Assembly Releases and Versions
Topics
List of UCSC genome releases
How do UCSC’s release numbers correspond to those of other organizations, such as NCBI?
The first release of an assembly is given a name using the first three characters of the organism’s genus and species classification in the format gggSss#, with subsequent assemblies incrementing the number. Assemblies predating the 2003 introduction of the six-letter naming system were given two-letter names in a similar gs# format and human assemblies are named hg# for human genome.
SPECIES
UCSC VERSION
RELEASE DATE
RELEASE NAME
STATUS
MAMMALS
Human
hg38
Dec. 2013
Genome Reference Consortium GRCh38
Available
hg19
Feb. 2009
Genome Reference Consortium GRCh37
Available
hg18
Mar. 2006
NCBI Build 36.1
Available
hg17
May 2004
NCBI Build 35
Available
hg16
Jul. 2003
NCBI Build 34
Available
hg15
Apr. 2003
NCBI Build 33
Archived
hg13
Nov. 2002
NCBI Build 31
Archived
hg12
Jun. 2002
NCBI Build 30
Archived
hg11
Apr. 2002
NCBI Build 29
Archived (data only)
hg10
Dec. 2001
NCBI Build 28
Archived (data only)
hg8
Aug. 2001
UCSC-assembled
Archived (data only)
hg7
Apr. 2001
UCSC-assembled
Archived (data only)
hg6
Dec. 2000
UCSC-assembled
Archived (data only)
hg5
Oct. 2000
UCSC-assembled
Archived (data only)
hg4
Sep. 2000
UCSC-assembled
Archived (data only)
hg3
Jul. 2000
UCSC-assembled
Archived (data only)
hg2
Jun. 2000
UCSC-assembled
Archived (data only)
hg1
May 2000
UCSC-assembled
Archived (data only)
Alpaca
vicPac2
Mar. 2013
Broad Institute Vicugna_pacos-2.0.1
Available
vicPac1
Jul. 2008
Broad Institute VicPac1.0
Available
Armadillo
dasNov3
Dec. 2011
Broad Institute DasNov3
Available
Baboon
papAnu4
Apr. 2017
Human Genome Sequencing Center
Available
papAnu2
Mar. 2012
Baylor College of Medicine Panu_2.0
Available
papHam1
Nov. 2008
Baylor College of Medicine HGSC Pham_1.0
Available
Bison
bisBis1
Oct. 2014
Univ. of Maryland Bison_UMD1.0
Available
Bonobo
panPan3
May 2020
University of Washington
Available
panPan2
Dec. 2015
Max-Planck Institute for Evolutionary Anthropology panpan1.1
Available
panPan1
May 2012
Max-Planck Institute panpan1
Available
Brown kiwi
aptMan1
Jun. 2015
Max-Planck Institute for Evolutionary Anthropology AptMant0
Available
Bushbaby
otoGar3
Mar. 2011
Broad Institute OtoGar3
Available
Cat
felCat9
Nov. 2017
Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine Felis_catus_9.0
Available
felCat8
Nov. 2014
ICGSC Felis_catus_8.0
Available
felCat5
Sep. 2011
ICGSC Felis_catus-6.2
Available
felCat4
Dec. 2008
NHGRI catChrV17e
Available
felCat3
Mar. 2006
Broad Institute Release 3
Available
Chimp
panTro6
Jan. 2018
Clint_PTRv2
Available
panTro5
May 2016
CGSC Build 3.0
Available
panTro4
Feb. 2011
CGSC Build 2.1.4
Available
panTro3
Oct. 2010
CGSC Build 2.1.3
Available
panTro2
Mar. 2006
CGSC Build 2.1
Available
panTro1
Nov. 2003
CGSC Build 1.1
Available
Chinese hamster
criGri1
Jul. 2013
Beijing Genomics Institution-Shenzhen C_griseus_v1.0
Available
Chinese hamster ovary cell line
criGriChoV2
Jun. 2017
Eagle Genomics Ltd CHOK1S_HZDv1
