCRECGQGFIQKSVLIRHQRTHTGEKP
YVCRECGQGFTWKSVLICHQRTHTGEKP
YVCRECGQGFTRKSYLICHQRTHTGEKP
YVCRECGQGFTWKSHLIRHQRTHTGEKP
YVCRECGQGFTRKSYLICHQRTHTGEKP
YVCRECGQGFIQKSHLICHQRTHTGEKP
YVCRECGQGFTRKSYLICHQRTHTGEKP
YVCRECGQGFTWKSVLIRHQRTHTAEK*

>PRDM7_merUng Meriones unguiculatus ADA68117 terminal fragment
 ESKRTMEELTTGQKTNTEDTVKSFIGSEIS
GTGRECGQCFSDKSNVSEHQRTHTGEKP
YVCRECGRGFMQRSNLISHQRTHTGEKP
YVCRECGRGFMQRSNLISHQRTHTGEKP
YVCRECGRGFTVKSVLISHQRTHTGEKP
YVCRECGRGFTVKPHLISHQRTHTGEKP
HVCRECGRGFTQRSNLIRHQRTHTGEKP
YVCRECGRGFTVKPHLISHQRTHTGEKP
YVCRECGRGFTVKPHLISHQRTHTGEKP
YVCRECGRGFTVKSVLISHQRTHTGEKP
YVCRECGRGFTVKSVLIRHQRTHTGEKP
YVCRECRRGFTQRSTLIRHQRTHTGEKP
HVCRECGRGFTRGSHLLRHQRTHTGEVLPFQ*

>PRDM7_apoSyl Apodemus sylvaticus ADA68116 terminal fragment
GGKRTVEEEIRTVQSTNTDDKVKSVIASEIS
RVERQRGQCFSDKSNVSERQGTHTGEKP
CVCRECGRGFTQKSHLNRHQRTHTGEKP
HVCRECGRGFTQKSHLNRHQRTHTGEKP
HVCRECGRGFTLKSNLNRHQRTHTGEKP
CVCRECGRAFTQKSDLIQHQRTHTGEKP
YVCRECGRGFTQKSNLNQHQRTHTGEKP
YVCRECGRGFTRKSLLIQHQRTHTGEKP
YVCRECGRGFTQKSDLNRHQRTHTGEKP
YVCRECGRGLTQKSNLIQHQRTHTGEKP
YVCRECGRGFTLKSDLIQHQRTHTGEKP
YVCRECGRGFTRKSDLNRHQRTHTGEKP
YVCRECGRGFTQKSNLIQHQRTHTGEKP
YVCRECGRGFTLKSDLIQHQRTHTGEKP
YVCRECGRGFTRKSDLNRHQRTHTGEK*

>PRDMx_monDom Monodelphis domestica (opossum) gene genome no GAS8 fragment KRAB SSXRD SET weak C2H2 domain
0 0  
0 GEDAFKDISTYFSKKQWVKLKEWEKVRLKNVKRNYEAMIKI 1 
2 GLSVPRPAFMCRGRQNKKVKVEESGDSDEEWIPKQL 1 
2 0  
0 1  
2 DCRRKDVEVHIYSLRERKYQVYQEMWDPQDDDYL 1 
2 yCEECQIFFLDSCPLHGPPTFVQDSAMVKGHPYCSAITLPPGLRIGLSGIPGAGLGVWNEASTLPLGLHFGPYKGKMTEDDEAANSGYSWM 0 
0 ITKGRNCYEYVDGKEESCSNWMR 2  
1 YVNCARDEEEQNLVAFQYHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKRPLPELTGE 1 
2 GKPGISLCPSTLWASPLIPSSINTRCSKQPP*VFLDSGTGKL*AGRSTAGPATSNRFQLLSDKETSPKEHPSSLWGKTKQVDRREKFSLPQSQQVRGKESSSGEDLSRIQGKSTRQTTMAFQERNR
KECE*GFTHQTNLVTHRWTHSGERP  
YVCV*GFTQKLGFSPYTWTL* 0  
 
