Control track and group visibility more selectively below.
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| Base Position |
| Chromosome position in bases. (Clicks here zoom in 3x) |
| STS Markers |
| STS Markers on Genetic and Radiation Hybrid Maps |
| Assembly |
| Assembly from Fragments |
| BAC End Pairs |
| BAC End Pairs |
| Chromosome Band |
| Chromosome Bands Based On Microscopy |
| Gap |
| Gap Locations |
| GC Percent |
| GC Percent in 5-Base Windows |
| GRC Incident |
| GRC Incident Database |
| Map Contigs |
| Physical Map Contigs |
Mappability |
| Mappability or Uniqueness of Reference Genome from ENCODE |
| MGI QTL |
| Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics |
| Restr Enzymes |
| Restriction Enzymes from REBASE |
| Short Match |
| Perfect Matches to Short Sequence () |
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| UCSC Genes |
| UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics) |
| Ensembl Genes |
| Ensembl Genes |
| Human Proteins |
| Human Proteins Mapped by Chained tBLASTn |
| RefSeq Genes |
| RefSeq Genes |
| Other RefSeq |
| Non-Mouse RefSeq Genes |
| AceView Genes |
| AceView Gene Models With Alt-Splicing |
| AUGUSTUS |
| AUGUSTUS ab initio gene predictions v3.1 |
| CCDS |
| Consensus CDS |
| CRISPR... |
| CRISPR/Cas9 Sp. Pyog. target sites |
| CRISPR Regions |
| Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 200 bp) |
| CRISPR Targets |
| CRISPR/Cas9 -NGG Targets |
| Exoniphy |
| Exoniphy Mouse/Rat/Human/Dog |
| Gene Trap |
| International Gene Trap Consortium Sequence Tag Alignments |
| Geneid Genes |
| Geneid Gene Predictions |
| Genscan Genes |
| Genscan Gene Predictions |
| IKMC Genes |
| International Knockout Mouse Consortium Genes |
| miRNA |
| MicroRNAs from miRBase |
| N-SCAN |
| N-SCAN Gene Predictions |
| NIA Gene Index |
| NIA Mouse Gene Index |
| Old UCSC Genes |
| Previous Version of UCSC Genes |
| ORFeome Clones |
| ORFeome Collaboration Gene Clones |
| Pfam in UCSC Gene |
| Pfam Domains in UCSC Genes |
| SGP Genes |
| SGP Gene Predictions Using Mouse/Human Homology |
| Transcriptome |
| TROMER Transcriptome database |
| tRNA Genes |
| Transfer RNA Genes Identified with tRNAscan-SE |
| UCSC Alt Events |
| Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes |
| Vega Genes |
| Vega Annotations |
| Yale Pseudo60 |
| Yale Pseudogenes based on Ensembl Release 60 |
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| Publications |
| Publications: Sequences in Scientific Articles |
| Web Sequences |
| DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research |
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| Spliced ESTs |
| Mouse ESTs That Have Been Spliced |
| Mouse mRNAs |
| Mouse mRNAs from GenBank |
| Mouse ESTs |
| Mouse ESTs Including Unspliced |
| Other mRNAs |
| Non-Mouse mRNAs from GenBank |
| PolyA-Seq |
| Poly(A)-sequencing from Merck Research Laboratories |
| SIB Alt-Splicing |
| Alternative Splicing Graph from Swiss Institute of Bioinformatics |
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| MGI Allele |
| Jackson Laboratory / Mouse Genome Informatics Allele |
| MGI Gene Trap |
| Jackson Laboratory / Mouse Genome Informatics DNA and RNA Gene Traps |
| MGI Phenotype |
| Jackson Laboratory / Mouse Genome Informatics Phenotype |
| MGI RepTranscrpt |
| Jackson Laboratory / Mouse Genome Informatics Representative Transcript |
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| Affy Exon... |
| Affymetrix All Exon Microarrays |
| Affy Exon Probes |
| Affymetrix Exon Array 1.0: Probesets |
| Affy Exon Tissues |
| Affymetrix Exon Array 1.0: Normal Tissues |
| Affy GNF1M |
| Alignments of Probes from Affymetrix GNF1M Chip |
| Affy MOE430 |
| Alignments of Affymetrix Consensus Sequences from Mouse MOE430 (A and B) |
| Affy U74 |
| Alignments of Affymetrix Consensus Sequences from MG-U74 v2 (A,B, and C) |
| Allen Brain |
| Allen Brain Atlas Probes |
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Caltech Histone |
| Histone Modifications by ChIP-seq from ENCODE/Caltech |
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Caltech RNA-seq |
| RNA-seq from ENCODE/Caltech |
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Caltech TFBS |
| Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech |
| CpG Islands... |
| CpG Islands (Islands < 300 Bases are Light Green) |
| CpG Islands |
| CpG Islands (Islands < 300 Bases are Light Green) |
| Unmasked CpG |
| CpG Islands on All Sequence (Islands < 300 Bases are Light Green) |
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CSHL Long RNA-seq |
| Long RNA-seq from ENCODE/Cold Spring Harbor Lab |
| FaceBase 24STypes |
| FaceBase 24 Sample Types Averaged |
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FSU Repli-chip |
| Replication Timing by Repli-chip from ENCODE/FSU |
| GNF Atlas 2 |
| GNF Expression Atlas 2 |
| GNF U74A |
| GNF Expression Atlas on Mouse Affymetrix U74A Chip |
| GNF U74B |
| GNF Expression Atlas on Mouse Affymetrix U74B Chip |
| GNF U74C |
| GNF Expression Atlas on Mouse Affymetrix U74C Chip |
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LICR Histone |
| Histone Mods by ChIP-seq from ENCODE/LICR |
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LICR RNA-seq |
| RNA-seq from ENCODE/LICR |
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LICR TFBS |
| Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR |
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NHGRI BiP |
| ENCODE NHGRI Elnitski Bidirectional Promoters |
| NKI Nuc Lamina... |
| NKI Nuclear Lamina Associated Domains (LaminB1 DamID) |
| mouse LaminB1 ESC |
| NKI LaminB1 (DamID of LaminB1 in mouse Embryonic Stem cells, log2-ratio) |
| mouse LaminB1 NPC |
| NKI LaminB1 (DamID of LaminB1 in mouse Neural Progenitor cells, log2-ratio) |
| mouse LaminB1 AC |
| NKI LaminB1 (DamID of LaminB1 in mouse Astrocytes, log2-ratio) |
| mouse LaminB1 MEF |
| NKI LaminB1 (DamID of LaminB1 in mouse Embryonic Fibroblasts, log2-ratio) |
| ORegAnno |
| Regulatory elements from ORegAnno |
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PSU DNaseI HS |
| DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU |
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PSU Histone |
| Histone Modifications by ChIP-seq from ENCODE/PSU |
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PSU RNA-seq |
| RNA-seq from ENCODE/PSU |
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PSU TFBS |
| Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU |
| REST |
| Repressor Element 1-Silencing Transcription Factor (REST) binding sites |
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Stan/Yale Histone |
| Histone Modifications by ChIP-seq from ENCODE/SYDH |
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Stan/Yale RNA-seq |
| RNA-seq from ENCODE/Stanford/Yale |
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Stan/Yale TFBS |
| Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale |
| TS miRNA sites |
| TargetScan miRNA Regulatory Sites |
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UW DNaseI DGF |
| DNaseI Digital Genomic Footprinting from ENCODE/University of Washington |
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UW DNaseI HS |
| DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington |
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UW RNA-seq |
| RNA-seq from ENCODE/UW |
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| Conservation |
| 30-Way Multiz Alignment & Conservation |
| GERP |
| GERP scores for mammalian alignments |
| Rat Chain/Net |
| Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments |
| Guinea pig Chain/Net |
| Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments |
| Rabbit Chain/Net |
| Rabbit (Apr. 2009 (Broad/oryCun2)), Chain and Net Alignments |
| Marmoset Chain/Net |
| Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments |
| Rhesus Chain/Net |
| Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments |
| Orangutan Chain/Net |
| Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments |
| Chimp Chain/Net |
| Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments |
| Human Chain/Net |
| Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments |
| Panda Chain/Net |
| Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments |
| Dog Chain/Net |
| Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments |
| Cat Chain/Net |
| Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments |
| Horse Chain/Net |
| Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments |
| Sheep Chain/Net |
| Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments |
| bosTau6 Chain/Net |
| Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments |
| Pig Chain/Net |
| Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments |
| Elephant Chain/Net |
| Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments |
| Opossum Chain/Net |
| Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments |
| Platypus Chain/Net |
| Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments |
| Lizard Chain/Net |
| Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments |
| Turkey Chain/Net |
| Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments |
| Chicken Chain/Net |
| Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments |
| X. tropicalis Chain/Net |
| X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments |
| Zebrafish Chain/Net |
| Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments |
| Stickleback Chain/Net |
| Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments |
| Medaka Chain/Net |
| Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments |
| Fugu Chain/Net |
| Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments |
| Tetraodon Chain/Net |
| Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments |
| Lamprey Chain/Net |
| Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments |
| Lancelet Chain/Net |
| Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments |
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| SNPs (128) |
| Simple Nucleotide Polymorphisms (dbSNP build 128) |
| RepeatMasker |
| Repeating Elements by RepeatMasker |
| Agilent CGH |
| Agilent CGH Microarray probesets |
| Microsatellite |
| