UCSC to RefSeq correspondence: Difference between revisions

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<table border=1>
{| border='1' style='border-collapse:collapse' class='wikitable sortable'
<tr><th>UCSC<br>browser</th>
|+ UCSC to Genbank assembly accession correspondence
<th>scientific<br>name(s)</th>
! count
<th>common<br>name</th>
! UCSC browser
<th>Entrez<br>assembly</th>
! scientific name(s)
<th>NCBI<br>FTP</th>
! common name
</tr>
! Entrez assembly
<tr><td>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ailMel1 ailMel1]
! NCBI FTP
<td>Ailuropoda&nbsp;melanoleuca</td>
|-
<td>Panda</td>
! 1
<td>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000004335.2/ GCF_000004335.2_AilMel_1.0]</td>
| [http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=CHM1 CHM1]
<td>[ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Ailuropoda_melanoleuca/all_assembly_versions/GCF_000004335.2_AilMel_1.0/ vertebrate_mammalian]</td>
| mole<br>Homo&nbsp;sapiens
</tr>
| Homo sapiens hydatidiform mole assembly chm1
<tr><td>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=balAcu1 balAcu1]
| [http://www.ncbi.nlm.nih.gov/assembly/GCF_000306695.2/ GCF_000306695.2_CHM1_1.1]
<td>Balaenoptera&nbsp;acutorostrata&nbsp;scammoni<br>Balaenoptera&nbsp;acutorostrata</td>
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000306695.2_CHM1_1.1/ vertebrate_mammalian]
<td>Minke whale</td>
|-
<td>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000493695.1/ GCF_000493695.1_BalAcu1.0]</td>
! 2
<td>[ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Balaenoptera_acutorostrata/all_assembly_versions/GCF_000493695.1_BalAcu1.0/ vertebrate_mammalian]</td>
| [http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=ailMel1 ailMel1]
</tr>
| Ailuropoda&nbsp;melanoleuca
<tr><td>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=bubBub1 bubBub1]
| Panda
<td>Bubalus&nbsp;bubalis</td>
| [http://www.ncbi.nlm.nih.gov/assembly/GCF_000004335.2/ GCF_000004335.2_AilMel_1.0]
<td>Water buffalo</td>
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Ailuropoda_melanoleuca/all_assembly_versions/GCF_000004335.2_AilMel_1.0/ vertebrate_mammalian]
<td>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000471725.1/ GCF_000471725.1_UMD_CASPUR_WB_2.0]</td>
|-
<td>[ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Bubalus_bubalis/all_assembly_versions/GCF_000471725.1_UMD_CASPUR_WB_2.0/ vertebrate_mammalian]</td>
! 3
</tr>
| [http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=balAcu1 balAcu1]
<tr><td>[http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=camFer1 camFer1]
| Balaenoptera&nbsp;acutorostrata&nbsp;scammoni<br>Balaenoptera&nbsp;acutorostrata
<td>Camelus&nbsp;ferus</td>
| Minke whale
<td>Bactrian camel</td>
| [http://www.ncbi.nlm.nih.gov/assembly/GCF_000493695.1/ GCF_000493695.1_BalAcu1.0]
<td>[http://www.ncbi.nlm.nih.gov/assembly/GCF_000311805.1/ GCF_000311805.1_CB1]</td>
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Balaenoptera_acutorostrata/all_assembly_versions/GCF_000493695.1_BalAcu1.0/ vertebrate_mammalian]
<td>[ftp://ftp.ncbi.