>PRDMx_macEug Macropus eugenii (wallaby) notDet genome ---- poor quality fragment
0 0  
0 1  
2 gFSAPRPTFMCHGKQNKEAKVEESGDFDEEWIRKQP 1 
2 0  
0 1  
2 1  
2 yCEECQTFFLETCAVHGPPKFVQDSVMVKGHPYCSAITLPPGLRIGLSGIPGAGLGIWNEASNLPLGLHFGPYEGQMTEDDEAANSGYSWM 0 
0 2  
1 YVNCARDEEEQNLVAFQYHRKIFYRTCQIIRPGCELLVWYGDEYGQELGIKWGSKWKRPPITLT 1 
2 * 0  

>PRDMx_sarHar Sarcophilus harrisii (tasmanian_devil) Chr3_supercontig_000000236
0 0  
0 1  
2 1 
2 0  
0 1  
2 1  
2 yCEECQTFFLETCAVHGPPKFVQDGAMIKGYPYCSAITLPPGLRIGLSGIPNAGLGVWNEGSNLPMGLHFGPYEGKSTEDDEAANSGYSWM 0 
0 2  
1 YVNCAREEEEQNLVAFQYQRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGRKWKRPLT 1 
2 * 0 

>PRDMxa_ornAna Ornithorhynchus anatinus (platypus) gene genome chrX5 fragment X5 +- 20577549 no iMet possible in first exon phase 2
0 0  
0 1  
2 1  
2 0  
0 1  
2 RIGKKPQVRDFNLRKQKRKIYNENYRPEDDDYL 1 
2 yCEICQTFFLEKCVLHGPPVFVQDLPVEKWRPNRSTITLPPGMQIKVSGIPNAGLGVWNQATSLPRGLHFGPYMGIRTKNEKESHSGYSWM 0 
2 IVRGKNYEYLDGKDKAFSNWMR 2  
1 YVNCARSEREQNLVAIQYQGEIYYRTCRVIPPGQELLVWYGLEYGRHLGILPNNNNPEP 1 
2 ERAKARVRKSERIEKAMARVRKSEQIERAKARVRTSERIERAMATV RKSERIERAKVTVKKSEQIERAMGRVRKSERIERAKDMGRKKALGGLPRPCRGGLSDETQQRKGGGHEQLGQKPGPSEA RAGPAEGSATPRR
HCCDVCRKAFKRLSHLRQHKRIHTGEKP  
LVCKVCRRTFSDPSNLNRHSRIHTGLRP  
YVCKLCRKAFADPSNLKRHVFSHTGHKP  
FVCEKCGKGFNRCDNLKDHSAKHSEDNSTPKP* 0 
 
>PRDMxb_ornAna Ornithorhynchus anatinus (platypus) gene genome chrX5 tandem fragment slight frameshift taa to ta YVN exon X5 +- 20605294 20611704 no iMet possible in first exon phase 2 gg as expected
0 0  
0 1  
2 1  
2 0  
0 1  
2 RSGKKPQVRDFNLRKQKRKMYTEESEPEDDDYL 1 
2 yCEDCQTFFLEKCSVHGPPVFVQDCEAKRCQQNRSEVTLPPGLLIKMSGIPNAGLGVWNQATSLPRGLYFGPFVGIRKNNVKDSLSGYSWAV 0 
0 ILRGRNYEYLDGKNTSFSNWMR 2  
1 YVNCPRTKYEQNLVAIQYHREIYYRTTPCDSTRSRVAGVVWRRVRSYLGIFWKSETPKS 1 
2 ERPHSSGGSFAPSARSGGVKQRIWSKRRSAALQRTRERRNSTHDFPPKHEDTAARQDERQCPDRGRAKQRGVRKSEQIERAKAMGRKKALGGLSPPRRERLSDEAGQRKKSGHEQFWQKPGPSEAWAGPAEGSTIPRR
HCCDVCGKAFNRLSRLKQHKRVHTGEKP  
LVCKICKRAFSDPSNLNRHAKRHTGEKP  
FVCRVCGRSFNRSDNMNEHRWKHTSNNIIP NTGHMSATVVENASLCINRNYQIYKERATYL* 0

