Data Releases: Tracks, Tables, and Assemblies

This page contains track and table release information for the following genome assemblies:

For older log entries, please see this page.

Last updated 07 Dec 2019. Inquiries and feedback welcome.

10 Latest Changes (all assemblies)

Track Name	Assembly
EPDnew Promoters track for human and mouse (hg19, hg38, mm10)	hg19 hg38 mm10
ENCODE Enhancer-Gene Map	mm10
LOVD update	hg19
CRISPR/Cas9 Sp. Pyog. target sites, whole genome	mm10
A comprehensive study of chromatin accessibility across these developmental stages	mm10
Chromatin state annotations derived from ChIP-seq of histone modifications	mm10
A comprehensive study of chromatin state across these developmental stages	mm10
LRG update	hg19 hg38
gnomAD Variants	hg38
Illumina Global Diversity Array	hg19

Human Dec. 2013 (GRCh38/hg38) (hg38, GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15))

Track Name
EPDnew Promoters track for human and mouse (hg19, hg38, mm10)
LRG update
gnomAD Variants
CRISPR/Cas9 Sp. Pyog. target sites, whole genome
GENCODE Genes v32
GENCODE release V31
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
GDC Cancer mutations: 33 TCGA Cancer Projects (Pan-Can 33)
Transcription Factor ChIP-seq Clusters (338 factors, 130 cell types) from ENCODE 3
Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3
NCBI RefSeq HGMD
CRISPR/Cas9 Sp. Pyog. target sites (exons +/- 10,000 bp)
Human Gene Mutation Database Public Variants 2018
Common SNPs(151), Flagged SNPs(151), Mult. SNPs(151), All SNPS(151) initial release
GENCODE Genes v29
GeneHancer Regulatory Elements and Gene Interactions
miRBase v22 data update
Detailed RepeatMasker Visualization using updated repeat libraries
NCBI RefSeq Genomic Differences
import of GENCODE V28 / Ensembl 92
NCBI RefSeq gene predictions
UCSC to RefSeq Chromosome names
Human Gene Mutation Database Public Variants (HGMD)
Newest MalaCards Links (hg38 & hg19)
Mammal 30-way Conservation (27 primates)
Hoffman Lab Umap and Bismap Mappability for human
NCBI RefSeq Functional Elements for human (hg38) and mouse (mm10)
X. tropicalis (xenTro9) Chain and Net
Transcript and Gene Expression in 33 TCGA Cancer Tissues (GENCODE v23)
Uniprot proteins
GENCODE V27 release
GTEx Transcript Expression
COSMIC: Catalogue Of Somatic Mutations In Cancer v82.
GRCh38 patch release 11, alternate sequences and reference sequence patches
Common SNPs(150), Flagged SNPs(150), Mult. SNPs(150), All SNPS(150) initial release
COSMIC: Catalogue Of Somatic Mutations In Cancer v81.
All GENCODE V26 release
Gene interactions and pathways from curated databases and text-mining
Human (hg38) and Horse (equCab2) Chain/Nets
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets
RefSeq gene predictions from NCBI
GRCh38 patch release 9, alternate sequences and reference sequence patches

Human Feb. 2009 (GRCh37/hg19) (hg19, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1))

Track Name
EPDnew Promoters track for human and mouse (hg19, hg38, mm10)
LOVD update
LRG update
Illumina Global Diversity Array
GENCODE release V31 mapped to GRCh37/hg19 (V31lift37)
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
CRISPR/Cas9 Sp. Pyog. target sites, whole genome
Database of Genomic Variants: Gold Standard Variants
Transcription Factor ChIP-seq Clusters (338 factors, 130 cell types) from ENCODE 3
Transcription Factor ChIP-seq Peaks (340 factors in 129 cell types) from ENCODE 3
Genomenon Mastermind Text-mined variants
NCBI RefSeq HGMD
CRISPR/Cas9 Sp. Pyog. target sites (exons +/- 10,000 bp)
Human Gene Mutation Database Public Variants 2018
Common SNPs(151), Flagged SNPs(151), Mult. SNPs(151), All SNPS(151) initial release
GeneHancer Regulatory Elements and Gene Interactions
DECIPHER Variants
Genome Aggregation Database (gnomAD) Variants and Coverage
GENCODE V28lift37, GENCODE V28 back-mapped to GRCh37/hg19
NCBI RefSeq gene predictions
Human Gene Mutation Database Public Variants (HGMD)
Newest MalaCards Links (hg38 & hg19)
GTEx Combined eQTL
GTEx Tissue eQTL
GENCODE V27lift37 release, mapped from GRCh38/hg38 to GRCh37/hg19
Uniprot proteins
GTEx Transcript Expression
COSMIC: Catalogue Of Somatic Mutations In Cancer v82.
Common SNPs(150), Flagged SNPs(150), Mult. SNPs(150), All SNPS(150) initial release
COSMIC: Catalogue Of Somatic Mutations In Cancer v81.
Gene interactions and pathways from curated databases and text-mining
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Pfam in UCSC Genes (update)

