UCSC to RefSeq correspondence: Difference between revisions

From genomewiki
Jump to navigationJump to search
(forgot to include everything)
(updated with RR references)
Line 7: Line 7:


The external links go to:
The external links go to:
* UCSC browser - genome-test genome browser
* test browser - genome-test.soe.ucsc.edu genome browser
* Entrez assembly - assembly information page at NCBI
** public browser - when available the genome.ucsc.edu browser
* NCBI FTP - ftp directory at NCBI where the assembly can be obtained
* RefSeq assembly - assembly information page at NCBI for the refseq version
** Genbank assembly - assembly information page at NCBI when equivalent, genbank version
* RefSeq FTP - ftp directory at NCBI where the RefSeq assembly can be obtained
** Genbank FTP - ftp directory for the genbank version when equivalent




Line 51: Line 54:
|+ UCSC to Genbank assembly accession correspondence
|+ UCSC to Genbank assembly accession correspondence
! count
! count
! UCSC browser
! test browser
public browser
! scientific name(s)
! scientific name(s)
! common name
! common name
! Entrez assembly
! RefSeq assembly
! NCBI FTP
Genbank assembly
! RefSeq FTP
Genbank FTP
|-
|-
! 1
! 1
Line 66: Line 72:
! 2
! 2
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ailMel1 ailMel1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ailMel1 ailMel1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ailMel1 public]
| Ailuropoda_melanoleuca
| Ailuropoda_melanoleuca
| Panda
| Panda
Line 73: Line 80:
! 3
! 3
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=balAcu1 balAcu1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=balAcu1 balAcu1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=balAcu1 public]
| Balaenoptera_acutorostrata<br>Balaenoptera&nbsp;acutorostrata&nbsp;scammoni
| Balaenoptera_acutorostrata<br>Balaenoptera&nbsp;acutorostrata&nbsp;scammoni
| Minke whale
| Minke whale
Line 80: Line 88:
! 4
! 4
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau8 bosTau8]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau8 bosTau8]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau8 public]
| Bos_taurus
| Bos_taurus
| Cow
| Cow
Line 94: Line 103:
! 6
! 6
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=calJac3 calJac3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=calJac3 calJac3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=calJac3 public]
| Callithrix_jacchus
| Callithrix_jacchus
| Marmoset
| Marmoset
Line 108: Line 118:
! 8
! 8
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=canFam3 canFam3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=canFam3 canFam3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=canFam3 public]
| Canis_lupus<br>Canis&nbsp;lupus&nbsp;familiaris
| Canis_lupus<br>Canis&nbsp;lupus&nbsp;familiaris
| Dog
| Dog
Line 122: Line 133:
! 10
! 10
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=cavPor3 cavPor3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=cavPor3 cavPor3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=cavPor3 public]
| Cavia_porcellus
| Cavia_porcellus
| Guinea pig
| Guinea pig
Line 129: Line 141:
! 11
! 11
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=cerSim1 cerSim1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=cerSim1 cerSim1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=cerSim1 public]
| Ceratotherium_simum
| Ceratotherium_simum
| White rhinoceros
| White rhinoceros
Line 157: Line 170:
! 15
! 15
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=dasNov3 dasNov3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=dasNov3 dasNov3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=dasNov3 public]
| Dasypus_novemcinctus
| Dasypus_novemcinctus
| Armadillo
| Armadillo
Line 164: Line 178:
! 16
! 16
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=echTel2 echTel2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=echTel2 echTel2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=echTel2 public]
| Echinops_telfairi
| Echinops_telfairi
| Tenrec
| Tenrec
Line 178: Line 193:
! 18
! 18
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=eriEur2 eriEur2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=eriEur2 eriEur2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=eriEur2 public]
| Erinaceus_europaeus
| Erinaceus_europaeus
| Hedgehog
| Hedgehog
Line 186: Line 202:
| style="color:red;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=felCat5 felCat5]
| style="color:red;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=felCat5 felCat5]
(has dups: 1)
(has dups: 1)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=felCat5 public]
| Felis_catus
| Felis_catus
| Cat
| Cat
Line 194: Line 211:
! 20
! 20
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=felCat8 felCat8]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=felCat8 felCat8]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=felCat8 public]
| Felis_catus
| Felis_catus
| Cat
| Cat
Line 201: Line 219:
! 21
! 21
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galVar1 galVar1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galVar1 galVar1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galVar1 public]
| Galeopterus_variegatus
| Galeopterus_variegatus
| Malayan flying lemur
| Malayan flying lemur
Line 208: Line 227:
! 22
! 22
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hetGla2 hetGla2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hetGla2 hetGla2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hetGla2 public]
| Heterocephalus_glaber
| Heterocephalus_glaber
| Naked mole-rat
| Naked mole-rat
Line 215: Line 235:
! 23
! 23
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hg38 hg38]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hg38 hg38]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hg38 public]
| Homo_sapiens
| Homo_sapiens
| Human
| Human
Line 236: Line 257:
! 26
! 26
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=macFas5 macFas5]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=macFas5 macFas5]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=macFas5 public]
| Macaca_fascicularis
| Macaca_fascicularis
| Crab-eating macaque
| Crab-eating macaque
Line 250: Line 272:
! 28
! 28
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=micMur2 micMur2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=micMur2 micMur2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=micMur2 public]
| Microcebus_murinus
| Microcebus_murinus
| Mouse lemur
| Mouse lemur
Line 278: Line 301:
! 32
! 32
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=myoLuc2 myoLuc2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=myoLuc2 myoLuc2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=myoLuc2 public]
| Myotis_lucifugus
| Myotis_lucifugus
| Microbat
| Microbat
Line 307: Line 331:
| style="color:red;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar3 otoGar3]
| style="color:red;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar3 otoGar3]
(has dups: 139)
(has dups: 139)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=otoGar3 public]
| Otolemur_garnettii
| Otolemur_garnettii
| Bushbaby
| Bushbaby
Line 315: Line 340:
! 37
! 37
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oviAri3 oviAri3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oviAri3 oviAri3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oviAri3 public]
| Ovis_aries
| Ovis_aries
| Sheep
| Sheep
Line 329: Line 355:
! 39
! 39
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panPan1 panPan1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panPan1 panPan1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panPan1 public]
| Pan_paniscus
| Pan_paniscus
| Bonobo
| Bonobo
Line 350: Line 377:
! 42
! 42
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panTro4 panTro4]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panTro4 panTro4]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panTro4 public]
| Pan_troglodytes