Available
criGriChoV1
Aug. 2011
Beijing Genomics Institute CriGri_1.0
Available
Chinese pangolin
manPen1
Aug. 2014
Washington University (WashU) M_pentadactyla-1.1.1
Available
Cow
bosTau9
Apr. 2018
USDA ARS
Available
bosTau8
Jun. 2014
University of Maryland v3.1.1
Available
bosTau7
Oct. 2011
Baylor College of Medicine HGSC Btau_4.6.1
Available
bosTau6
Nov. 2009
University of Maryland v3.1
Available
bosTau4
Oct. 2007
Baylor College of Medicine HGSC Btau_4.0
Available
bosTau3
Aug. 2006
Baylor College of Medicine HGSC Btau_3.1
Available
bosTau2
Mar. 2005
Baylor College of Medicine HGSC Btau_2.0
Available
bosTau1
Sep. 2004
Baylor College of Medicine HGSC Btau_1.0
Archived
Crab-eating macaque
macFas5
Jun. 2013
Washington University Macaca_fascicularis_5.0
Available
Dog
canFam6
Oct. 2020
Dog Genome Sequencing Consortium Dog10K_Boxer_Tasha
Available
canFam5
May 2019
University of Michigan
Available
canFam4
Mar. 2020
Uppsala University
Available
canFam3
Sep. 2011
Broad Institute v3.1
Available
canFam2
May 2005
Broad Institute v2.0
Available
canFam1
Jul. 2004
Broad Institute v1.0
Available
Dolphin
turTru2
Oct. 2011
Baylor College of Medicine Ttru_1.4
Available
Elephant
loxAfr3
Jul. 2009
Broad Institute LoxAfr3
Available
Ferret
musFur1
Apr. 2011
Ferret Genome Sequencing Consortium MusPutFur1.0
Available
Garter snake
thaSir1
Jun. 2015
Washington University Thamnophis_sirtalis-6.0
Available
Gibbon
nomLeu3
Oct. 2012
Gibbon Genome Sequencing Consortium Nleu3.0
Available
nomLeu2
Jun. 2011
Gibbon Genome Sequencing Consortium Nleu1.1
Available
nomLeu1
Jan. 2010
Gibbon Genome Sequencing Consortium Nleu1.0
Available
Golden eagle
aquChr2
Oct. 2014
University of Washington aquChr2-1.0.2
Available
Golden snub-nosed monkey
rhiRox1
Oct. 2014
Novogene Rrox_v1
Available
Gorilla
gorGor6
Aug. 2019
University of Washington
Available
gorGor5
Mar. 2016
University of Washington GSMRT3
Available
gorGor4
Dec. 2014
Wellcome Trust Sanger Institute gorGor4
Available
gorGor3
May 2011
Wellcome Trust Sanger Institute gorGor3.1
Available
Green Monkey
chlSab2
Mar. 2014
Vervet Genomics Consortium 1.1
Available
Guinea pig
cavPor3
Feb. 2008
Broad Institute cavPor3
Available
Hawaiian monk seal
neoSch1
Jun. 2017
Johns Hopkins University ASM220157v1
Available
Hedgehog
eriEur2
May 2012
Broad Institute EriEur2.0
Available
eriEur1
Jun. 2006
Broad Institute Draft_v1
Available
Horse
equCab3
Jan. 2018
University of Louisville
Available
equCab2
Sep. 2007
Broad Institute EquCab2
Available
equCab1
Jan. 2007
Broad Institute EquCab1
Available
Kangaroo rat
dipOrd1
Jul. 2008
Baylor/Broad Institute DipOrd1.0
Available
Little brown bat
myoLuc2
Jul. 2010
Broad Institute MyoLuc2.0
Available
Malayan flying lemur
galVar1
Jul. 2014
WashU G_variegatus-3.0.2
Available
Manatee
triMan1
Oct. 2011
Broad Institute TriManLat1.0
Available
Marmoset
calJac4
May 2020
Washington University Callithrix_jacchus_cj1700_1.1
Available
Marmoset
calJac3
Mar. 2009
WUSTL Callithrix_jacchus-v3.2
Available
calJac1
Jun. 2007
WUSTL Callithrix_jacchus-v2.0.2
Available