|-
! 4
| [http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau8 bosTau8]
| Bos&nbsp;taurus
| Cow
| [http://www.ncbi.nlm.nih.gov/assembly/GCF_000003055.5/ GCF_000003055.5_Bos_taurus_UMD_3.1.1]
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Bos_taurus/all_assembly_versions/GCF_000003055.5_Bos_taurus_UMD_3.1.1/ vertebrate_mammalian]
|-
! 5
| [http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=bubBub1 bubBub1]
| Bubalus&nbsp;bubalis
| Water buffalo
| [http://www.ncbi.nlm.nih.gov/assembly/GCF_000471725.1/ GCF_000471725.1_UMD_CASPUR_WB_2.0]
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Bubalus_bubalis/all_assembly_versions/GCF_000471725.1_UMD_CASPUR_WB_2.0/ vertebrate_mammalian]
|-
! 6
| [http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=calJac3 calJac3]
| Callithrix&nbsp;jacchus
| Marmoset
| [http://www.ncbi.nlm.nih.gov/assembly/GCF_000004665.1/ GCF_000004665.1_Callithrix_jacchus-3.2]
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Callithrix_jacchus/all_assembly_versions/GCF_000004665.1_Callithrix_jacchus-3.2/ vertebrate_mammalian]
|-
! 7
| [http://genome-preview.cse.ucsc.edu/cgi-bin/hgTracks?db=camFer1 camFer1]
| Camelus&nbsp;ferus
| Bactrian camel
| [http://www.ncbi.nlm.nih.gov/assembly/GCF_000311805.1/ GCF_000311805.1_CB1]
| [ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Camelus_ferus/all_assembly_versions/GCF_000311805.1_CB1/ vertebrate_mammalian]
|-
! 8
| [http://genome-

Revision as of 22:51, 10 August 2016

UCSC to Genbank assembly accession correspondence
count UCSC browser scientific name(s) common name Entrez assembly NCBI FTP
1 CHM1 mole
Homo sapiens 		Homo sapiens hydatidiform mole assembly chm1 GCF_000306695.2_CHM1_1.1 vertebrate_mammalian
2 ailMel1 Ailuropoda melanoleuca Panda GCF_000004335.2_AilMel_1.0 vertebrate_mammalian
3 balAcu1 Balaenoptera acutorostrata scammoni
Balaenoptera acutorostrata 		Minke whale GCF_000493695.1_BalAcu1.0 vertebrate_mammalian
4 bosTau8 Bos taurus Cow GCF_000003055.5_Bos_taurus_UMD_3.1.1 vertebrate_mammalian
5 bubBub1 Bubalus bubalis Water buffalo GCF_000471725.1_UMD_CASPUR_WB_2.0 vertebrate_mammalian
6 calJac3 Callithrix jacchus Marmoset GCF_000004665.1_Callithrix_jacchus-3.2 vertebrate_mammalian
7 camFer1 Camelus ferus Bactrian camel GCF_000311805.1_CB1 vertebrate_mammalian
8 canFam3 Canis lupus familiaris
Canis lupus 		Dog GCF_000002285.3_CanFam3.1 vertebrate_mammalian
9 capHir1 Capra hircus Domestic goat GCF_000317765.1_CHIR_1.0 vertebrate_mammalian
10 cavPor3 Cavia porcellus Guinea pig GCF_000151735.1_Cavpor3.0 vertebrate_mammalian
11 cerSim1 Ceratotherium simum White rhinoceros GCF_000283155.1_CerSimSim1.0 vertebrate_mammalian
12 chlSab2 Chlorocebus sabaeus Green monkey GCF_000409795.2_Chlorocebus_sabeus_1.1 vertebrate_mammalian
13 chrAsi1 Chrysochloris asiatica Cape golden mole GCF_000296735.1_ChrAsi1.0 vertebrate_mammalian
14 colAng1 Colobus angolensis palliatus
Colobus angolensis 		Angolan colobus GCF_000951035.1_Cang.pa_1.0 vertebrate_mammalian
15 dasNov3 Dasypus novemcinctus Armadillo GCF_000208655.1_Dasnov3.0 vertebrate_mammalian
16 echTel2 Echinops telfairi Tenrec GCF_000313985.1_EchTel2.0 vertebrate_mammalian
17 eleEdw1 Elephantulus edwardii Cape elephant shrew GCF_000299155.1_EleEdw1.0 vertebrate_mammalian