| Pan_troglodytes
| Chimp
| Chimp
Line 364: Line 392:
! 44
! 44
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=papAnu2 papAnu2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=papAnu2 papAnu2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=papAnu2 public]
| Papio_anubis
| Papio_anubis
| Baboon
| Baboon
Line 385: Line 414:
! 47
! 47
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rheMac8 rheMac8]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rheMac8 rheMac8]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rheMac8 public]
| Macaca_mulatta
| Macaca_mulatta
| Rhesus
| Rhesus
Line 406: Line 436:
! 50
! 50
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sarHar1 sarHar1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sarHar1 sarHar1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sarHar1 public]
| Sarcophilus_harrisii
| Sarcophilus_harrisii
| Tasmanian devil
| Tasmanian devil
Line 413: Line 444:
! 51
! 51
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sorAra2 sorAra2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sorAra2 sorAra2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sorAra2 public]
| Sorex_araneus
| Sorex_araneus
| Shrew
| Shrew
Line 420: Line 452:
! 52
! 52
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=speTri2 speTri2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=speTri2 speTri2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=speTri2 public]
| Ictidomys_tridecemlineatus<br>Spermophilus&nbsp;tridecemlineatus
| Ictidomys_tridecemlineatus<br>Spermophilus&nbsp;tridecemlineatus
| Squirrel
| Squirrel
Line 427: Line 460:
! 53
! 53
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=susScr3 susScr3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=susScr3 susScr3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=susScr3 public]
| Sus_scrofa
| Sus_scrofa
| Pig
| Pig
Line 434: Line 468:
! 54
! 54
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=tarSyr2 tarSyr2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=tarSyr2 tarSyr2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=tarSyr2 public]
| Carlito_syrichta<br>Tarsius&nbsp;syrichta
| Carlito_syrichta<br>Tarsius&nbsp;syrichta
| Tarsier
| Tarsier
Line 441: Line 476:
! 55
! 55
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=tarSyr2 tarSyr2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=tarSyr2 tarSyr2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=tarSyr2 public]
| Tarsius_syrichta
| Tarsius_syrichta
| Tarsier
| Tarsier
Line 448: Line 484:
! 56
! 56
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=triMan1 triMan1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=triMan1 triMan1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=triMan1 public]
| Trichechus_manatus<br>Trichechus&nbsp;manatus&nbsp;latirostris
| Trichechus_manatus<br>Trichechus&nbsp;manatus&nbsp;latirostris
| Manatee
| Manatee
Line 470: Line 507:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]
(subset: 66 of 179)
(subset: 66 of 179)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 public]
| Mus_musculus
| Mus_musculus
| Mouse
| Mouse
Line 478: Line 516:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]
(subset: 66 of 182)
(subset: 66 of 182)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 public]
| Mus_musculus
| Mus_musculus
| Mouse
| Mouse
Line 486: Line 525:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]
(subset: 66 of 196)
(subset: 66 of 196)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 public]
| Mus_musculus
| Mus_musculus
| Mouse
| Mouse
Line 494: Line 534:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 mm10]
(subset: 66 of 207)
(subset: 66 of 207)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=mm10 public]
| Mus_musculus
| Mus_musculus
| Mouse
| Mouse
Line 502: Line 543:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rn6 rn6]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rn6 rn6]
(subset: 953 of 953)
(subset: 953 of 953)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rn6 public]
| Rattus_norvegicus
| Rattus_norvegicus
| Rat
| Rat
Line 511: Line 553:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=gorGor3 gorGor3]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=gorGor3 gorGor3]
(subset: 46823 of 50196)
(subset: 46823 of 50196)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=gorGor3 public]
| Gorilla_gorilla<br>Gorilla&nbsp;gorilla&nbsp;gorilla
| Gorilla_gorilla<br>Gorilla&nbsp;gorilla&nbsp;gorilla
| Gorilla
| Gorilla
Line 519: Line 562:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=vicPac2 vicPac2]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=vicPac2 vicPac2]
(subset: 276611 of 276611)
(subset: 276611 of 276611)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=vicPac2 public]
| Vicugna_pacos
| Vicugna_pacos
| Alpaca
| Alpaca
Line 528: Line 572:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=saiBol1 saiBol1]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=saiBol1 saiBol1]
(subset: 2685 of 2686)
(subset: 2685 of 2686)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=saiBol1 public]
| Saimiri_boliviensis
| Saimiri_boliviensis
| Squirrel monkey
| Squirrel monkey
Line 571: Line 616:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ochPri3 ochPri3]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ochPri3 ochPri3]
(subset: 10420 of 10420)
(subset: 10420 of 10420)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ochPri3 public]
| Ochotona_princeps
| Ochotona_princeps
| Pika
| Pika
Line 604: Line 650:
! 75
! 75
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=loxAfr3 loxAfr3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=loxAfr3 loxAfr3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=loxAfr3 public]
| Loxodonta_africana
| Loxodonta_africana
| Elephant
| Elephant
Line 612: Line 659:
! 76
! 76
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ornAna1 ornAna1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ornAna1 ornAna1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ornAna1 public]
| Ornithorhynchus_anatinus
| Ornithorhynchus_anatinus
| Platypus
| Platypus
Line 620: Line 668:
! 77
! 77
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau6 bosTau6]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau6 bosTau6]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau6 public]
| Bos_taurus
| Bos_taurus
| Cow
| Cow
Line 628: Line 677:
! 78
! 78
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oryCun2 oryCun2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oryCun2 oryCun2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oryCun2 public]
| Oryctolagus_cuniculus
| Oryctolagus_cuniculus
| Rabbit
| Rabbit
Line 636: Line 686:
! 79
! 79
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=nomLeu3 nomLeu3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=nomLeu3 nomLeu3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=nomLeu3 public]
| Nomascus_leucogenys
| Nomascus_leucogenys
| Gibbon
| Gibbon
Line 645: Line 696:
| style="color:red;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=turTru2 turTru2]
| style="color:red;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=turTru2 turTru2]
(has dups: 9)
(has dups: 9)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=turTru2 public]
| Tursiops_truncatus
| Tursiops_truncatus
| Dolphin
| Dolphin
Line 654: Line 706:
! 81
! 81
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=vicPac2 vicPac2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=vicPac2 vicPac2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=vicPac2 public]
| Vicugna_pacos
| Vicugna_pacos
| Alpaca
| Alpaca
Line 663: Line 716:
! 82
! 82
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=criGri1 criGri1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=criGri1 criGri1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=criGri1 public]
| Cricetulus_griseus
| Cricetulus_griseus
| Chinese hamster
| Chinese hamster
Line 679: Line 733:
! 84
! 84
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panTro3 panTro3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panTro3 panTro3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=panTro3 public]
| Pan_troglodytes
| Pan_troglodytes
| Chimp
| Chimp
Line 687: Line 742:
! 85
! 85
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ornAna2 ornAna2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ornAna2 ornAna2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ornAna2 public]
| Ornithorhynchus_anatinus
| Ornithorhynchus_anatinus
| Platypus
| Platypus
Line 696: Line 752:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rheMac2 rheMac2]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rheMac2 rheMac2]
(near match: 21 of 22)
(near match: 21 of 22)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=rheMac2 public]
| Macaca_mulatta
| Macaca_mulatta
| Rhesus
| Rhesus
Line 704: Line 761:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 monDom5]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 monDom5]
(near match: 10 of 11)
(near match: 10 of 11)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=monDom5 public]
| Monodelphis_domestica
| Monodelphis_domestica
| Opossum
| Opossum
Line 712: Line 770:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=equCab2 equCab2]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=equCab2 equCab2]
(near match: 33 of 34)
(near match: 33 of 34)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=equCab2 public]
| Equus_caballus
| Equus_caballus
| Horse
| Horse
Line 720: Line 779:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau7 bosTau7]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau7 bosTau7]
(near match: 11691 of 11692)
(near match: 11691 of 11692)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=bosTau7 public]
| Bos_taurus
| Bos_taurus
| Cow
| Cow
Line 872: Line 932:
! 108
! 108
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=allMis1 allMis1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=allMis1 allMis1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=allMis1 public]
| Alligator_mississippiensis
| Alligator_mississippiensis
| American alligator
| American alligator
Line 893: Line 954:
! 111
! 111
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=anoCar2 anoCar2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=anoCar2 anoCar2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=anoCar2 public]
| Anolis_carolinensis
| Anolis_carolinensis
| Lizard
| Lizard
Line 928: Line 990:
! 116
! 116
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=calMil1 calMil1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=calMil1 calMil1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=calMil1 public]
| Callorhinchus_milii
| Callorhinchus_milii
| Elephant shark
| Elephant shark
Line 1,005: Line 1,068:
! 127
! 127
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer10 danRer10]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer10 danRer10]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer10 public]
| Danio_rerio
| Danio_rerio
| Zebrafish
| Zebrafish
Line 1,012: Line 1,076:
! 128
! 128
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer7 danRer7]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer7 danRer7]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=danRer7 public]
| Danio_rerio
| Danio_rerio
| Zebrafish
| Zebrafish
Line 1,054: Line 1,119:
! 134
! 134
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=fr3 fr3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=fr3 fr3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=fr3 public]
| Takifugu_rubripes
| Takifugu_rubripes
| Fugu
| Fugu
Line 1,068: Line 1,134:
! 136
! 136
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal4 galGal4]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal4 galGal4]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=galGal4 public]
| Gallus_gallus
| Gallus_gallus
| Chicken
| Chicken
Line 1,096: Line 1,163:
! 140
! 140
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=geoFor1 geoFor1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=geoFor1 geoFor1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=geoFor1 public]
| Geospiza_fortis
| Geospiza_fortis
| Medium ground finch
| Medium ground finch
Line 1,117: Line 1,185:
! 143
! 143
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=latCha1 latCha1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=latCha1 latCha1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=latCha1 public]
| Latimeria_chalumnae
| Latimeria_chalumnae
| Coelacanth
| Coelacanth
Line 1,138: Line 1,207:
! 146
! 146
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melUnd1 melUnd1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melUnd1 melUnd1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melUnd1 public]
| Melopsittacus_undulatus
| Melopsittacus_undulatus
| Budgerigar
| Budgerigar
Line 1,181: Line 1,251:
| style="color:red;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oreNil2 oreNil2]
| style="color:red;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oreNil2 oreNil2]
(has dups: 170)
(has dups: 170)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=oreNil2 public]
| Oreochromis_niloticus
| Oreochromis_niloticus
| Nile tilapia
| Nile tilapia
Line 1,266: Line 1,337:
! 164
! 164
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=taeGut2 taeGut2]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=taeGut2 taeGut2]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=taeGut2 public]
| Taeniopygia_guttata
| Taeniopygia_guttata
| Zebra finch
| Zebra finch
Line 1,301: Line 1,373:
! 169
! 169
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=xenTro7 xenTro7]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=xenTro7 xenTro7]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=xenTro7 public]
| Xenopus_Silurana_tropicalis<br>Xenopus&nbsp;tropicalis
| Xenopus_Silurana_tropicalis<br>Xenopus&nbsp;tropicalis
| X. tropicalis
| X. tropicalis
Line 1,308: Line 1,381:
! 170
! 170
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=xenTro7 xenTro7]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=xenTro7 xenTro7]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=xenTro7 public]
| Xenopus_tropicalis
| Xenopus_tropicalis
| X. tropicalis
| X. tropicalis
Line 1,448: Line 1,522:
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melGal1 melGal1]
| style="color:green;" | [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melGal1 melGal1]
(near match: 5890 of 5891)
(near match: 5890 of 5891)
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=melGal1 public]
| Meleagris_gallopavo
| Meleagris_gallopavo
| Turkey
| Turkey
Line 1,547: Line 1,622:
! 200
! 200
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ce11 ce11]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ce11 ce11]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ce11 public]
| Caenorhabditis_elegans
| Caenorhabditis_elegans
| C. elegans
| C. elegans
Line 1,568: Line 1,644:
! 203
! 203
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=dm6 dm6]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=dm6 dm6]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=dm6 public]
| Drosophila_melanogaster
| Drosophila_melanogaster
| D. melanogaster
| D. melanogaster
Line 1,654: Line 1,731:
! 215
! 215
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=droPer1 droPer1]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=droPer1 droPer1]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=droPer1 public]
| Drosophila_persimilis
| Drosophila_persimilis
| D. persimilis
| D. persimilis
Line 1,800: Line 1,878:
! 235
! 235
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sacCer3 sacCer3]
| [http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sacCer3 sacCer3]
[http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=sacCer3 public]
| Saccharomyces_cerevisiae
| Saccharomyces_cerevisiae
| S. cerevisiae
| S. cerevisiae