Megabat
pteVam1
Jul. 2008
Broad Institute Ptevap1.0
Available
Minke whale
balAcu1
Oct. 2013
KORDI BalAcu1.0
Available
Mouse
mm39
Jun. 2020
Genome Reference Consortium Mouse Build 39
Available
mm10
Dec. 2011
Genome Reference Consortium GRCm38
Available
mm9
Jul. 2007
NCBI Build 37
Available
mm8
Feb. 2006
NCBI Build 36
Available
mm7
Aug. 2005
NCBI Build 35
Available
mm6
Mar. 2005
NCBI Build 34
Archived
mm5
May 2004
NCBI Build 33
Archived
mm4
Oct. 2003
NCBI Build 32
Archived
mm3
Feb. 2003
NCBI Build 30
Archived
mm2
Feb. 2002
MGSCv3
Archived
mm1
Nov. 2001
MGSCv2
Archived (data only)
Mouse lemur
micMur2
May 2015
Baylor/Broad Institute Mmur_2.0
Available
micMur1
Jul. 2007
Broad Institute MicMur1.0
Available
Naked mole-rat
hetGla2
Jan. 2012
Broad Institute HetGla_female_1.0
Available
hetGla1
Jul. 2011
Beijing Genomics Institute HetGla_1.0
Available
Opossum
monDom5
Oct. 2006
Broad Institute release MonDom5
Available
monDom4
Jan. 2006
Broad Institute release MonDom4
Available
monDom1
Oct. 2004
Broad Institute release MonDom1
Available
Orangutan
ponAbe2
Jul. 2007
WUSTL Pongo_albelii-2.0.2
Available
ponAbe3
Jan. 2018
Susie_PABv2/ponAbe3
Available
Panda
ailMel1
Dec. 2009
BGI-Shenzhen AilMel 1.0
Available
Pig
susScr11
Feb. 2017
Swine Genome Sequencing Consortium Sscrofa11.1
Available
susScr3
Aug. 2011
Swine Genome Sequencing Consortium Sscrofa10.2
Available
susScr2
Nov. 2009
Swine Genome Sequencing Consortium Sscrofa9.2
Available
Pika
ochPri3
May 2012
Broad Institute OchPri3.0
Available
ochPri2
Jul. 2008
Broad Institute OchPri2
Available
Platypus
ornAna2
Feb. 2007
WUSTL v5.0.1
Available
ornAna1
Mar. 2007
WUSTL v5.0.1
Available
Proboscis Monkey
nasLar1
Nov. 2014
Proboscis Monkey Functional Genome Consortium Charlie1.0
Available
Rabbit
oryCun2
Apr. 2009
Broad Institute release OryCun2
Available
Rat
rn7
Nov. 2020
Wellcome Sanger Institute mRatBN7.2
Available
rn6
Jul. 2014
RGSC Rnor_6.0
Available
rn5
Mar. 2012
RGSC Rnor_5.0
Available
rn4
Nov. 2004
Baylor College of Medicine HGSC v3.4
Available
rn3
Jun. 2003
Baylor College of Medicine HGSC v3.1
Available
rn2
Jan. 2003
Baylor College of Medicine HGSC v2.1
Archived
rn1
Nov. 2002
Baylor College of Medicine HGSC v1.0
Archived
Rhesus
rheMac10
Feb. 2019
The Genome Institute at Washington University School of Medicine Mmul_10
Available
rheMac8
Nov. 2015
Baylor College of Medicine HGSC Mmul_8.0.1
Available
rheMac3
Oct. 2010
Beijing Genomics Institute CR_1.0
Available
rheMac2
Jan. 2006
Baylor College of Medicine HGSC v1.0 Mmul_051212
Available
rheMac1
Jan. 2005
Baylor College of Medicine HGSC Mmul_0.1
Archived
Rock hyrax
proCap1
Jul. 2008
Baylor College of Medicine HGSC Procap1.0
Available
Sheep
oviAri4
Dec. 2015
ISGC Oar_v4.0
Available
oviAri3
Aug. 2012
ISGC Oar_v3.1
Available
oviAri1
Feb. 2010
ISGC Ovis aries 1.0
Available
Shrew
sorAra2
Aug. 2008
Broad Institute SorAra2.0
Available
sorAra1
Jun. 2006
Broad Institute SorAra1.0
Available
Sloth
choHof1
Jul. 2008
Broad Institute ChoHof1.0
Available
Squirrel
speTri2
Nov. 2011
Broad Institute SpeTri2.0
Available