18 eriEur2 Erinaceus europaeus Hedgehog GCF_000296755.1_EriEur2.0 vertebrate_mammalian
19 felCat5 Felis catus Cat GCF_000181335.1_Felis_catus-6.2 vertebrate_mammalian
20 felCat8 Felis catus Cat GCF_000181335.2_Felis_catus_8.0 vertebrate_mammalian
21 galVar1 Galeopterus variegatus Malayan flying lemur GCF_000696425.1_G_variegatus-3.0.2 vertebrate_mammalian
22 hetGla2 Heterocephalus glaber Naked mole-rat GCF_000247695.1_HetGla_female_1.0 vertebrate_mammalian
23 hg38 Homo sapiens Human GCF_000001405.26_GRCh38 vertebrate_mammalian
24 lepWed1 Leptonychotes weddellii Weddell seal GCF_000349705.1_LepWed1.0 vertebrate_mammalian
25 lipVex1 Lipotes vexillifer Yangtze river dolphin GCF_000442215.1_Lipotes_vexillifer_v1 vertebrate_mammalian
26 macFas5 Macaca fascicularis Crab-eating macaque GCF_000364345.1_Macaca_fascicularis_5.0 vertebrate_mammalian
27 mesAur1 Mesocricetus auratus Golden hamster GCF_000349665.1_MesAur1.0 vertebrate_mammalian
28 micMur2 Microcebus murinus Mouse lemur GCF_000165445.1_Mmur_2.0 vertebrate_mammalian
29 micOch1 Microtus ochrogaster Prairie vole GCF_000317375.1_MicOch1.0 vertebrate_mammalian
30 myoBra1 Myotis brandtii Brandt's myotis (bat) GCF_000412655.1_ASM41265v1 vertebrate_mammalian
31 myoDav1 Myotis davidii David's myotis (bat) GCF_000327345.1_ASM32734v1 vertebrate_mammalian
32 myoLuc2 Myotis lucifugus Microbat GCF_000147115.1_Myoluc2.0 vertebrate_mammalian
33 nanGal1 Nannospalax galili Upper Galilee mountains blind mole rat GCF_000622305.1_S.galili_v1.0 vertebrate_mammalian
34 orcOrc1 Orcinus orca Killer whale GCF_000331955.2_Oorc_1.1 vertebrate_mammalian
35 otoGar3 Otolemur garnettii Bushbaby GCF_000181295.1_OtoGar3 vertebrate_mammalian
36 oviAri3 Ovis aries Sheep GCF_000298735.1_Oar_v3.1 vertebrate_mammalian
37 panHod1 Pantholops hodgsonii Tibetan antelope GCF_000400835.1_PHO1.0 vertebrate_mammalian
38 panPan1 Pan paniscus Bonobo GCF_000258655.1_panpan1 vertebrate_mammalian
39 panPan2 Pan paniscus Bonobo GCF_000258655.2_panpan1.1 vertebrate_mammalian
40 panTig1 Panthera tigris altaica
Panthera tigris 		Amur tiger GCF_000464555.1_PanTig1.0 vertebrate_mammalian
41 panTro4 Pan troglodytes Chimp GCF_000001515.6_Pan_troglodytes-2.1.4 vertebrate_mammalian
42 panTro5 Pan troglodytes Chimp GCF_000001515.7_Pan_tro_3.0 vertebrate_mammalian
43 papAnu2 Papio anubis Baboon GCF_000264685.1_Panu_2.0 vertebrate_mammalian
44 perManBai1 Peromyscus maniculatus bairdii
Peromyscus maniculatus 		Prairie deer mouse GCF_000500345.1_Pman_1.0 vertebrate_mammalian
45 phyCat1 Physeter catodon Sperm whale GCF_000472045.1_Physeter_macrocephalus-2.0.2 vertebrate_mammalian
46 rheMac8 Macaca mulatta Rhesus GCF_000772875.2_Mmul_8.0.1 vertebrate_mammalian
47 rhiRox1 Rhinopithecus roxellana Golden snub-nosed monkey GCF_000769185.1_Rrox_v1 vertebrate_mammalian
48 rouAeg1 Rousettus aegyptiacus Egyptian rousette GCF_001466805.2_Raegyp2.0 vertebrate_mammalian
49 sarHar1 Sarcophilus harrisii Tasmanian devil GCF_000189315.1_Devil_ref_v7.0 vertebrate_mammalian
50 sorAra2 Sorex araneus Shrew GCF_000181275.1_SorAra2.0 vertebrate_mammalian
51 speTri2 Spermophilus tridecemlineatus
Ictidomys tridecemlineatus 		Squirrel GCF_000236235.1_SpeTri2.0 vertebrate_mammalian
52 tarSyr2 Tarsius syrichta
Carlito syrichta 		Tarsier GCF_000164805.1_Tarsius_syrichta-2.0.1 vertebrate_mammalian
53 triMan1 Trichechus manatus latirostris
Trichechus manatus 		Manatee GCF_000243295.1_TriManLat1.0 vertebrate_mammalian
54 tupChi1 Tupaia chinensis Chinese tree shrew GCF_000334495.1_TupChi_1.0 vertebrate_mammalian
55 ursMar1 Ursus maritimus Polar bear GCF_000687225.1_UrsMar_1.0 vertebrate_mammalian
56 allMis1 Alligator mississippiensis American alligator GCF_000281125.1_allMis0.2 vertebrate_other
57 allSin1 Alligator sinensis Chinese alligator GCF_000455745.1_ASM45574v1 vertebrate_other
58 anaPla1 Anas platyrhynchos Mallard duck GCF_000355885.1_BGI_duck_1.0 vertebrate_other
59 anoCar2 Anolis carolinensis Lizard GCF_000090745.1_AnoCar2.0 vertebrate_other
60 apaVit1 Apaloderma vittatum Bar tailed trogon GCF_000703405.1_ASM70340v1 vertebrate_other
61 aptFor1 Aptenodytes forsteri Emperor penguin GCF_000699145.1_ASM69914v1 vertebrate_other
62 bucRhi1 Buceros rhinoceros silvestris
Buceros rhinoceros 		Rhinoceros hornbill GCF_000710305.1_ASM71030v1 vertebrate_other
63 calAnn1 Calypte anna Anna's hummingbird GCF_000699085.1_ASM69908v1 vertebrate_other
64 calMil1 Callorhinchus milii Elephant shark GCF_000165045.1_Callorhinchus_milii-6.1.3 vertebrate_other
65 capCar1 Caprimulgus carolinensis Chuck-will's-widow GCF_000700745.1_ASM70074v1 vertebrate_other
66 carCri1 Cariama cristata Red-legged seriema GCF_000690535.1_ASM69053v1 vertebrate_other
67 chaVoc2 Charadrius vociferus Killdeer GCF_000708025.1_ASM70802v2 vertebrate_other
68 cheMyd1 Chelonia mydas Green seaturtle GCF_000344595.1_CheMyd_1.0 vertebrate_other
69 chlUnd1 Chlamydotis undulata macqueenii
Chlamydotis macqueenii 		Houbara bustard GCF_000695195.1_ASM69519v1 vertebrate_other
70 colLiv1 Columba livia Rock pigeon GCF_000337935.1_Cliv_1.0 vertebrate_other
71 colStr1 Colius striatus Speckled mousebird GCF_000690715.1_ASM69071v1 vertebrate_other
72 corBra1 Corvus brachyrhynchos American crow GCF_000691975.1_ASM69197v1 vertebrate_other
73 cucCan1 Cuculus canorus Common cuckoo GCF_000709325.1_ASM70932v1 vertebrate_other
74 cynSem1 Cynoglossus semilaevis Tongue sole GCF_000523025.1_Cse_v1.0 vertebrate_other
75 danRer10 Danio rerio Zebrafish GCF_000002035.5_GRCz10 vertebrate_other
76 danRer7 Danio rerio Zebrafish GCF_000002035.4_Zv9 vertebrate_other
77 egrGar1 Egretta garzetta Little egret GCF_000687185.1_ASM68718v1 vertebrate_other
78 eurHel1 Eurypyga helias Sunbittern GCF_000690775.1_ASM69077v1 vertebrate_other
79 falChe1 Falco cherrug Saker falcon GCF_000337975.1_F_cherrug_v1.0 vertebrate_other
80 falPer1 Falco peregrinus Peregrine falcon GCF_000337955.1_F_peregrinus_v1.0 vertebrate_other
81 ficAlb2 Ficedula albicollis Collared flycatcher GCF_000247815.1_FicAlb1.5 vertebrate_other
82 fr3 Takifugu rubripes Fugu GCF_000180615.1_FUGU5 vertebrate_other
83 fulGla1 Fulmarus glacialis Northern fulmar GCF_000690835.1_ASM69083v1 vertebrate_other
84 galGal4 Gallus gallus Chicken GCF_000002315.3_Gallus_gallus-4.0 vertebrate_other
85 galGal5 Gallus gallus Chicken GCF_000002315.4_Gallus_gallus-5.0 vertebrate_other
86 gavSte1 Gavia stellata Red-throated loon GCF_000690875.1_ASM69087v1 vertebrate_other
87 gekJap0 Gekko japonicus notFound GCF_001447785.1_Gekko_japonicus_V1.1 vertebrate_other
88 geoFor1 Geospiza fortis Medium ground finch GCF_000277835.1_GeoFor_1.0 vertebrate_other