Mouse Dec. 2011 (GRCm38/mm10) (mm10, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2))

Track Name
EPDnew Promoters track for human and mouse (hg19, hg38, mm10)
ENCODE Enhancer-Gene Map
CRISPR/Cas9 Sp. Pyog. target sites, whole genome
A comprehensive study of chromatin accessibility across these developmental stages
Chromatin state annotations derived from ChIP-seq of histone modifications
A comprehensive study of chromatin state across these developmental stages
GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Tabula Muris
Detailed RepeatMasker Visualization using updated repeat libraries
GENCODE Mouse VM18 release
Crispr Targets 10K
UCSC Genes v17 for GRCm38/mm10
GENCODE Mouse release VM16
NCBI RefSeq Functional Elements for human (hg38) and mouse (mm10)
X. tropicalis (xenTro9) Chain and Net
NCBI RefSeq gene predictions
Uniprot proteins
Mouse SNPs
GENCODE VM14 Release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

A. gambiae Oct. 2006 (AgamP3/anoGam3) (anoGam3, The International Consortium for the Sequencing of Anopheles Genome)

Track Name
Initial anoGam3 release (using The International Consortium for the Sequencing of Anopheles Genome AgamP3 (NCBI project 1438, GCF_000005575.2) A. gambiae Chain/Net AUGUSTUS Assembly Chromosome Band (Ideogram) CpG Islands D. melanogaster Chain and Net GC Percent Gap Genscan Genes INSDC Interrupted Rpts Microsatellite RefSeq Acc RepeatMasker Simple Repeats Unmasked CpG WM + SDust

African clawed frog Aug. 2016 (Xenopus_laevis_v2/xenLae2) (xenLae2, International Xenopus Sequencing Consortium)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
X. tropicalis (xenTro9) Chain and Net
Initial xenLae2 release (using International Xenopus Sequencing Consortium Xenopus_laevis_v2 (NCBI project 338693, GCF_001663975.1)), AUGUSTUS, African clawed frog Chain/Net, Assembly, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Gap Overlaps, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust, X. tropicalis Chain and Net

Alpaca Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2) (vicPac2, Broad Institute)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Alpaca Jul. 2008 (Broad/vicPac1) (vicPac1, Broad Institute vicPac1)

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

American alligator Aug. 2012 (allMis0.2/allMis1) (allMis1, International Crocodilian Genomes Working Group)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Armadillo Dec. 2011 (Baylor/dasNov3) (dasNov3, Baylor College of Medicine Dasnov3.0 (GCA_000208655.2))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Atlantic cod May 2010 (Genofisk GadMor_May2010/gadMor1) (gadMor1, Genofisk GadMor_May2010 (GCA_000231765.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Baboon Apr. 2017 (Panu_3.0/papAnu4) (papAnu4, Human Genome Sequencing Center)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
AUGUSTUS, Assembly, Baboon Chain/Net, Chromosome Band (Ideogram), CpG Islands, Ensembl Genes, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust

Baboon Mar. 2012 (Baylor Panu_2.0/papAnu2) (papAnu2, Baylor College of Medicine)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v90 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Bison Oct. 2014 (Bison_UMD1.0/bisBis1) (bisBis1, U. Maryland)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
TransMap Alignments (AUGUSTUS, Assembly, Bison Chain/Net, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust)

Bonobo Aug. 2015 (MPI-EVA panpan1.1/panPan2) (panPan2, Max-Planck Institute for Evolutionary Anthropology)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Initial panPan2 release (using Max-Planck Institute for Evolutionary Anthropology MPI-EVA panpan1.1 (NCBI project 169343, GCF_000258655.2): AUGUSTUS, Assembly, Bonobo Chain/Net, Chimp Chain/Net, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Gorilla Chain/Net, Human Chain/Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain/Net, RefSeq Acc, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust.