Squirrel monkey
saiBol1
Oct. 2011
Broad Institute SaiBol1.0
Available
Tarsier
tarSyr2
Sep. 2013
WashU Tarsius_syrichta-2.0.1
Available
tarSyr1
Aug. 2008
WUSTL/Broad Institute Tarsyr1.0
Available
Tasmanian devil
sarHar1
Feb. 2011
Wellcome Trust Sanger Institute Devil_refv7.0
Available
Tenrec
echTel2
Nov. 2012
Broad Institute EchTel2.0
Available
echTel1
Jul. 2005
Broad Institute echTel1
Available
Tree shrew
tupBel1
Dec. 2006
Broad Institute Tupbel1.0
Available
Wallaby
macEug2
Sep. 2009
Tammar Wallaby Genome Sequencing Consortium Meug_1.1
Available
White rhinoceros
cerSim1
May 2012
Broad Institute CerSimSim1.0
Available
VERTEBRATES
African clawed frog
xenLae2
Aug. 2016
Int. Xenopus Sequencing Consortium
Available
American alligator
allMis1
Aug. 2012
Int. Crocodilian Genomes Working Group allMis0.2
Available
Atlantic cod
gadMor1
May 2010
Genofisk GadMor_May2010
Available
Budgerigar
melUnd1
Sep. 2011
WUSTL v6.3
Available
Chicken
galGal6
Mar. 2018
GRCg6 Gallus-gallus-6.0
Available
galGal5
Dec. 2015
ICGC Gallus-gallus-5.0
Available
galGal4
Nov. 2011
ICGC Gallus-gallus-4.0
Available
galGal3
May 2006
WUSTL Gallus-gallus-2.1
Available
galGal2
Feb. 2004
WUSTL Gallus-gallus-1.0
Available
Coelacanth
latCha1
Aug. 2011
Broad Institute LatCha1
Available
Elephant shark
calMil1
Dec. 2013
IMCB Callorhinchus_milli_6.1.3
Available
Fugu
fr3
Oct. 2011
JGI v5.0
Available
fr2
Oct. 2004
JGI v4.0
Available
fr1
Aug. 2002
JGI v3.0
Available
Lamprey
petMar3
Dec. 2017
University of Kentucky Pmar_germline 1.0
Available
petMar2
Sep. 2010
WUGSC 7.0
Available
petMar1
Mar. 2007
WUSTL v3.0
Available
Lizard
anoCar2
May 2010
Broad Institute AnoCar2
Available
anoCar1
Feb. 2007
Broad Institute AnoCar1
Available
Medaka
oryLat2
Oct. 2005
NIG v1.0
Available
Medium ground finch
geoFor1
Apr. 2012
BGI GeoFor_1.0 / NCBI 13302
Available
Nile tilapia
oreNil2
Jan. 2011
Broad Institute Release OreNil1.1
Available
Painted turtle
chrPic1
Dec. 2011
IPTGSC Chrysemys_picta_bellii-3.0.1
Available
Stickleback
gasAcu1
Feb. 2006
Broad Institute Release 1.0
Available
Tetraodon
tetNig2
Mar. 2007
Genoscope v7
Available
tetNig1
Feb. 2004
Genoscope v7
Available
Tibetan frog
nanPar1
Mar. 2015
Beijing Genomics Institute BGI_ZX_20015
Available
Turkey
melGal5
Nov. 2014
Turkey Genome Consortium v5.0
Available
melGal1
Dec. 2009
Turkey Genome Consortium v2.01
Available
X. tropicalis
xenTro10
Nov. 2019
University of California, Berkeley UCB_Xtro_10.0
Available
xenTro9
Jul. 2016
JGI v.9.1
Available
xenTro7
Sep. 2012
JGI v.7.0
Available
xenTro3
Nov. 2009
JGI v.4.2
Available
xenTro2
Aug. 2005
JGI v.4.1
Available
xenTro1
Oct. 2004
JGI v.3.0
Available
Zebra finch
taeGut2
Feb. 2013
WashU taeGut324
Available
taeGut1
Jul. 2008
WUSTL v3.2.4
Available
Zebrafish
danRer11
May 2017
Genome Reference Consortium GRCz11
Available
danRer10
Sep. 2014
Genome Reference Consortium GRCz10
Available
danRer7
Jul. 2010
Sanger Institute Zv9
Available
danRer6
Dec. 2008
Sanger Institute Zv8
Available
danRer5
Jul. 2007
Sanger Institute Zv7
Available
danRer4
Mar. 2006