89 halAlb1 Haliaeetus albicilla White-tailed eagle GCF_000691405.1_ASM69140v1 vertebrate_other
90 halLeu1 Haliaeetus leucocephalus Bald eagle GCF_000737465.1_Haliaeetus_leucocephalus-4.0 vertebrate_other
91 latCha1 Latimeria chalumnae Coelacanth GCF_000225785.1_LatCha1 vertebrate_other
92 lepDis1 Leptosomus discolor Cuckoo roller GCF_000691785.1_ASM69178v1 vertebrate_other
93 mayZeb1 Maylandia zebra Zebra mbuna GCF_000238955.1_MetZeb1.1 vertebrate_other
94 melUnd1 Melopsittacus undulatus Budgerigar GCF_000238935.1_Melopsittacus_undulatus_6.3 vertebrate_other
95 merNub1 Merops nubicus Northern carmine bee-eater GCF_000691845.1_ASM69184v1 vertebrate_other
96 mesUni1 Mesitornis unicolor Brown roatelo GCF_000695765.1_ASM69576v1 vertebrate_other
97 nipNip1 Nipponia nippon Crested ibis GCF_000708225.1_ASM70822v1 vertebrate_other
98 notCor1 Notothenia coriiceps Black rockcod GCF_000735185.1_NC01 vertebrate_other
99 opiHoa1 Opisthocomus hoazin Hoatzin GCF_000692075.1_ASM69207v1 vertebrate_other
100 oreNil2 Oreochromis niloticus Nile tilapia GCF_000188235.2_Orenil1.1 vertebrate_other
101 pelCri1 Pelecanus crispus Dalmatian pelican GCF_000687375.1_ASM68737v1 vertebrate_other
102 pelSin1 Pelodiscus sinensis Chinese softshell turtle GCF_000230535.1_PelSin_1.0 vertebrate_other
103 phaCar1 Phalacrocorax carbo Great cormorant GCF_000708925.1_ASM70892v1 vertebrate_other
104 phaLep1 Phaethon lepturus White-tailed tropicbird GCF_000687285.1_ASM68728v1 vertebrate_other
105 picPub1 Picoides pubescens Downy woodpecker GCF_000699005.1_ASM69900v1 vertebrate_other
106 poeFor1 Poecilia formosa Amazon molly GCF_000485575.1_Poecilia_formosa-5.1.2 vertebrate_other
107 pseHum1 Pseudopodoces humilis Tibetan ground jay GCF_000331425.1_PseHum1.0 vertebrate_other
108 pteGut1 Pterocles gutturalis Yellow-throated sandgrouse GCF_000699245.1_ASM69924v1 vertebrate_other
109 pytBiv0 Python bivittatus notFound GCF_000186305.1_Python_molurus_bivittatus-5.0.2 vertebrate_other
110 pytBiv1 Python bivittatus Burmese python GCF_000186305.1_Python_molurus_bivittatus-5.0.2 vertebrate_other
111 strCam1 Struthio camelus australis
Struthio camelus 		Ostrich GCF_000698965.1_ASM69896v1 vertebrate_other
112 taeGut2 Taeniopygia guttata Zebra finch GCF_000151805.1_Taeniopygia_guttata-3.2.4 vertebrate_other
113 tauEry1 Tauraco erythrolophus Red crested turaco GCF_000709365.1_ASM70936v1 vertebrate_other
114 thaSir0 Thamnophis sirtalis notFound GCF_001077635.1_Thamnophis_sirtalis-6.0 vertebrate_other
115 tinGut2 Tinamus guttatus White throated tinamou GCF_000705375.1_ASM70537v2 vertebrate_other
116 tytAlb1 Tyto alba Barn owl GCF_000687205.1_ASM68720v1 vertebrate_other
117 xenTro7 Xenopus tropicalis
Xenopus Silurana tropicalis 		X. tropicalis GCF_000004195.2_Xtropicalis_v7 vertebrate_other
118 xenTro7 Xenopus tropicalis X. tropicalis GCF_000004195.2_Xtropicalis_v7 vertebrate_other
119 xipMac1 Xiphophorus maculatus Southern platyfish GCF_000241075.1_Xiphophorus_maculatus-4.4.2 vertebrate_other
120 zonAlb1 Zonotrichia albicollis White-throated sparrow GCF_000385455.1_Zonotrichia_albicollis-1.0.1 vertebrate_other
121 acrEch0 Acromyrmex echinatior notFound GCF_000204515.1_Aech_3.9 invertebrate
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