Bonobo May 2012 (Max-Planck/panPan1) (panPan1, Max-Planck Institute panpan1 (GCA_000258655.1))

Track Name
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names

Brown kiwi Jun. 2015 (MPI-EVA AptMant0/aptMan1) (aptMan1, Max-Plank Institute for Evolutionary Anthropology AptMant0)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.

Budgerigar Sep. 2011 (WUSTL v6.3/melUnd1) (melUnd1, WUSTL Melopsittacus undulatus Budgerigar Version 6.3 (GCA_000238935.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Bushbaby Mar. 2011 (Broad/otoGar3) (otoGar3, Broad Institute (GCA_000181295.3))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

C. elegans Feb. 2013 (WBcel235/ce11) (ce11, C. elegans Sequencing Consortium WBcel235 (GCA_000002985.3))

Track Name
Ensembl Genes v95 Jan 2019
Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis)
Ensembl v92 release
CRISPR track for ce11
NCBI RefSeq gene predictions
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
Uniprot proteins

C. elegans Oct. 2010 (WS220/ce10) (ce10, Washington University School of Medicine GSC and Sanger Institute WS220)

Track Name
Uniprot proteins

C. intestinalis Apr. 2011 (Kyoto KH/ci3) (ci3, Kyoto KH)

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Initial ci3 release (using Kyoto KH Kyoto KH (NCBI project 187185, GCF_000224145.1) Assembly, C. elegans Chain and Net, C. intestinalis Chain/Net, C. savignyi Cha, Chromosome Band (Ideogram), CpG Islands, Ensembl Genes, GC Percent, Gap, Genscan Genes, INSDC, Interrupted Rpts, Microsatellite, RefSeq Acc, RepeatMasker, S. purp, Simple Repeats, Unmasked CpG, WM + SDust.

Cat Nov. 2017 (Felis_catus_9.0/felCat9) (felCat9, Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial felCat9 release (using Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine Felis_catus_9.0 (NCBI project 16726, GCF_000181335.3), AUGUSTUS, Assembly, Cat Chain/Net, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RefSeq Alignments, RefSeq All, RefSeq Curated, RefSeq Other, RefSeq Predicted, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust

Cat Nov. 2014 (ICGSC Felis_catus_8.0/felCat8) (felCat8, International Cat Genome Sequencing Consortium)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Cat Sep. 2011 (ICGSC Felis_catus 6.2/felCat5) (felCat5, International Cat Genome Sequencing Consortium Felis_catus-6.2 (NCBI project 16726, accession AANG00000000.2, GCA_000181335.2))

Track Name
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v90 release

Chicken Mar. 2018 (GRCg6a/galGal6) (galGal6, Genome Reference Consortium)

Track Name
GRC Incident track
Vertebrate Multiz Alignment & Conservation (77 Species)
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Initial galGal6 release (using Genome Reference Consortium GRCg6a (NCBI project 13342, GCF_000002315.5), AUGUSTUS, Assembly, CRISPR Regions 10K, CRISPR Targets 10K, Chicken Chain/Net, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RefSeq Alignments, RefSeq All, RefSeq Curated, RefSeq Other, RefSeq Predicted, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust

Chicken Dec 2015 (Gallus_gallus-5.0/galGal5) (galGal5, ICGC Gallus_gallus-5.0 (GCA_000002315.3))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl v92 release
Ensembl v91 release
X. tropicalis (xenTro9) Chain and Net
Ensembl v89 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
All SNPs(147), Mult SNPs(147) Initial Release
Rat (rn6) Chain/Nets

Chicken Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) (galGal4, ICGSC Gallus_gallus-4.0 (GCA_000002315.2))

Track Name
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names

Chimp Jan. 2018 (Clint_PTRv2/panTro6) (panTro6, University of Washington)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial panTro6 release (using University of Washington Clint_PTRv2 (NCBI project 369439, GCF_002880755.1): AUGUSTUS, Assembly, Chimp Chain/Net, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RefSeq Alignments, RefSeq All, RefSeq Curated, RefSeq Other, RefSeq Predicted, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust

Chimp May 2016 (Pan_tro 3.0/panTro5) (panTro5, Chimpanzee Sequencing and Analysis Consortium)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Chimp Feb. 2011 (CSAC 2.1.4/panTro4) (panTro4, CSAC Pan_troglodytes-2.1.4 (GCA_000001515.4))