Sanger Institute Zv6
Available
danRer3
May 2005
Sanger Institute Zv5
Available
danRer2
Jun. 2004
Sanger Institute Zv4
Archived
danRer1
Nov. 2003
Sanger Institute Zv3
Archived
DEUTEROSTOMES
C. intestinalis
ci3
Apr. 2011
Kyoto KH
Available
C. intestinalis
ci2
Mar. 2005
JGI v2.0
Available
ci1
Dec. 2002
JGI v1.0
Available
Lancelet
braFlo1
Mar. 2006
JGI v1.0
Available
S. purpuratus
strPur2
Sep. 2006
Baylor College of Medicine HGSC v. Spur 2.1
Available
strPur1
Apr. 2005
Baylor College of Medicine HGSC v. Spur_0.5
Available
INSECTS
A. mellifera
apiMel2
Jan. 2005
Baylor College of Medicine HGSC v.Amel_2.0
Available
apiMel1
Jul. 2004
Baylor College of Medicine HGSC v.Amel_1.2
Available
A. gambiae
anoGam3
Oct. 2006
International Consortium for the Sequencing of Anopheles Genome AgamP3
Available
anoGam1
Feb. 2003
IAGP v.MOZ2
Available
D. ananassae
droAna2
Aug. 2005
Agencourt Arachne release
Available
droAna1
Jul. 2004
TIGR Celera release
Available
D. erecta
droEre1
Aug. 2005
Agencourt Arachne release
Available
D. grimshawi
droGri1
Aug. 2005
Agencourt Arachne release
Available
D. melanogaster
dm6
Aug. 2014
BDGP Release 6 + ISO1 MT
Available
dm3
Apr. 2006
BDGP Release 5
Available
dm2
Apr. 2004
BDGP Release 4
Available
dm1
Jan. 2003
BDGP Release 3
Available
D. mojavensis
droMoj2
Aug. 2005
Agencourt Arachne release
Available
droMoj1
Aug. 2004
Agencourt Arachne release
Available
D. persimilis
droPer1
Oct. 2005
Broad Institute release
Available
D. pseudoobscura
dp3
Nov. 2004
FlyBase Release 1.0
Available
dp2
Aug. 2003
Baylor College of Medicine HGSC Freeze 1
Available
D. sechellia
droSec1
Oct. 2005
Broad Institute Release 1.0
Available
D. simulans
droSim1
Apr. 2005
WUSTL Release 1.0
Available
D. virilis
droVir2
Aug. 2005
Agencourt Arachne release
Available
droVir1
Jul. 2004
Agencourt Arachne release
Available
D. yakuba
droYak2
Nov. 2005
WUSTL Release 2.0
Available
droYak1
Apr. 2004
WUSTL Release 1.0
Available
NEMATODES
C. brenneri
caePb2
Feb. 2008
WUSTL 6.0.1
Available
caePb1
Jan. 2007
WUSTL 4.0
Available
C. briggsae
cb3
Jan. 2007
WUSTL Cb3
Available
cb1
Jul. 2002
WormBase v. cb25.agp8
Available
C. elegans
ce11
Feb. 2013
elegans Sequencing Consortium WBcel235
Available
ce10
Oct. 2010
WormBase v. WS220
Available
ce6
May 2008
WormBase v. WS190
Available
ce4
Jan. 2007
WormBase v. WS170
Available
ce2
Mar. 2004
WormBase v. WS120
Available
ce1
May 2003
WormBase v. WS100
Archived
C. japonica
caeJap1
Mar. 2008
WUSTL 3.0.2
Available
C. remanei
caeRem3
May 2007
WUSTL 15.0.1
Available
caeRem2
Mar. 2006
WUSTL 1.0
Available
P. pacificus
priPac1
Feb. 2007
WUSTL 5.0
Available
OTHER
Sea Hare
aplCal1
Sep. 2008
Broad Release Aplcal2.0
Available
Yeast
sacCer3
April 2011
SGD April 2011 sequence
Available
sacCer2
June 2008
SGD June 2008 sequence
Available
sacCer1
Oct. 2003
SGD 1 Oct 2003 sequence
Available
VIRUSES
Ebola Virus
eboVir3
June 2014
Sierra Leone 2014 (G3683/KM034562.1)
Available
SARS-CoV-2
wuhCor1
Jan. 2020
SARS-CoV-2 ASM985889v3
Available
Initial assembly release dates
When will the next assembly be out?