>PRDMx_danRer Danio rerio (zebrafish) Q6P2A1 transcript BC064665 no KRAB false homolog
0 MSLSP 1
2 DLPPSEEQNLEIQGSATNCYSVVIIEEQDDTFNDQPF 1
2 YCEMCQQHFIDQCETHGPPSFTCDSPAALGTPQRALLTLPQGLVIGRSSISHAGLGVFNQGQTVPLGMHFGPFDGEEISEEKALDSANSWV 0
0 ICRGNNQYSYIDAEKDTHSNWMK 2
1 FVVCSRSETEQNLVAFQQNGRILFRCCRPISPGQEFRVWYAEEYAQGLGAIWDKIWDNKCISQ 1
2 GSTEEQATQNCPCPFCHYSFPTLVYLHAHVKRTHPNEYAQFTQTHPLESEAHTPITEVEQCLVASDEALSTQTQPVTESPQEQISTQNGQPIHQTENSDEPDASDIYTAAGEISDEI
HACVDCGRSFLRSCHLKRHQRTIHSKEKP
YCCSQCKKCFSQATGLKRHQHTHQEQEKNIESPDRPSDI
YPCTKCTLSFVAKINLHQHLKRHHHGEYLRLVESGSLTAETEEDHT
EVCFDKQDPNYEPPSRGRKSTKNSLKG
RGCPKKVAVGRPRGRPPKNKNLEVEVQKIS
PICTNCEQSFSDLETLKTHQCPRRDDEGDNVEHPQEASQ
YICGECIRAFSNLDLLKAHECIQQGEGS
YCCPHCDLYFNRMCNLRRHERTIHSKEKP
YCCTVCLKSFTQSSGLKRHQQSHLRRKSHRQSSALFTAAI
FPCAYCPFSFTDERYLYKHIRRHHPEMSLKYLSFQEGGVLSVEKP
HSCSQCCKSFSTIKGFKNHSCFKQGEKV
YLCPDCGKAFSWFNSLKQHQRIHTGEKP
YTCSQCGKSFVHSGQLNVHLRTHTGEKP
FLCSQCGESFRQSGDLRRHEQKHSGVRP
CQCPDCGKSFSRPQSLKAHQQLHVGTKL
FPCTQCGKSFTRRYHLTRHHQKMHS* 0

>ZNF133_homSap Homo sapiens (human) NP_001076799 KRAB Krueppel-associated box and zinc fingers
0 MAFRDVAVDFTQDEWRLLSPAQRTLYREVMLENYSNLVSL 1
2 GISFSKPELITQLEQGKETWREEKKCSPATCP 1
2 DPEPELYLDPFCPPGFSSQKFPMQHVLCNHPPWIFTCLCAEGNIQPGDPGPGDQ EKQQQASEGRPWSDQAEGPE GEGAMPLFGRTKKRTLG AFSRPPQRQPVSSRNGLRGVELEASPAQTGNPEETDKLLKRIEVLGFGT
VNCGECGLSFSKMTNLLSHQRIHSGEKP
YVCGVCEKGFSLKKSLARHQKAHSGEKP
IVCRECGRGFNRKSTLIIHERTHSGEKP
YMCSECGRGFSQKSNLIIHQRTHSGEKP
YVCRECGKGFSQKSAVVRHQRTHLEEKT
IVCSDCGLGFSDRSNLISHQRTHSGEKP
YACKECGRCFRQRTTLVNHQRTHSKEKP
YVCGVCGHSFSQNSTLISHRRTHTGEKP
YVCGVCGRGFSLKSHLNRHQNIHSGEKP
IVCKDCGRGFSQQSNLIRHQRTHSGEKP
MVCGECGRGFSQKSNLVAHQRTHSGERP
YVCRECGRGFSHQAGLIRHKRKHSREKP
YMCRQCGLGFGNKSALITHKRAHSEEKP
CVCRECGQGFLQKSHLTLHQMTHTGEKP
YVCKTCGRGFSLKSHLSRHRKTTSVHHR LPVQPDPEPCAGQPSDSLYSL* 0

>ZNF343_homSap Homo sapiens (human) KRAB Krueppel-associated box and zinc fingers
0 MMLPYPSALGDQYWEEILLPKNGENVETMKKLTQNHKAK 1
2 GLPSNDTDCPQKKEGKAQIV 0
0 VPVTFRDVTVIFTEAEWKRLSPEQRNLYKEVMLENYRNLLSL 1
2 AEPKPEIYTCSSCLLAFSCQQFLSQHVLQIFLGLCAENHFHPGNSSPGHWKQQGQQYSHVSCWFENAEGQERGGGSKPWSARTEERETSRAFPSPLQRQSASPRKGNMVVETEPSSAQRPNPVQLDKGLKELETLRFGA
INCREYEPDHNLESNFITNPRTLLGKKP
YICSDCGRSFKDRSTLIRHHRIHSMEKP
YVCSECGRGFSQKSNLSRHQRTHSEEKP
YLCRECGQSFRSKSILNRHQWTHSEEKP
YVCSECGRGFSEKSSFIRHQRTHSGEKP
YVCLECGRSFCDKSTLRKHQRIHSGEKP
YVCRECGRGFSQNSDLIKHQRTHLDEKP
YVCRECGRGFCDKSTLIIHERTHSGEKP
YVCGECGRGFSRKSLLLVHQRTHSGEKH
YVCRECRRGFSQKSNLIRHQRTHSNEKP
YICRECGRGFCDKSTLIVHERTHSGEKP
YVCSECGRGFSRKSLLLVHQRTHSGEKH
YVCRECGRGFSHKSNLIRHQRTH* 0

>ZNF169_homSap Homo sapiens (human) KRAB Krueppel-associated box and zinc fingers
0 MSPGLLTTRKEALMAFRDVAVAFTQKEWKLLSSAQRTLYREVMLENYSHLVSL 1
2 GIAFSKPKLIEQLEQGDEPWREENEHLLDLCP 1
2 EPRTEFQPSFPHLVAFSSSQLLRQYALSGHPTQIFPSSSAGGDFQLEAPRCSSEKGESGETEGPDSSLRKRPSRISRTFFSPHQGDPVEWVEGNREGGTDLRLAQRMSLGGSDTMLKGADTSESGAVIRGNYRLGLSKKSSLFSHQKH
HVCPECGRGFCQRSDLIKHQRTHTGEKP
YLCPECGRRFSQKASLSIHQRKHSGEKP
YVCRECGRHFRYTSSLTNHKRIHSGERP
FVCQECGRGFRQKIALLLHQRTHLEEKP
FVCPECGRGFCQKASLLQHQSSHTGERP
FLCLECGRSFRQQSLLLSHQVTHSGEKP
YVCAECGHSFRQKVTLIRHQRTHTGEKP
YLCPQCGRGFSQKVTLIGHQRTHTGEKP
YLCPDCGRGFGQKVTLIRHQRTHTGEKP
YLCPKCGRAFGFKSLLTRHQRTHSEEEL
YVDRVCGQGLGQKSHLISDQRTHSGEKP
CICDECGRGFGFKSALIRHQRTHSGEKP
YVCRECGRGFSQKSHLHRHRRTKSGHQL LPQEVF* 0

>ZNF596_homSap Homo sapiens (human) KRAB Krueppel-associated box and zinc fingers
0 MESQESVTFQDVAVDFTQEEWALLDTSQRTLFREVMLENISHLVSV 1
2 GNQLYKSDVISHLEQGEQLSREGLGFLQGQSPVISDREDDPKKQEMLSMQHICKKDAPLISAMQWSHTQEDPLECNNFREKFTEILPLTQYVIPQVGKKPFISQDVGKAISYLPSFNIQKQIHSRSKS
YECHQRRNTFIQSSAHRQHNNTQTGEKT
FECHVCRKAFSKSSNLRRHEMIHTGVKP
HGCHLCGKSFTHCSDLRKHERIHTGEKL
YGCHLCGKAFSKSYNLRRHEVIHTKEKP
NECHLCGKAFAHCSDLRKHERTHFGEKP
YGCHLCGKTFSKTSYLRQHERTHNGEKP
YGCHLCGKAFTHCSHLRKHERTHTGEKP
YECHLCGKAFTESSVLRRHERTHTGEKP
YECHLCWKAFTDSSVLKRHERTHTGEKP
YECHLCGKTFNHSSVLRRHERTHTGEKP
YECNICGKAFNRSYNFRLHKRIHTGEKP
YKCYLCGKAFSKYFNLRQHENSCYKGNK* 0