Revision as of 23:19, 17 August 2016

The correspondences show here are exact, subset, and near match. NCBI assemblies with no equivalent UCSC database are listed.

The columns can be sorted. Click on the small arrow icon next to the column header label.

The external links go to:

  • test browser - genome-test.soe.ucsc.edu genome browser
    • public browser - when available the genome.ucsc.edu browser
  • RefSeq assembly - assembly information page at NCBI for the refseq version
    • Genbank assembly - assembly information page at NCBI when equivalent, genbank version
  • RefSeq FTP - ftp directory at NCBI where the RefSeq assembly can be obtained
    • Genbank FTP - ftp directory for the genbank version when equivalent


Note about the (has dups N) indication. Some older assemblies have entire sequences duplicated in multiple contigs in both the NCBI assembly and the UCSC assembly. Most newer UCSC assemblies have removed the duplicate contigs, and newer NCBI assemblies now also remove the duplicate contigs. The N indicates how many duplicate sequences are in the assembly. These duplicate contigs will cause confusion when coordinating chromosome names.

Note about the (subset N of M) indication. When all contigs of one assembly are completely found in the other assembly, it is marked as a (subset N of M). This is often the result of one assembly including a chrM/chrMT sequence, or duplicate sequences removed from one of the assemblies. The N of M counts the number of sequences in the subset vs. the superset after duplicate sequences have been removed.

Note about the (near match N of M) indication. When almost all contigs of one assembly are completely found in the other assembly, it is marked as a (near match N of M). This is often the result of different sequences for chrM/chrMT, included in each of the assemblies, or a different combination rearrangement of sequences in one assembly. For example monDom5 at UCSC combines all unplaced contigs into a single chrUn sequence whereas NCBI keeps those contigs as separate sequences. The N of M counts the number of sequences identical vs. the total sequences in the other assembly. The limit in this notation is a maximum difference of two sequences in the smaller assembly, and only for vertebrate_mammalian and vertebrate_other assemblies.


NCBI assemblies for the sub-groups vertebrate_mammalian and vertebrate_other with no equivalent UCSC database are indicated as (N sequences) where N is the number of sequences in the NCBI assembly.

UCSC to Genbank assembly accession correspondence
count test browser

public browser

scientific name(s) common name RefSeq assembly

Genbank assembly

RefSeq FTP

Genbank FTP

1 CHM1 Homo_sapiens
mole 		Homo sapiens hydatidiform mole assembly chm1 GCF_000306695.2_CHM1_1.1 vertebrate_mammalian
2 ailMel1

public

Ailuropoda_melanoleuca Panda GCF_000004335.2_AilMel_1.0 vertebrate_mammalian
3 balAcu1

public

Balaenoptera_acutorostrata
Balaenoptera acutorostrata scammoni 		Minke whale GCF_000493695.1_BalAcu1.0 vertebrate_mammalian
4 bosTau8

public

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

public

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

public

Canis_lupus
Canis lupus familiaris 		Dog GCF_000002285.3_CanFam3.1 vertebrate_mammalian
9 capHir1 Capra_hircus Domestic goat GCF_000317765.1_CHIR_1.0 vertebrate_mammalian
10 cavPor3

public

Cavia_porcellus Guinea pig GCF_000151735.1_Cavpor3.0 vertebrate_mammalian
11 cerSim1

public

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
Colobus angolensis palliatus 		Angolan colobus GCF_000951035.1_Cang.pa_1.0 vertebrate_mammalian
15 dasNov3

public

Dasypus_novemcinctus Armadillo GCF_000208655.1_Dasnov3.0 vertebrate_mammalian
16 echTel2

public

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

public

Erinaceus_europaeus Hedgehog GCF_000296755.1_EriEur2.0 vertebrate_mammalian
19 felCat5

(has dups: 1) public

Felis_catus Cat GCF_000181335.1_Felis_catus-6.2

(has dups: 1)

vertebrate_mammalian
20 felCat8

public

Felis_catus Cat GCF_000181335.2_Felis_catus_8.0 vertebrate_mammalian
21 galVar1

public

Galeopterus_variegatus Malayan flying lemur GCF_000696425.1_G_variegatus-3.0.2 vertebrate_mammalian
22 hetGla2

public

Heterocephalus_glaber Naked mole-rat GCF_000247695.1_HetGla_female_1.0 vertebrate_mammalian
23 hg38

public

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

public

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

public

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

public

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 oryAfe1 Orycteropus_afer
Orycteropus afer afer 		Aardvark GCF_000298275.1_OryAfe1.0 vertebrate_mammalian
36 otoGar3

(has dups: 139) public

Otolemur_garnettii Bushbaby GCF_000181295.1_OtoGar3

(has dups: 139)

vertebrate_mammalian
37 oviAri3

public

Ovis_aries Sheep GCF_000298735.1_Oar_v3.1 vertebrate_mammalian
38 panHod1 Pantholops_hodgsonii Tibetan antelope GCF_000400835.1_PHO1.0 vertebrate_mammalian
39 panPan1

public

Pan_paniscus Bonobo GCF_000258655.1_panpan1 vertebrate_mammalian
40 panPan2 Pan_paniscus Bonobo GCF_000258655.2_panpan1.1 vertebrate_mammalian
41 panTig1 Panthera_tigris
Panthera tigris altaica 		Amur tiger GCF_000464555.1_PanTig1.0 vertebrate_mammalian
42 panTro4

public

Pan_troglodytes Chimp GCF_000001515.6_Pan_troglodytes-2.1.4 vertebrate_mammalian
43 panTro5 Pan_troglodytes Chimp GCF_000001515.7_Pan_tro_3.0 vertebrate_mammalian
44 papAnu2

public

Papio_anubis Baboon GCF_000264685.1_Panu_2.0 vertebrate_mammalian
45 perManBai1 Peromyscus_maniculatus
Peromyscus maniculatus bairdii 		Prairie deer mouse GCF_000500345.1_Pman_1.0 vertebrate_mammalian
46 phyCat1 Physeter_catodon Sperm whale GCF_000472045.1_Physeter_macrocephalus-2.0.2 vertebrate_mammalian
47 rheMac8

public

Macaca_mulatta Rhesus GCF_000772875.2_Mmul_8.0.1 vertebrate_mammalian
48 rhiRox1 Rhinopithecus_roxellana Golden snub-nosed monkey GCF_000769185.1_Rrox_v1 vertebrate_mammalian
49 rouAeg1 Rousettus_aegyptiacus Egyptian rousette GCF_001466805.2_Raegyp2.0 vertebrate_mammalian
50 sarHar1

public

Sarcophilus_harrisii Tasmanian devil GCF_000189315.1_Devil_ref_v7.0 vertebrate_mammalian
51 sorAra2

public

Sorex_araneus Shrew GCF_000181275.1_SorAra2.0 vertebrate_mammalian
52 speTri2

public

Ictidomys_tridecemlineatus
Spermophilus tridecemlineatus 		Squirrel GCF_000236235.1_SpeTri2.0 vertebrate_mammalian
53 susScr3

public

Sus_scrofa Pig GCF_000003025.5_Sscrofa10.2 vertebrate_mammalian
54 tarSyr2

public

Carlito_syrichta
Tarsius syrichta 		Tarsier GCF_000164805.1_Tarsius_syrichta-2.0.1 vertebrate_mammalian
55 tarSyr2

public

Tarsius_syrichta Tarsier GCF_000164805.1_Tarsius_syrichta-2.0.1 vertebrate_mammalian
56 triMan1

public

Trichechus_manatus
Trichechus manatus latirostris 		Manatee GCF_000243295.1_TriManLat1.0 vertebrate_mammalian
57 tupChi1 Tupaia_chinensis Chinese tree shrew GCF_000334495.1_TupChi_1.0 vertebrate_mammalian
58 ursMar1 Ursus_maritimus Polar bear GCF_000687225.1_UrsMar_1.0 vertebrate_mammalian
59 mm10

(subset: 66 of 179) public

Mus_musculus Mouse GCF_000001635.22_GRCm38.p2 vertebrate_mammalian
60 mm10

(subset: 66 of 182) public

Mus_musculus Mouse GCF_000001635.23_GRCm38.p3 vertebrate_mammalian
61 mm10

(subset: 66 of 196) public

Mus_musculus Mouse GCF_000001635.24_GRCm38.p4 vertebrate_mammalian
62 mm10

(subset: 66 of 207) public

Mus_musculus Mouse GCF_000001635.25_GRCm38.p5 vertebrate_mammalian
63 rn6

(subset: 953 of 953) public

Rattus_norvegicus Rat GCF_000001895.5_Rnor_6.0

(has dups: 1)

vertebrate_mammalian
64 gorGor3

(subset: 46823 of 50196) public

Gorilla_gorilla
Gorilla gorilla gorilla 		Gorilla GCF_000151905.1_gorGor3.1 vertebrate_mammalian
65 vicPac2

(subset: 276611 of 276611) public

Vicugna_pacos Alpaca GCF_000164845.1_Vicugna_pacos-2.0.1

(has dups: 115)

vertebrate_mammalian
66 saiBol1

(subset: 2685 of 2686) public

Saimiri_boliviensis Squirrel monkey GCF_000235385.1_SaiBol1.0 vertebrate_mammalian
67 octDeg1

(subset: 7134 of 7134)

Octodon_degus Brush-tailed rat GCF_000260255.1_OctDeg1.0

(has dups: 1)

vertebrate_mammalian
68 conCri1

(subset: 2038 of 2038)

Condylura_cristata Star-nosed mole GCF_000260355.1_ConCri1.0

(has dups: 2)

vertebrate_mammalian
69 chiLan1

(subset: 2838 of 2839)

Chinchilla_lanigera Chinchilla GCF_000276665.1_ChiLan1.0 vertebrate_mammalian
70 jacJac1

(subset: 10896 of 10896)

Jaculus_jaculus Lesser Egyptian jerboa GCF_000280705.1_JacJac1.0

(has dups: 2)

vertebrate_mammalian
71 ochPri3

(subset: 10420 of 10420) public

Ochotona_princeps Pika GCF_000292845.1_OchPri3.0

(has dups: 1)

vertebrate_mammalian
72 bosMut1

(subset: 41191 of 41192)

Bos_mutus
Bos grunniens mutus 		Wild yak GCF_000298355.1_BosGru_v2.0 vertebrate_mammalian
73 eptFus1

(subset: 6788 of 6788)

Eptesicus_fuscus Big brown bat GCF_000308155.1_EptFus1.0

(has dups: 1)

vertebrate_mammalian
74 pteAle1

(subset: 65597 of 65598)

Pteropus_alecto Black flying-fox GCF_000325575.1_ASM32557v1 vertebrate_mammalian
75 loxAfr3

public

Loxodonta_africana Elephant GCF_000001905.1_Loxafr3.0

(subset: 2352 of 2353)

vertebrate_mammalian
76 ornAna1

public

Ornithorhynchus_anatinus Platypus GCF_000002275.2_Ornithorhynchus_anatinus_5.0.1

(subset: 200154 of 201523)

vertebrate_mammalian
77 bosTau6

public

Bos_taurus Cow GCF_000003055.6_Bos_taurus_UMD_3.1.1

(subset: 3144 of 3317)

vertebrate_mammalian
78 oryCun2

public

Oryctolagus_cuniculus Rabbit GCF_000003625.3_OryCun2.0

(subset: 3241 of 3242)

vertebrate_mammalian
79 nomLeu3

public

Nomascus_leucogenys Gibbon GCF_000146795.2_Nleu_3.0

(subset: 17484 of 17492)

vertebrate_mammalian
80 turTru2

(has dups: 9) public

Tursiops_truncatus Dolphin GCF_000151865.2_Ttru_1.4

(has dups: 9) (subset: 240548 of 240891)

vertebrate_mammalian
81 vicPac2

public

Vicugna_pacos Alpaca GCF_000164845.2_Vicugna_pacos-2.0.2

(has dups: 115) (subset: 276610 of 276611)

vertebrate_mammalian
82 criGri1

public

Cricetulus_griseus Chinese hamster GCF_000419365.1_C_griseus_v1.0

(subset: 52710 of 52711)

vertebrate_mammalian
83 bisBis1 Bison_bison
Bison bison bison 		Bison GCF_000754665.1_Bison_UMD1.0

(subset: 128431 of 450182)

vertebrate_mammalian
84 panTro3

public

Pan_troglodytes Chimp GCF_000001515.5_Pan_troglodytes-2.1.4

(near match: 24127 of 24129)

vertebrate_mammalian
85 ornAna2

public

Ornithorhynchus_anatinus Platypus GCF_000002275.2_Ornithorhynchus_anatinus_5.0.1

(near match: 200153 of 200154)

vertebrate_mammalian
86 rheMac2

(near match: 21 of 22) public

Macaca_mulatta Rhesus GCF_000002255.3_Mmul_051212 vertebrate_mammalian
87 monDom5

(near match: 10 of 11) public

Monodelphis_domestica Opossum GCF_000002295.2_MonDom5 vertebrate_mammalian
88 equCab2

(near match: 33 of 34) public

Equus_caballus Horse GCF_000002305.2_EquCab2.0 vertebrate_mammalian
89 bosTau7

(near match: 11691 of 11692) public

Bos_taurus Cow GCF_000003205.5_Btau_4.6.1 vertebrate_mammalian
90 equPrz1

(near match: 53096 of 53097)

Equus_przewalskii Przewalski horse GCF_000696695.1_Burgud vertebrate_mammalian
91 notFound Homo_sapiens Human GCF_000001405.30_GRCh38.p4

(510 sequences)

vertebrate_mammalian
92 notFound Homo_sapiens Human GCF_000001405.32_GRCh38.p6

(521 sequences)

vertebrate_mammalian
93 notFound Rattus_norvegicus Norway rat GCF_000002265.2_Rn_Celera

(has dups: 5) (7041 sequences)

vertebrate_mammalian
94 notFound Homo_sapiens Human GCF_000001405.31_GRCh38.p5

(517 sequences)

vertebrate_mammalian
95 notFound Ovis_aries
Ovis aries musimon 		Mouflon GCF_000765115.1_Oori1

(6173 sequences)

vertebrate_mammalian
96 notFound Pteropus_vampyrus Large flying fox GCF_000151845.1_Pvam_2.0

(36094 sequences)

vertebrate_mammalian
97 notFound Homo_sapiens Human GCF_000001405.33_GRCh38.p7

(525 sequences)

vertebrate_mammalian
98 notFound Mus_musculus House mouse GCF_000002165.2_Mm_Celera

(12503 sequences)

vertebrate_mammalian
99 notFound Homo_sapiens Human GCF_000001405.34_GRCh38.p8

(543 sequences)

vertebrate_mammalian
100 notFound Homo_sapiens Human GCF_000001405.27_GRCh38.p1

(471 sequences)

vertebrate_mammalian
101 notFound Ovis_aries Sheep GCF_000298735.2_Oar_v4.0

(5466 sequences)

vertebrate_mammalian
102 notFound Homo_sapiens Human GCF_000001405.28_GRCh38.p2

(486 sequences)

vertebrate_mammalian
103 notFound Cricetulus_griseus Chinese hamster GCF_000223135.1_CriGri_1.0

(109152 sequences)

vertebrate_mammalian
104 notFound Bos_taurus Cattle GCF_000003205.7_Btau_5.0.1

(3143 sequences)

vertebrate_mammalian
105 notFound Pongo_abelii Sumatran orangutan GCF_000001545.4_P_pygmaeus_2.0.2

(61535 sequences)

vertebrate_mammalian
106 notFound Homo_sapiens Human GCF_000001405.29_GRCh38.p3

(494 sequences)

vertebrate_mammalian
107 notFound Dipodomys_ordii Ord's kangaroo rat GCF_000151885.1_Dord_2.0

(65193 sequences)

vertebrate_mammalian
108 allMis1

public

Alligator_mississippiensis American alligator GCF_000281125.1_allMis0.2 vertebrate_other
109 allSin1 Alligator_sinensis Chinese alligator GCF_000455745.1_ASM45574v1 vertebrate_other
110 anaPla1 Anas_platyrhynchos Mallard duck GCF_000355885.1_BGI_duck_1.0 vertebrate_other
111 anoCar2

public

Anolis_carolinensis Lizard GCF_000090745.1_AnoCar2.0 vertebrate_other
112 apaVit1 Apaloderma_vittatum Bar tailed trogon GCF_000703405.1_ASM70340v1 vertebrate_other
113 aptFor1 Aptenodytes_forsteri Emperor penguin GCF_000699145.1_ASM69914v1 vertebrate_other
114 bucRhi1 Buceros_rhinoceros
Buceros rhinoceros silvestris 		Rhinoceros hornbill GCF_000710305.1_ASM71030v1 vertebrate_other
115 calAnn1 Calypte_anna Anna's hummingbird GCF_000699085.1_ASM69908v1 vertebrate_other
116 calMil1

public

Callorhinchus_milii Elephant shark GCF_000165045.1_Callorhinchus_milii-6.1.3 vertebrate_other
117 capCar1 Caprimulgus_carolinensis Chuck-will's-widow GCF_000700745.1_ASM70074v1 vertebrate_other
118 carCri1 Cariama_cristata Red-legged seriema GCF_000690535.1_ASM69053v1 vertebrate_other
119 chaVoc2 Charadrius_vociferus Killdeer GCF_000708025.1_ASM70802v2 vertebrate_other
120 cheMyd1 Chelonia_mydas Green seaturtle GCF_000344595.1_CheMyd_1.0 vertebrate_other
121 chlUnd1 Chlamydotis_macqueenii
Chlamydotis undulata macqueenii 		Houbara bustard GCF_000695195.1_ASM69519v1 vertebrate_other
122 colLiv1 Columba_livia Rock pigeon GCF_000337935.1_Cliv_1.0 vertebrate_other
123 colStr1 Colius_striatus Speckled mousebird GCF_000690715.1_ASM69071v1 vertebrate_other
124 corBra1 Corvus_brachyrhynchos American crow GCF_000691975.1_ASM69197v1 vertebrate_other
125 cucCan1 Cuculus_canorus Common cuckoo GCF_000709325.1_ASM70932v1 vertebrate_other
126 cynSem1 Cynoglossus_semilaevis Tongue sole GCF_000523025.1_Cse_v1.0 vertebrate_other
127 danRer10

public

Danio_rerio Zebrafish GCF_000002035.5_GRCz10 vertebrate_other
128 danRer7

public

Danio_rerio Zebrafish GCF_000002035.4_Zv9 vertebrate_other
129 egrGar1 Egretta_garzetta Little egret GCF_000687185.1_ASM68718v1 vertebrate_other
130 eurHel1 Eurypyga_helias Sunbittern GCF_000690775.1_ASM69077v1 vertebrate_other
131 falChe1 Falco_cherrug Saker falcon GCF_000337975.1_F_cherrug_v1.0 vertebrate_other
132 falPer1 Falco_peregrinus Peregrine falcon GCF_000337955.1_F_peregrinus_v1.0 vertebrate_other
133 ficAlb2 Ficedula_albicollis Collared flycatcher GCF_000247815.1_FicAlb1.5 vertebrate_other
134 fr3

public

Takifugu_rubripes Fugu GCF_000180615.1_FUGU5 vertebrate_other
135 fulGla1 Fulmarus_glacialis Northern fulmar GCF_000690835.1_ASM69083v1 vertebrate_other
136 galGal4

public

Gallus_gallus Chicken GCF_000002315.3_Gallus_gallus-4.0 vertebrate_other
137 galGal5 Gallus_gallus Chicken GCF_000002315.4_Gallus_gallus-5.0 vertebrate_other
138 gavSte1 Gavia_stellata Red-throated loon GCF_000690875.1_ASM69087v1 vertebrate_other
139 gekJap0 Gekko japonicus notFound GCF_001447785.1_Gekko_japonicus_V1.1 vertebrate_other
140 geoFor1

public

Geospiza_fortis Medium ground finch GCF_000277835.1_GeoFor_1.0 vertebrate_other
141 halAlb1 Haliaeetus_albicilla White-tailed eagle GCF_000691405.1_ASM69140v1 vertebrate_other
142 halLeu1 Haliaeetus_leucocephalus Bald eagle GCF_000737465.1_Haliaeetus_leucocephalus-4.0 vertebrate_other
143 latCha1