Track Name
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v90 release

Chinese hamster Jun. 2017 (CHOK1S_HZDv1/criGriChoV2) (criGriChoV2, Eagle Genomics Ltd)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial criGriChoV2 release (using Eagle Genomics Ltd CHOK1S_HZDv1 (NCBI project 0, GCA_900186095.1) AUGUSTUS Assembly Chinese hamster Chain/Net Chromosome Band (Ideogram) CpG Islands Ensembl Genes GC Percent Gap Genscan Genes Human Chain and Net INSDC Interrupted Rpts Microsatellite Mouse Chain and Net RefSeq Acc RepeatMasker Simple Repeats Unmasked CpG WM + SDust

Chinese hamster Aug. 2011 (CHO K1 cell line/criGriChoV1) (criGriChoV1, Beijing Genomics Institute)

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
Initial criGriChoV1 release (using Beijing Genomics Institute CHO K1 cell line (NCBI project 69991, GCF_000223135.1)) AUGUSTUS, Assembly, Chinese hamster Chain and Net, Chinese hamster Chain/Net, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Gap Overlaps, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust

Chinese hamster Jul. 2013 (C_griseus_v1.0/criGri1) (criGri1, Beijing Genomics Institution-Shenzhen)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Crispr track for criGri1
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Chinese pangolin Aug 2014 (M_pentadactyla-1.1.1/manPen1) (manPen1, Washington University (WashU) GCA_000738955.1)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial manPen1 release (Chinese Pangolin, Manis pentadactyla, NCBI Bioproject: 20331, Accession ID: GCA_000738955.1) Assembly, AUGUSTUS, Chain/Net, Chromosome Band (Ideogram), CpG Islands, GC Percent Gap, Genscan Genes, Human (hg38) Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse (mm10) Chain and Net, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust, supporting tables and files.

Coelacanth Aug. 2011 (Broad/latCha1) (latCha1, Broad LatCha1 (GCA_000225785.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Cow Apr. 2018 (ARS-UCD1.2/bosTau9) (bosTau9, USDA ARS)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
AUGUSTUS, Assembly, CRISPR Regions 10K, CRISPR Targets 10K, Chromosome Band (Ideogram), Cow Chain/Net, CpG Islands, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RefSeq Alignments, RefSeq All, RefSeq Curated, RefSeq Other, RefSeq Predicted, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust

Cow Jun. 2014 (Bos_taurus_UMD_3.1.1/bosTau8) (bosTau8, University of Maryland Bos_taurus_UMD_3.1.1)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Cow Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) (bosTau6, UMD_3.1 (NCBI project 10708, accession GCA_000003055.3))

Track Name
Ensembl v92 release
Ensembl v91 release

Crab-eating macaque Jun. 2013 (Macaca_fascicularis_5.0/macFas5) (macFas5, Washington University (WashU) GCA_000364345.1)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) (dm6, The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics (GCA_000001215.4))

Track Name
Ensembl Genes v95 Jan 2019
Multiz Alignment & Conservation (124 Insects)
Ensembl v92 release
NCBI RefSeq gene predictions
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
Uniprot proteins

D. persimilis Oct. 2005 (Broad/droPer1) (droPer1, Broad 28 Oct. 2005)

Track Name
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names

Dog Sep. 2011 (Broad CanFam3.1/canFam3) (canFam3, Broad CanFam3.1 (GCA_000002285.2))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
X. tropicalis (xenTro9) Chain and Net
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Dolphin Oct. 2011 (Baylor Ttru_1.4/turTru2) (turTru2, Baylor College of Medicine Ttru_1.4 (NCBI project 20365, GCA_000151865.2, WGS ABRN02))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3, Broad Institute loxAfr3 (NCBI project 12569, AAGU03000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Elephant shark Dec. 2013 (Callorhinchus_milii-6.1.3/calMil1) (calMil1, Institute of Molecular and Cell Biology, Singapore)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Ferret Apr. 2011 (MusPutFur1.0/musFur1) (musFur1, Ferret Genome Sequencing Consortium)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Fugu Oct. 2011 (FUGU5/fr3) (fr3, Fugu Genome Sequencing Consortium - FUGU5 (NCBI project 1434, GCA_000180615.2))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
X. tropicalis (xenTro9) Chain and Net
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Fugu Oct. 2004 (JGI 4.0/fr2) (fr2, JGI V4.0)

Track Name
Ensembl v92 release
Ensembl v91 release

GRCh37.p13 Jun. 2013 (hg19Patch13, GRCh37 patch 13 Genome Reference Consortium Human Reference 37)