>HKR1_homSap Homo sapiens (human) KRAB Krueppel-associated box and zinc fingers
0 MRVNHTVSTMLPTCMVHRQTMSCSGAGGITAFVAFRDVAVYFTQEEWRLLSPAQRTLHREVMLETYNHLVSL 1
2 EIPSSKPKLIAQLERGEAPWREERKCPLDLCP 1
2 ESKPEIQLSPSCPLIFSSQQALSQHVWLSHLSQLFSSLWAGNPLHLGKHYPEDQ KQQQDPFCFSGKAEWIQE GEDSRLLFGRVSKNGTSKALSSPPEEQQPAQSKEDNTVVDIGSSPERRADLEETDKVLHGLEVSGFGE
IKYEEFGPGFIKESNLLSLQKTQTGETP
YMYTEWGDSFGSMSVLIKNPRTHSGGKP
YVCRECGRGFTWKSNLITHQRTHSGEKP
YVCKDCGRGFTWKSNLFTHQRTHSGLKP
YVCKECGQSFSLKSNLITHQRAHTGEKP
YVCRECGRGFRQHSHLVRHKRTHSGEKP
YICRECEQGFSQKSHLIRHLRTHTGEKP
YVCTECGRHFSWKSNLKTHQRTHSGVKP
YVCLECGQCFSLKSNLNKHQRSHTGEKP
FVCTECGRGFTRKSTLSTHQRTHSGEKP
FVCAECGRGFNDKSTLISHQRTHSGEKP
FMCRECGRRFRQKPNLFRHKRAHSGA
FVCRECGQGFCAKLTLIKHQRAHAGGKP
HVCRECGQGFSRQSHLIRHQRTHSGEKP
YICRKCGRGFSRKSNLIRHQRTHSG* 0

>PRDM11_homSap Homo sapiens (human) 511 aa 7 exons chr11:45115564 44% id PRDM9 SET
0 MLKMAEPIASLMIVECRACLRCSPLFLYQREK 0
0 DRMTENMKECLAQTNAAVGDMVTVVKTEVCSPLRDQEYGQPC 2
1 SRRPDSSAMEVEPKKLKGKRDLIVPKSFQQVDFW 1
2 FCESCQEYFVDECPNHGPPVFVSDTPVPVGIPDRAALTIPQGMEVVKDTSGESDVRCVNEVIPKGHIFGPYEGQISTQDKSAGFFSWL 0
0 IVDKNNRYKSIDGSDETKANWMR 2
1 YVVISREEREQNLLAFQHSERIYFRACRDIRPGEWLRVWYSEDYMKRLHSMSQETIHRNLAR 1
2 GEKRLQREKSEQVLDNPEDLRGPIHLSVLRQGKSPYKRGFDEGDVHPQAKKKKIDLIFKDVLEASLESAKVEAHQLALSTSLVIRKVPKYQDDAYSQCATTMTHGVQNIGQTQG
EGDWKVPQGVSKEPGQLEDEEEEPSSFKADSPAEASLASDPHELPTTSFCPNCIRLKKKVRELQAELDMLKSGKLPEPPVLPPQVLELPEFSDPAGKLVWMRLLSEGRVRSGLCGG* 0