public

Latimeria_chalumnae Coelacanth GCF_000225785.1_LatCha1 vertebrate_other
144 lepDis1 Leptosomus_discolor Cuckoo roller GCF_000691785.1_ASM69178v1 vertebrate_other
145 mayZeb1 Maylandia_zebra Zebra mbuna GCF_000238955.1_MetZeb1.1 vertebrate_other
146 melUnd1

public

Melopsittacus_undulatus Budgerigar GCF_000238935.1_Melopsittacus_undulatus_6.3 vertebrate_other
147 merNub1 Merops_nubicus Northern carmine bee-eater GCF_000691845.1_ASM69184v1 vertebrate_other
148 mesUni1 Mesitornis_unicolor Brown roatelo GCF_000695765.1_ASM69576v1 vertebrate_other
149 nipNip1 Nipponia_nippon Crested ibis GCF_000708225.1_ASM70822v1 vertebrate_other
150 notCor1 Notothenia_coriiceps Black rockcod GCF_000735185.1_NC01 vertebrate_other
151 opiHoa1 Opisthocomus_hoazin Hoatzin GCF_000692075.1_ASM69207v1 vertebrate_other
152 oreNil2

(has dups: 170) public

Oreochromis_niloticus Nile tilapia GCF_000188235.2_Orenil1.1

(has dups: 170)

vertebrate_other
153 pelCri1 Pelecanus_crispus Dalmatian pelican GCF_000687375.1_ASM68737v1 vertebrate_other
154 pelSin1 Pelodiscus_sinensis Chinese softshell turtle GCF_000230535.1_PelSin_1.0 vertebrate_other
155 phaCar1 Phalacrocorax_carbo Great cormorant GCF_000708925.1_ASM70892v1 vertebrate_other
156 phaLep1 Phaethon_lepturus White-tailed tropicbird GCF_000687285.1_ASM68728v1 vertebrate_other
157 picPub1 Picoides_pubescens Downy woodpecker GCF_000699005.1_ASM69900v1 vertebrate_other
158 poeFor1 Poecilia_formosa Amazon molly GCF_000485575.1_Poecilia_formosa-5.1.2 vertebrate_other
159 pseHum1 Pseudopodoces_humilis Tibetan ground jay GCF_000331425.1_PseHum1.0 vertebrate_other
160 pteGut1 Pterocles_gutturalis Yellow-throated sandgrouse GCF_000699245.1_ASM69924v1 vertebrate_other
161 pytBiv0 Python bivittatus notFound GCF_000186305.1_Python_molurus_bivittatus-5.0.2 vertebrate_other
162 pytBiv1 Python_bivittatus Burmese python GCF_000186305.1_Python_molurus_bivittatus-5.0.2 vertebrate_other
163 strCam1 Struthio_camelus
Struthio camelus australis 		Ostrich GCF_000698965.1_ASM69896v1 vertebrate_other
164 taeGut2

public

Taeniopygia_guttata Zebra finch GCF_000151805.1_Taeniopygia_guttata-3.2.4 vertebrate_other
165 tauEry1 Tauraco_erythrolophus Red crested turaco GCF_000709365.1_ASM70936v1 vertebrate_other
166 thaSir0 Thamnophis sirtalis notFound GCF_001077635.1_Thamnophis_sirtalis-6.0 vertebrate_other
167 tinGut2 Tinamus_guttatus White throated tinamou GCF_000705375.1_ASM70537v2 vertebrate_other
168 tytAlb1 Tyto_alba Barn owl GCF_000687205.1_ASM68720v1 vertebrate_other
169 xenTro7

public

Xenopus_Silurana_tropicalis
Xenopus tropicalis 		X. tropicalis GCF_000004195.2_Xtropicalis_v7 vertebrate_other
170 xenTro7

public

Xenopus_tropicalis X. tropicalis GCF_000004195.2_Xtropicalis_v7 vertebrate_other
171 xipMac1 Xiphophorus_maculatus Southern platyfish GCF_000241075.1_Xiphophorus_maculatus-4.4.2 vertebrate_other
172 zonAlb1 Zonotrichia_albicollis White-throated sparrow GCF_000385455.1_Zonotrichia_albicollis-1.0.1 vertebrate_other
173 punNye1

(subset: 7233 of 7233)

Pundamilia_nyererei Pundamilia nyererei GCF_000239375.1_PunNye1.0

(has dups: 3)

vertebrate_other
174 neoBri1

(subset: 9083 of 9083)

Neolamprologus_brichardi Princess of Burundi GCF_000239395.1_NeoBri1.0

(has dups: 16)

vertebrate_other
175 hapBur1

(subset: 7994 of 7994)

Haplochromis_burtoni Burton's mouthbreeder GCF_000239415.1_AstBur1.0

(has dups: 7)

vertebrate_other
176 lepOcu1

(subset: 1925 of 1925)

Lepisosteus_oculatus Spotted gar GCF_000242695.1_LepOcu1

(has dups: 1)

vertebrate_other
177 serCan1

(subset: 304397 of 304397)

Serinus_canaria Canary GCF_000534875.1_SCA1

(has dups: 3)

vertebrate_other
178 stePar1

(subset: 5817 of 5817)

Stegastes_partitus Bicolor damselfish GCF_000690725.1_Stegastes_partitus-1.0.2

(has dups: 1)

vertebrate_other
179 pygAde1

(subset: 19264 of 19265)

Pygoscelis_adeliae Adelie penguin GCF_000699105.1_ASM69910v1 vertebrate_other
180 esoLuc1

(subset: 5325 of 5326)

Esox_lucius Northern pike GCF_000721915.1_EsoLuc1.0 vertebrate_other
181 cypVar1

(subset: 9258 of 9259)

Cyprinodon_variegatus Sheepshead minnow GCF_000732505.1_C_variegatus-1.0 vertebrate_other
182 corCor1

(subset: 1298 of 1299)

Corvus_cornix
Corvus cornix cornix 		Hooded crow GCF_000738735.1_Hooded_Crow_genome vertebrate_other
183 aquChr2

(subset: 1141 of 1142)

Aquila_chrysaetos
Aquila chrysaetos canadensis 		Golden eagle GCF_000766835.1_Aquila_chrysaetos-1.0.2 vertebrate_other
184 astMex1 Astyanax_mexicanus Mexican tetra (cavefish) GCF_000372685.1_Astyanax_mexicanus-1.0.2

(subset: 10735 of 10736)

vertebrate_other
185 manVit1 Manacus_vitellinus Golden-collared manakin GCF_000692015.1_ASM69201v2

(subset: 92755 of 92789)

vertebrate_other
186 acaChl1 Acanthisitta_chloris Rifleman GCF_000695815.1_ASM69581v1

(subset: 53875 of 53876)

vertebrate_other
187 melGal1

(near match: 5890 of 5891) public

Meleagris_gallopavo Turkey GCF_000146605.1_Turkey_2.01 vertebrate_other
188 chrPic2

(near match: 78594 of 78595)

Chrysemys_picta
Chrysemys picta bellii 		Painted turtle GCF_000241765.3_Chrysemys_picta_bellii-3.0.3 vertebrate_other
189 poeRet1

(near match: 2766 of 2767)

Poecilia_reticulata Guppy GCF_000633615.1_Guppy_female_1.0_MT

(has dups: 1)

vertebrate_other
190 notFound Nestor_notabilis Kea GCF_000696875.1_ASM69687v1

(42180 sequences)

vertebrate_other
191 notFound Coturnix_japonica Japanese quail GCF_001577835.1_Coturnix_japonica_2.0

(2012 sequences)

vertebrate_other
192 notFound Esox_lucius Northern pike GCF_000721915.2_ASM72191v2

(1520 sequences)

vertebrate_other
193 notFound Meleagris_gallopavo Turkey GCF_000146605.2_Turkey_5.0

(231286 sequences)

vertebrate_other
194 notFound Oryzias_latipes Japanese medaka GCF_000313675.1_ASM31367v1

(7189 sequences)

vertebrate_other
195 acrEch0 Acromyrmex echinatior notFound GCF_000204515.1_Aech_3.9 invertebrate
196 apiMel4 Apis_mellifera A. mellifera GCF_000002195.4_Amel_4.5 invertebrate
197 attCep0 Atta cephalotes notFound GCF_000143395.1_Attacep1.0 invertebrate
198 caeRem4 Caenorhabditis_remanei C. remanei GCF_000149515.1_ASM14951v1 invertebrate
199 camFlo0 Camponotus floridanus notFound GCF_000147175.1_CamFlo_1.0 invertebrate
200 ce11

public

Caenorhabditis_elegans C. elegans GCF_000002985.6_WBcel235 invertebrate
201 cerBir0 Cerapachys biroi notFound GCF_000611835.1_CerBir1.0 invertebrate
202 ci3 Ciona_intestinalis C. intestinalis GCF_000224145.1_KH invertebrate
203 dm6

public

Drosophila_melanogaster D. melanogaster GCF_000001215.4_Release_6_plus_ISO1_MT invertebrate
204 droAna3

(has dups: 2)

Drosophila_ananassae D. ananassae GCF_000005115.1_dana_caf1

(has dups: 2)

invertebrate
205 droBia2 Drosophila_biarmipes D. biarmipes GCF_000233415.1_Dbia_2.0 invertebrate
206 droBip2 Drosophila_bipectinata D. bipectinata GCF_000236285.1_Dbip_2.0 invertebrate
207 droEle2 Drosophila_elegans D. elegans GCF_000224195.1_Dele_2.0 invertebrate
208 droEre2 Drosophila_erecta D. erecta GCF_000005135.1_dere_caf1 invertebrate
209 droEug2 Drosophila_eugracilis D. eugracilis GCF_000236325.1_Deug_2.0 invertebrate
210 droFic2 Drosophila_ficusphila D. ficusphila GCF_000220665.1_Dfic_2.0 invertebrate
211 droGri2 Drosophila_grimshawi D. grimshawi GCF_000005155.2_dgri_caf1 invertebrate
212 droKik2 Drosophila_kikkawai D. kikkawai GCF_000224215.1_Dkik_2.0 invertebrate
213 droMir2 Drosophila_miranda D. miranda GCF_000269505.1_DroMir_2.2 invertebrate
214 droMoj3 Drosophila_mojavensis D. mojavensis GCF_000005175.2_dmoj_caf1 invertebrate
215 droPer1

public

Drosophila_persimilis D. persimilis GCF_000005195.2_dper_caf1 invertebrate
216 droRho2 Drosophila_rhopaloa D. rhopaloa GCF_000236305.1_Drho_2.0 invertebrate
217 droSuz1 Drosophila_suzukii D. suzukii GCF_000472105.1_Dsuzukii.v01 invertebrate
218 droTak2 Drosophila_takahashii D. takahashii GCF_000224235.1_Dtak_2.0 invertebrate
219 droVir3

(has dups: 1)

Drosophila_virilis D. virilis GCF_000005245.1_dvir_caf1

(has dups: 1)

invertebrate
220 droWil2 Drosophila_willistoni D. willistoni GCF_000005925.1_dwil_caf1 invertebrate
221 droYak3 Drosophila_yakuba D. yakuba GCF_000005975.2_dyak_caf1 invertebrate
222 harSal0 Harpegnathos saltator notFound GCF_000147195.1_HarSal_1.0 invertebrate
223 linHum0

(has dups: 1)

Linepithema humile notFound GCF_000217595.1_Lhum_UMD_V04

(has dups: 1)

invertebrate
224 lotGig0 Lottia_gigantea Limpet GCF_000327385.1_Helro1 invertebrate
225 pogBar0 Pogonomyrmex barbatus notFound GCF_000187915.1_Pbar_UMD_V03 invertebrate
226 solInv0 Solenopsis invicta notFound GCF_000188075.1_Si_gnG invertebrate
227 strPur4

(has dups: 1)

Strongylocentrotus_purpuratus S. purpuratus GCF_000002235.3_Spur_3.1

(has dups: 1)

invertebrate
228 araTha1 Arabidopsis thaliana notFound GCF_000001735.3_TAIR10 plant
229 ricCom1 Ricinus communis notFound GCF_000151685.1_JCVI_RCG_1.1 plant
230 bunEbo1 Bundibugyo_virus
Bundibugyo ebolavirus 		Bundibugyo ebolavirus GCF_000889155.1_ViralProj51245 viral
231 resEbo1 Reston_ebolavirus Reston ebolavirus GCF_000854085.1_ViralProj15006 viral
232 sudEbo1 Sudan_ebolavirus Sudan ebolavirus GCF_000855585.1_ViralProj15012 viral
233 taiEbo1 Tai_Forest_ebolavirus Tai forest ebolavirus GCF_000888475.1_ViralProj51257 viral
234 zaiEbo1 Zaire_ebolavirus Zaire ebolavirus GCF_000848505.1_ViralProj14703 viral
235 sacCer3

public

Saccharomyces_cerevisiae S. cerevisiae GCF_000146045.2_R64 fungi
Retrieved from "https://genomewiki.ucsc.edu/index.php?title=UCSC_to_RefSeq_correspondence&oldid=23355"