UCSC does not produce its own genome assemblies, but instead obtains them from standard sources. Because of this, you can expect us to release a new version of a genome soon after the assembling organization has released the version. A new assembly release initially consists of the genome sequence and a small set of aligned annotation tracks. Additional annotation tracks are added as they are obtained or generated. Bulk downloads of the data are typically available in the first week after the assembly is released in the browser.
Data sources - UCSC assemblies
Where does UCSC obtain the assembly and annotation data displayed in the Genome Browser?
All the assembly data displayed in the UCSC Genome Browser are obtained from external sequencing centers. To determine the data source and version for a given assembly, see the assembly’s description on the Genome Browser Gateway page or the List of UCSC Genome Releases.
The annotations accompanying an assembly are obtained from a variety of sources. The UCSC Genome Bioinformatics Group generates several of the tracks; the remainder are contributed by collaborators at other sites. Each track has an associated description page that credits the authors of the annotation.
For detailed information about the individuals and organizations who contributed to a specific assembly, see the Credits page.
Which UCSC assemblies are equivalent to Ensembl or NCBI assemblies?
The asmEquivalent table on the hgFixed database is available on the public MySQL server to show which assemblies versions are identical (or almost identical) to each other between UCSC, Ensembl, Genbank, and RefSeq assemblies.
mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -e 'desc asmEquivalent;' hgFixed
+----------------------+-------------------------------------------+
| Field | Type |
+----------------------+-------------------------------------------+
| source | varchar(255) |
| destination | varchar(255) |
| sourceAuthority | enum('ensembl','ucsc','genbank','refseq') |
| destinationAuthority | enum('ensembl','ucsc','genbank','refseq') |
| matchCount | bigint(20) |
| sourceCount | bigint(20) |
| destinationCount | bigint(20) |
+----------------------+-------------------------------------------+
The “Count” indications are the count of individual sequences in the
assembly. When all three counts are identical,
matchCount == sourceCount == destinationCount, then the match
between genome assemblies is perfectly identical.
Non-perfect matches can be due to a number of factors:
different or not included chrMT genome sequences in an assembly
identical duplicated sequences present or absent from an assembly
some smaller contigs not included in an assembly
slight differences in versions of assemblies where some contain sequences not in the other assembly
Comparison of UCSC and NCBI human assemblies
How do the human assemblies displayed in the UCSC Genome Browser differ from the NCBI human assemblies?
Human assemblies displayed in the Genome Browser (hg10 and higher) are near identical to the NCBI assemblies when it comes to primary sequence. Minor differences may be present, however. Sources include:
NCBI genomes are repeat masked with RepeatMasker, however, UCSC genomes are independently masked with both RepeatMasker (with different flags) and WindowMasker, ultimately using the program output with the highest percentage masked for the base sequence
In genome download files, UCSC uses the ‘chr1’ nomenclature for sequence identifiers, whereas the primary NCBI sequence identifiers are RefSeq accessions
The original mitochondrion (chrM) for hg19 differs from the one in NCBI (GRCh37)
The mitochondrion released by NCBI after the hg19 browser was built has been added to the assemby as chrMT. See our documentation for details.
Looking for a genome assembly not shown in the tree?
When looking for a specific assembly, the best place to start is the Gateway page. If you begin to type the common name, species name, or NCBI RefSeq accession number in the search box on the left side of the screen, suggestions will appear if any matches are found. This search will also match any assembly hubs that are listed in UCSC’s Public Hubs. Nearly every NCBI RefSeq assembly and Vertebrate Genomes Project assembly is included here within the GenArk hubs. NCBI RefSeq assemblies can be loaded with direct links such as http://genome.ucsc.edu/h/GCF_001984765.1 with the GCF accession. These assembly hubs are automatically updated, but not reviewed by UCSC. The species tree shows all genomes reviewed by UCSC.