>PRDM1_homSap Homo sapiens (human) 825 aa 7 exons chr6 106,546,004 3DAL:KMDM..NLTQ SET + 5 C2H2
0 MLDICLEKRVGTTL 0
0 AAPKCNSSTVRFQGLAEGTKGTMKMDMEDADMTLWTEAEFEEKCTYIVNDHPWDSGADGGTSVQAEASLPRNLLFKYATNSEE 0
0 VIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWR 0
0 IYSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGELTMMNL 1
2 TQTQSSLKQPSTEKNELCPKNVPKREYSVKEILKLDSNPSKGKDLYRSNISPLTSEKDLDDFRRRGSPEMPFYPRVVYPIRAPLPEDFLKASLAYGIERPTYITRSPIPSSTTPSPSARSS
PDQSLKSSSPHSSPGNTVSPVGPGSQEHRDSYAYLNASYGTEGLGSYPGYAPLPHLPPAFIPSYNAHYPKFLLPPYGMNCNGLSAVSSMNGINNFGLFPRLCPVYSNLLGGGSLPHPMLNPTS
LPSSLPSDGARRLLQPEHPREVLVPAPHSAFSFTGAAASMKDKACSPTSGSPTAGTAATAEHVVQPKATSAAMAAPSSDEAMNLIKNKRNMTGYKTLPYPLKKQNGKIKYECNVCAKTFGQLSNLK 0
0 VHLRVHSGERPFKCQTCNKGFTQLAHLQKHYLVHTGEKPHECQ 0
0 VCHKRFSSTSNLKTHLRLHSGEKPYQCKVCPAKFTQFVHLKLHKRLHTRERPHKCSQCHKNYIHLCSLKVHLKGNCAAAPAPGLPLEDLTRINEEIEKFDISD
NADRLEDVEDDISVISVVEKEILAVVRKEKEETGLKVSLQRNMGNGLLSSGCSLYESSDLPLMKLPPSNPLPLVPVKVKQETVEPMDP*

>PRDM4_homSap Homo sapiens (human) 801 aa 11 exons chr12:108126644 3DB5:EHGPV..IGVPE SET + 1 + 6 C2H2 domaians
0 MHHR 2
1 MNEMNLSPVGMEQLTSSSVSNALPVSGSHLGLAASPTHSAIPAP 1
2 GLPVAIPNLGPSLSSLPSALSLMLPMGIGDRGVMCGLPERNYTLPPPPYPHLESSYFRTILP 1
2 GILSYLADRPPPQYIHPNSINVDGNTALSITNNPSALDPYQSNGNVGLEPGIVSIDSRSVNTHGAQSLHPSDGHEVALDTAITMENVSRVTSPISTDGMAEELTMDGVAGEHSQIPNGSRSHEPLSVDSVSN
NLAADAVGHGGVIPMHGNGLELPVVMETDHIASRVNGMSDSALSDSIHTVAMSTNSVSVALSTSHNLASLESVSLHEVGLSLEPVAVSSITQEVAMGTGHVDVSSDSLSFVSPSLQMEDSNSNKENMATLFTI 1
2 WCTLCDRAYPSDCPEHGPVTFVPDTPIESRARLSLPKQLVLRQSIVGAEV 1
2 GVWTGETIPVRTCFGPLIGQQSHSMEVAEWTDKAVNHIWK 0
0 IYHNGVLEFCIITTDENECNWMMFVRKAR 2
1 NREEQNLVAYPHDGKIFFCTSQDIPPENELLFYYSRDYAQQI 1
2 GVPEHPDVHLCNCGKECNSYTEFKAHLTSHIHNHLPTQGHSGSHGPSHSKERKWKCSMCPQAFISPSKLHVHFMGHMGMKPHKCDFCSKAFSDPSNLRTHLKIHT 1
2 GQKNYRCTLCDKSFTQKAHLESHMVIHTGEKNLKCDYCDKLFMRRQDLKQHVLIHTQ 2
1 ERQIKCPKCDKLFLRTNHLKKHLNSHEGKRDYVCEKCTKAYLTKYHLTRHLKTCKGPTSSSSAPEEEEEDDSEEEDLADSVGTEDCRINSAVYSADESLSAHK* 0

>GAS8_homSap Homo sapiens (human) synteny marker right centromeric positive strand C16orf3- in second intron growth arrest-specific del cancer
MAPKKKGKKGKAKGTPIVDGLAPEDMSKEQVEEHVSRIREELDREREERNYFQLERDKIHTFWEITRRQLEEKKAELRNKDREMEEAEERHQVEIKVYKQKVKHLLYEHQNNLTEMKAEG
TVVMKLAQKEHRIQESVLRKDMRALKVELKEQELASEVVVKNLRLKHTEEITRMRNDFERQVREIEAKYDKKMKMLRDELDLRRKTELHEVEERKNGQIHTLMQRHEEAFTDIKNYYNDI
TLNNLALINSLKEQMEDMRKKEDHLEREMAEVSGQNKRLADPLQKAREEMSEMQKQLANYERDKQILLCTKARLKVREKELKDLQWEHEVLEQRFTKVQQERDELYRKFTAAIQEVQQKT
GFKNLVLERKLQALSAAVEKKEVQFNEVLAASNLDPAALTLVSRKLEDVLESKNSTIKDLQYELAQVCKAHNDLLRTYEAKLLAFGIPLDNVGFKPLETAVIGQTLGQGPAGLVGTPT*

>CDH12_homSap Homo sapiens (human) synteny marker chr 5 794 aa
MLTRNCLSLLLWVLFDGGLLTPLQPQPQQTLATEPRENVIHLPGQRSHFQRVKRGWVWNQFFVLEEYVGSEPQYVGKLHSDLDKGEGTVKYTLSGDGAGTVFTIDETTGDIHAIRSLDRE
EKPFYTLRAQAVDIETRKPLEPESEFIIKVQDINDNEPKFLDGPYVATVPEMSPVGAYVLQVKATDADDPTYGNSARVVYSILQGQPYFSIDPKTGVIRTALPNMDREVKEQYQVLIQAK
DMGGQLGGLAGTTIVNITLTDVNDNPPRFPKSIFHLKVPESSPIGSAIGRIRAVDPDFGQNAEIEYNIVPGDGGNLFDIVTDEDTQEGVIKLKKPLDFETKKAYTFKVEASNLHLDHRFH
SAGPFKDTATVKISVLDVDEPPVFSKPLYTMEVYEDTPVGTIIGAVTAQDLDVGSSAVRYFIDWKSDGDSYFTIDGNEGTIATNELLDRESTAQYNFSIIASKVSNPLLTSKVNILINVL
DVNEFPPEISVPYETAVCENAKPGQIIQIVSAADRDLSPAGQQFSFRLSPEAAIKPNFTVRDFRNNTAGIETRRNGYSRRQQELYFLPVVIEDSSYPVQSSTNTMTIRVCRCDSDGTILS
CNVEAIFLPVGLSTGALIAILLCIVILLAIVVLYVALRRQKKKDTLMTSKEDIRDNVIHYDDEGGGEEDTQAFDIGALRNPKVIEENKIRRDIKPDSLCLPRQRPPMEDNTDIRDFIHQR
LQENDVDPTAPPYDSLATYAYEGSGSVAESLSSIDSLTTEADQDYDYLTDWGPRFKVLADMFGEEESYNPDKVT*

Online References

Open 38 abstracts on PRDM9 and related issues. Or the reverse chronological list below provides free full text for individual articles when that is available:

abs 2011  Neaves       Unisexual reproduction among vertebrates.  Trends Genet. 2011 Mar;27(3):81-8.
abs 2011  Ponting      What are the genomic drivers of the rapid evolution of PRDM9?  Trends Genetics (2011) 1–7
htm 2011  Yanover      Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.  Nucleic Acids Res. 2011 Feb 22
pdf 2011  Ubeda        Red Queen theory of recombination hotspots.  J Evol Biol. 2011 Mar;24(3):541-53.
abs 2010  Hochwagen    Meiosis: a PRDM9 guide to the hotspots of recombination.  Curr Biol. 2010 Mar 23;20(6):R271-4.
abs 2010  Klug         The discovery of zinc fingers and practical applications in gene regulation and genome manipulation.  Q Rev Biophys. 2010 Feb;43(1):1-21.
abs 2010  Berg         PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans.  Nat Genet. 2010 Oct;42(10):859-63.
abs 2010  McVean       PRDM9 marks the spot.  Nat Genet. 2010 Oct;42(10):821-2.
pdf 2010  Kong         Fine-scale recombination rate differences between sexes, populations and individuals.  Nature. 2010 Oct 28;467(7319):1099-103.
pmc 2010  Parvanov     Prdm9 controls activation of mammalian recombination hotspots.  Science. 2010 Feb 12;327(5967):835.
pmc 2010  Lorenz       The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3  BMC Genomics. 2010 Mar 26;11:206. 
pmc 2010  Neale        PRDM9 points the zinc finger at meiotic recombination hotspots.  Genome Biol. 2010;11(2):104.
pmc 2010  Sandovici    PRDM9 sticks its zinc fingers into recombination hotspots and between species.  F1000 Biol Rep. 2010 May 24;2.
pmc 2010  Billings     Patterns of recombination activity on mouse chromosome 11 revealed by high resolution mapping.  PLoS One. 2010 Dec 8;5(12):e15340.
htm 2010  Cheung       Genetic control of hotspots.  Science. 2010 Feb 12;327(5967):791-2.
pdf 2010  Urnov        Highly efficient endogenous human gene correction using designed zinc-finger nucleases.  Nature. 2005 Jun 2;435(7042):646-51.
htm 2010  Zheng        Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome.  Genome Biol. 2010;11(10):R103.
htm 2010  Baudat       PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice.  Science. 2010 Feb 12;327(5967):836-40.
htm 2010  Myers        Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination.  Science. 2010 Feb 12;327(5967):876-9.
pmc 2009  Berglund     Hotspots of biased nucleotide substitutions in human genes.  PLoS Biol. 2009 Jan 27;7(1):e26.
pmc 2009  Thomas       Evolution of C2H2-zinc finger genes revisited.  BMC Evol Biol. 2009 Mar 4;9:51.
pmc 2009  Oliver       Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa.  PLoS Genet. 2009 Dec;5(12):e1000753.
pmc 2009  Thomas       Extraordinary molecular evolution in the PRDM9 fertility gene.  PLoS One. 2009 Dec 30;4(12):e8505.
htm 2009  Willis       Origin of species in overdrive.  Science. 2009 Jan 16;323(5912):350-1.
htm 2009  Irie         Single-nucleotide polymorphisms of the PRDM9 (MEISETZ) gene in patients with nonobstructive azoospermia.  J Androl. 2009 Jul-Aug;30(4):426-31.
htm 2009  Mihola       A mouse speciation gene encodes a meiotic histone H3 methyltransferase.  Science. 2009 Jan 16;323(5912):373-5.
abs 2008  Brayer       The protein-binding potential of C2H2 zinc finger domains.  Cell Biochem Biophys. 2008;51(1):9-19.
pmc 2008  Duret        The impact of recombination on nucleotide substitutions in  the human genome.  PLoS Genet. 2008 May 9;4(5):e1000071.
pmc 2008  Miyamoto     Two single nucleotide polymorphisms in PRDM9 (MEISETZ) gene may be a genetic risk factor for Japanese patients with azoospermia by meiotic arrest.  J Assist Reprod Genet. 2008 Nov-Dec;25(11-12):553-7.
htm 2008  Cho          Prediction of DNA binding sites for zinc finger proteins.  BBRC 2008 May 9;369(3):845-8.
pmc 2007  Coop         Live hot, die young: transmission distortion in recombination hotspots.  PLoS Genet. 2007 Mar 9;3(3):e35.
pmc 2007  Fumasoni     Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates.  BMC Evol Biol. 2007 Oct 4;7:187.
pdf 2006  Phillips     A family of zinc-finger proteins is required for chromosome-specific pairing and synapsis during meiosis.  Dev Cell. 2006 Dec;11(6):817-29.
htm 2006  Birtle       Meisetz and the birth of the KRAB motif.  Bioinformatics. 2006 Dec 1;22(23):2841-5. 
pdf 2006  Hayashi      Meisetz, a novel histone tri-methyltransferase, regulates meiosis-specific epigenesis.  Cell Cycle. 2006 Mar;5(6):615-20.
pdf 2005  Hayashi      A histone H3 methyltransferase controls epigenetic events required for meiotic prophase. Nature 2005 Nov 17;438(7066):374-8.
abs 2000  Laity        DNA-induced alpha-helix capping in conserved linker sequences is a determinant of binding affinity in Cys(2)-His(2) zinc fingers.  J Mol Biol. 2000 Jan 28;295(4):719-27.