Track Name
GRCh37 patch release 13, alternate sequences and reference sequence patches

Garter snake Jun. 2015 (Thamnophis_sirtalis-6.0/thaSir1) (thaSir1, The Genome Institute at Washington University School of Medicine (WUGSC))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial thaSir1 release (using The Genome Institute at Washington University School of Medicine (WUGSC) Thamnophis_sirtalis-6.0 (NCBI project 189551, GCF_001077635.1): AUGUSTUS,Assembly,Chromosome Band (Ideogram),CpG Islands,GC Percent,Gap,Garter snake Chain/Net,Genscan Genes,Human Chain and Net,INSDC,Interrupted Rpts,Microsatellite,Mouse Chain and Net,RefSeq Acc,RefSeq Alignments,RefSeq All,RefSeq Other,RefSeq Predicted,RepeatMasker,Simple Repeats,Unmasked CpG,WM + SDust

Gibbon Oct. 2012 (GGSC Nleu3.0/nomLeu3) (nomLeu3, Gibbon Genome Sequencing Consortium )

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Gibbon Jan. 2010 (GGSC Nleu1.0/nomLeu1) (nomLeu1, GGSC (NCBI project 13975, accession GCA_000146795.1))

Track Name
Ensembl v90 release

Golden eagle Oct. 2014 (aquChr-1.0.2/aquChr2) (aquChr2, WashU)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial aquChr2 release (using WashU aquChr-1.0.2 (NCBI project 256103, GCA_000766835.1): AUGUSTUS, Assembly, Chicken Chain and Net, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Golden eagle Chain/Net, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust, supporting tables and files.

Golden snub-nosed monkey Oct. 2014 (Rrox_v1/rhiRox1) (rhiRox1, Novogene)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
Initial rhiRox1 release (using Novogene Rrox_v1 (NCBI project 266995, GCA_000769185.1): Assembly, Gap, GC Percent, INSDC, Short Match, Restr Enzymes, AUGUSTUS, Genscan Genes, Other RefSeq, CpG Islands, Human Chain/Net, Tarsier Chain/Net, RepeatMasker, Microsatellite, Interrupted Rpts, WM + SDust, Simple Repeats.

Gorilla Mar. 2016 (GSMRT3/gorGor5) (gorGor5, UNIVERSITY OF WASHINGTON)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Gorilla Dec 2014 (gorGor4.1/gorGor4) (gorGor4, Wellcome Trust Sanger Institute Dec 2014 (NCBI project 31265, GCA_000151905.1))

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

Gorilla May 2011 (gorGor3.1/gorGor3) (gorGor3, Wellcome Trust Sanger Institute May 2011 (NCBI project 31265, GCA_000151905.1))

Track Name
Ensembl v90 release

Green monkey Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) (chlSab2, Vervet Genomics Consortium GCA_000409795.2)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Ensembl genes v86 for Green Monkey (chlSab2)

Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3, Broad Institute cavPor3)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Hedgehog May 2012 (EriEur2.0/eriEur2) (eriEur2, Broad Institute EriEur2.0)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Hedgehog June 2006 (Broad/eriEur1) (eriEur1, Broad Institute eriEur1 (Draft_v1, NCBI project 12575))

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

Horse Jan. 2018 (EquCab3.0/equCab3) (equCab3, University of Louisville)

Track Name
AUGUSTUS, Assembly, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Horse Chain/Net, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust

Horse Sep. 2007 (Broad/equCab2) (equCab2, Broad Institute EquCab2)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl v92 release
Ensembl v91 release
Human (hg38) and Horse (equCab2) Chain/Nets
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Japanese quail Mar. 2016 (Coturnix japonica 2.0/cotJap2) (cotJap2, McDonnell Genome Institute - Washington University School of Medicine)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.

Kangaroo rat Jul. 2008 (Broad/dipOrd1) (dipOrd1, Broad Institute dipOrd1 (NCBI project 20385, ABRO01000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Lamprey Dec. 2017 (Pmar_germline 1.0/petMar3) (petMar3, University of Kentucky)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial petMar3 release (using University of Kentucky Pmar_germline 1.0 (NCBI project 357048, GCA_002833325.1): AUGUSTUS, Assembly, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Lamprey Chain/Net, Microsatellite, Mouse Chain and Net, RefSeq Acc, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust.

Lamprey Sep. 2010 (WUGSC 7.0/petMar2) (petMar2, GSC Washington University School of Medicine)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Lizard May 2010 (Broad AnoCar2.0/anoCar2) (anoCar2, Broad Institute of MIT and Harvard AnoCar 2.0 (GCA_000090745.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
X. tropicalis (xenTro9) Chain and Net
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Malayan flying lemur Jun. 2014 (G_variegatus-3.0.2/galVar1) (galVar1, Washington University (WashU))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Manatee Oct. 2011 (Broad v1.0/triMan1) (triMan1, Broad Institute of MIT and Harvard TriManLat1.0 (GCA_000243295.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3, WUSTL 3.2 (GCA_000004665.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2, NIG and Tokyo Univ MEDAKA1 (NCBI project 16702, BAAF04000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Medium ground finch Apr. 2012 (GeoFor_1.0/geoFor1) (geoFor1, Beijing Genomics Institute)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Megabat Jul. 2008 (Broad/pteVam1) (pteVam1, Broad Institute pteVam1 (NCBI project 20325, ABRP01000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Microbat Jul. 2010 (Broad Institute Myoluc2.0/myoLuc2) (myoLuc2, Broad Institute (NCBI Project ID: 16951, Accession: GCA_000147115.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Minke whale Oct. 2013 (BalAcu1.0/balAcu1) (balAcu1, Korea Ocean Research & Development Institute)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names

Mouse lemur May 2015 (Mouse lemur/micMur2) (micMur2, Broad Institute and Baylor College of Medicine Mmur_2.0)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
UCSC to RefSeq Chromosome names
Ensembl v90 release
Ensembl v89 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Naked mole-rat Jan. 2012 (Broad HetGla_female_1.0/hetGla2) (hetGla2, Broad Institute HetGla_female_1.0 (NCBI project 72441, GCA_000247695.1, WGS AHKG01))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Naked mole-rat Jul. 2011 (BGI HetGla_1.0/hetGla1) (hetGla1, HetGla_1.0 (NCBI project 68323, accession GCA_000230445.1)

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

Nile tilapia Nov. 2016 (ASM185804v2/oreNil3) (oreNil3, University of Maryland)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.

Nile tilapia Jan. 2011 (Broad oreNil1.1/oreNil2) (oreNil2, Broad Institute of MIT and Harvard Orenil1.1 (GCA_000188235.2))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Opossum Oct. 2006 (Broad/monDom5) (monDom5, Broad Institute monDom5 (NCBI project 12561, accession AAFR03000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
X. tropicalis (xenTro9) Chain and Net
Ensembl v89 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Orangutan Jan. 2018 (Susie_PABv2/ponAbe3) (ponAbe3, University of Washington)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial ponAbe3 release (using University of Washington Susie_PABv2 (NCBI project 369439, GCF_002880775.1), AUGUSTUS, Assembly, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, Orangutan Chain/Net, RefSeq Acc, RefSeq Alignments, RefSeq All, RefSeq Curated, RefSeq Other, RefSeq Predicted, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust

Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2, WUSTL 3.0)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1, BGI-Shenzhen AilMel 1.0 Dec. 2009)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Pig Feb. 2017 (Sscrofa11.1/susScr11) (susScr11, The Swine Genome Sequencing Consortium (SGSC))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
Initial susScr11 release (using The Swine Genome Sequencing Consortium (SGSC) Sscrofa11.1 (NCBI project 13421, GCF_000003025.6)) AUGUSTUS, Assembly, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, Pig Chain/Net, RefSeq Acc, RepeatMasker, Simple Repeats, Unmasked CpG, WM + SDust.

Pig Aug. 2011 (SGSC Sscrofa10.2/susScr3) (susScr3, SGSC Sscrofa10.2 (NCBI project 13421, GCA_000003025.4, WGS AEMK01))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Pika May 2012 (OchPri3.0/ochPri3) (ochPri3, Broad Institute)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Pika Jul. 2008 (Broad/ochPri2) (ochPri2, Broad Institute ochPri2)

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

Platypus Feb. 2007 (ASM227v2/ornAna2) (ornAna2, WUGSC ASM227v2)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
Ensembl v89 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1, WUSTL version 5.0.1)

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
Ensembl v89 release

Proboscis monkey Nov. 2014 (Charlie1.0/nasLar1) (nasLar1, Proboscis Monkey Functional Genome Consortium)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial nasLar1 release (using Proboscis Monkey Functional Genome Consortium): Assembly, Augustus, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genbank-process tracks and supporting tables, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, RepeatMasker, Simple Repeats, Tarsier Chain and Net, Unmasked CpG, WM + SDust, supporting tables and files.

Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2, Broad Institute oryCun2 (NCBI project 12819, AAGW00000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Rat Jul. 2014 (RGSC 6.0/rn6) (rn6, RGSC Rnor_6.0 (GCA_000001895.4))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
NCBI RefSeq gene predictions
Ensembl v91 release
Uniprot proteins
Ensembl v89 release
Mouse SNPs
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets
Vertebrate 20-way Conservation

Rhesus Feb. 2019 (Mmul_10/rheMac10) (rheMac10, The Genome Institute at Washington University School of Medicine)

Track Name
AUGUSTUS, Assembly, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Gap Overlaps, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Microsatellite, Mouse Chain and Net, RefSeq Acc, RefSeq Alignments, RefSeq All, RefSeq Curated, RefSeq Other, RefSeq Predicted, RepeatMasker, Rhesus Chain/Net, Simple Repeats, Tandem Dups, Unmasked CpG, WM + SDust

Rhesus Nov. 2015 (BCM Mmul_8.0.1/rheMac8) (rheMac8, Baylor College of Medicine Genome Sequencing Center)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Rock hyrax Jul. 2008 (Broad/proCap1) (proCap1, Broad Institute proCap1 (NCBI project 13972, ABRQ01000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database (GCA_000146045.2))

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
NCBI RefSeq gene predictions
Ensembl v91 release

Sheep Nov. 2015 (Oar_v4.0/oviAri4) (oviAri4, International Sheep Genome Consortium)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Initial oviAri4 release (using International Sheep Genome Consortium Oar_v4.0 (NCBI project 169880, GCF_000298735.2) AUGUSTUS Assembly Chromosome Band (Ideogram) CpG Islands GC Percent Gap Genscan Genes Human Chain and Net INSDC Interrupted Rpts Microsatellite Mouse Chain and Net RefSeq Acc RefSeq Alignments RefSeq All RefSeq Curated RefSeq Other RefSeq Predicted RepeatMasker Sheep Chain/Net Simple Repeats Unmasked CpG WM + SDust

Sheep Aug. 2012 (ISGC Oar_v3.1/oviAri3) (oviAri3, International Sheep Genome Consortium)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Shrew Aug. 2008 (Broad/sorAra2) (sorAra2, Broad Institute SorAra2.0)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Shrew June 2006 (Broad/sorAra1) (sorAra1, Broad Institute sorAra1 (Draft_v2))

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

Sloth Jul. 2008 (Broad/choHof1) (choHof1, Broad Institute choHof1)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Squirrel Nov. 2011 (Broad/speTri2) (speTri2, Broad Institute (GCA_000236235.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Squirrel monkey Oct. 2011 (Broad/saiBol1) (saiBol1, Broad SaiBol1.0 (GCA_000235385.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1, Broad Institute gasAcu1 (1.0) (NCBI project 13579, AANH01000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Tarsier Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) (tarSyr2, Washington University)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Tarsier Aug. 2008 (Broad/tarSyr1) (tarSyr1, Broad Institute tarSyr1 (NCBI project 20335, ABRT000000000))

Track Name
Ensembl v90 release

Tasmanian devil Feb. 2011 (WTSI Devil_ref v7.0/sarHar1) (sarHar1, Wellcome Trust Sanger Institute Devil_ref v7.0 (GCA_000189315.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Tenrec Nov. 2012 (Broad/echTel2) (echTel2, Broad/EchTel2.0)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Tenrec July 2005 (Broad/echTel1) (echTel1, Broad July 2005)

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2, Genoscope Tetraodon v8.0 (NCBI project 12350, CAAE01000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Tibetan frog Mar. 2015 (BGI_ZX_2015/nanPar1) (nanPar1, ASM93562v1)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
X. tropicalis (xenTro9) Chain and Net
Initial nanPar1 release (using ASM93562v1 BGI_ZX_2015 (NCBI project 243398, GCA_000935625.1): Assembly, AUGUSTUS, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genscan Genes, INSDC, Interrupted Rpts, Microsatellite, RefSeq Acc, RepeatMasker, Simple Repeats, Tibetan frog Chain/Net, Unmasked CpG, WM + SDust, X. tropicalis Chain and Net, supporting tables and files.

Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1, Broad Institute tupBel1 (NCBI project 13971, AAPY01000000))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Turkey Nov. 2014 (Turkey_5.0/melGal5) (melGal5, Turkey Genome Consortium)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
Rat (rn6) Chain/Nets
nitial melGal5 release (using Turkey Genome Consortium): AUGUSTUS, Assembly, Chicken Chain and Net, Chromosome Band (Ideogram), CpG Islands, GC Percent, Gap, Genbank-process tracks and supporting tables, Genscan Genes, Human Chain and Net, INSDC, Interrupted Rpts, Medium ground finch Chain and Net, Microsatellite, Mouse Chain and Net, Opossum Chain and Net, Peregrine falcon Chain and Net, Rat Chain and Net, RefSeq Acc, RepeatMasker, Simple Repeats, Turkey Chain/Net, Unmasked CpG, WM + SDust, X. tropicalis Chain and Net, Zebra finch Chain and Net, Zebrafish Chain and Net, supporting tables and files.

Turkey Dec. 2009 (TGC Turkey_2.01/melGal1) (melGal1, TGC (NCBI Project ID: 10805, Accession: GCA_000146605.1))

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

Wallaby Sep. 2009 (TWGS Meug_1.1/macEug2) (macEug2, TWGS (NCBI Project ID: 12586, Accession: GCA_000004035.1))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

White rhinoceros May 2012 (CerSimSim1.0/cerSim1) (cerSim1, Broad Institute)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

X. tropicalis Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) (xenTro9, DOE Joint Genome Institute)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
NCBI RefSeq gene predictions
Initial xenTro9 release (using DOE Joint Genome Institute Xenopus_tropicalis_v9.1 (GCA_000004195.3)): African clawed frog Chain and Net, AUGUSTUS Genes, Assembly, CpG Islands, Chicken Chain and Net, Dog Chain and Net, X. tropicalis ESTs, Other ESTs, Fugu Chain and Net, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Repeats, Lizard Chain and Net, Microsatellite, Mouse Chain and Net, X. tropicalis mRNAs, Other mRNAs, Opossum Chain and Net, Other RefSeq Genes, RefSeq Genes, RepeatMasker, Simple Repeats, Tibetan frog Chain and Net, WindowMasker + SDust

X. tropicalis Sep. 2012 (JGI 7.0/xenTro7) (xenTro7, US DOE Joint Genome Institute (JGI-PGF))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
NCBI RefSeq gene predictions
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

X. tropicalis Nov. 2009 (JGI 4.2/xenTro3) (xenTro3, US DOE Joint Genome Institute (JGI-PGF) (GCA_000004195.1))

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

Zebra finch Feb. 2013 (WashU taeGut324/taeGut2) (taeGut2, Washington University School of Medicine)

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)

Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1, Washington University taeGut1)

Track Name
Ensembl Genes v95 Jan 2019
Ensembl v92 release
Ensembl v91 release

Zebrafish May 2017 (GRCz11/danRer11) (danRer11, Genome Reference Consortium Zebrafish Build 11 (GCA_000002035.4))

Track Name
GRC Incident track
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
Ensembl Genes v95 Jan 2019
Ensembl v92 release
NCBI RefSeq gene predictions
Initial danRer11 release (using Genome Reference Consortium GRCz11 (NCBI project 11776, GCA_000002035.4)): AUGUSTUS Genes, Assembly, Zebgrafish ESTs, Other ESTs, GC Percent, Gap, Genscan Genes, Human Chain and Net, INSDC, Interrupted Repeats, Microsatellite, Mouse Chain and Net, Zebrafish mRNAs, Other mRNAs, Other RefSeq Genes, RefSeq Genes, RepeatMasker, Simple Repeats, CpG Islands, WindowMasker + SDust

Zebrafish Sep. 2014 (GRCz10/danRer10) (danRer10, Genome Reference Consortium Zebrafish Build 10 (GCA_000002035.3))

Track Name
TransMap V5 release. Update of TransMap for 120 assemblies. This now uses the NCBI RefSeq RNA mappings instead of the UCSC ones.
NCBI RefSeq gene predictions
UCSC to RefSeq Chromosome names
Ensembl v91 release
Uniprot proteins
Ensembl v89 release
TransMap Alignments (Ensembl, RefSeq, GenBank RNAs, and GenBank ESTs)
Rat (rn6) Chain/Nets

Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7, Wellcome Trust Sanger Institute Zv9 (GCA_000002035.2))

Track Name
Search support for chromosome aliases from Ensembl, GenBank, and RefSeq.
UCSC to RefSeq Chromosome names