If the assembly of interest is not found, you may write in to our mailing list (genome@soe.ucsc.edu) including the NCBI Genbank assembly accession for the requested assembly in the message. These will start with either GCA_ or GCF_. Our agreement with the genomics community is that we wait until the assembly has been deposited into Genbank at NCBI before we process it. See the Assembly Submission Guidelines page at NCBI for directions on their submission process.
Another option available to all users is to create an assembly hub. These are assemblies created and hosted by users and displayed on the Genome Browser. This requires no intervention by the UCSC Genome Browser and can be done for any assembly. See our Quick Start Guide to Assembly Hubs page for additional information and resources. If you create an assembly hub, consider sharing it with others as a Public Hub.
Differences between UCSC and NCBI mouse assemblies
Is the mouse genome assembly displayed in the UCSC Genome Browser the same as the one on the NCBI website?
The mouse genome assemblies featured in the UCSC Genome Browser are the same as those on the NCBI web site with one difference: the UCSC versions contain only the reference strain data (C57BL/6J). NCBI provides data for several additional strains in their builds.
Accessing older assembly versions
I need to access an older version of a genome assembly that’s no longer listed in the Genome Browser menu. What should I do?
In addition to the assembly versions currently available in the Genome Browser, you can access the data for older assemblies of the browser through our Downloads page.
Frequency of GenBank data updates
How frequently does UCSC update its databases with new data from GenBank?
GenBank updates for mRNA, RefSeq, and EST data occur on a semi-quarterly basis, following major NCBI releases. These updates are in place for most Genome Browser assemblies. Assemblies that are not on an incremental update schedule are updated whenever we load a new assembly or make a major revision to a table.
Coordinate changes between assemblies
I noticed that the chromosomal coordinates for a particular gene that I’m looking at have changed since the last time I used your browser. What happened?
A common source of confusion for users arises from mixing up different assemblies. It is very important to be aware of which assembly you are looking at. Within the Genome Browser display, assemblies are labeled by organism and date. To look up the corresponding UCSC database name or NCBI build number, use the release table.
UCSC database labels are of the form hg#, panTro#, etc. The letters designate the organism, e.g. hg for human genome or panTro for Pan troglodytes. The number denotes the UCSC assembly version for that organism. For example, ce1 refers to the first UCSC assembly of the C. elegans genome.
The coordinates of your favorite gene in one assembly may not be the same as those in the next release of the assembly unless the gene happens to lie on a completely sequenced and unrevised chromosome. For information on integrating data from one assembly into another, see the Converting positions between assembly versions section.
Converting positions between assembly versions
I’ve been researching a specific area of the human genome on the current assembly, and now you’ve just released a new version. Is there an easy way to locate my area of interest on the new assembly?
See the section on converting coordinates for information on assembly migration tools.
Missing annotation tracks
Why is my favorite annotation track missing from your latest release?
The initial release of a new genome assembly typically contains a small subset of core annotation tracks. New tracks are added as they are generated. In many cases, our annotation tracks are contributed by scientists not affiliated with UCSC who must first obtain the sequence, repeatmasked data, etc. before they can produce their tracks. If you have need of an annotation that has not appeared on an assembly within a month or so of its release, feel free to send an inquiry to genome@soe.ucsc.edu. **Messages sent to this address will be posted to the moderated genome mailing list, which is archived on a SEARCHABLE, PUBLIC**Google Groups forum.
What next with the human genome?
Now that the human genome is “finished”, will there be any more releases?
Rest assured that work will continue. There will be updates to the assembly over the next several years. This has been the case for all other finished (i.e. essentially complete) genome assemblies as gaps are closed. For example, the C. elegans genome has been “finished” for several years, but small bits of sequence are still being added and corrections are being made. NCBI will continue to coordinate the human genome assemblies in collaboration with the individual chromosome coordinators, and UCSC will continue to QC the assembly in conjunction with NCBI (and, to a lesser extent, Ensembl). UCSC, NCBI, Ensembl, and others will display the new releases on their sites as they become available.
Mouse strain used for mouse genome sequence
What strain of mouse was used for the Mus musculus genome?
C57BL/6J.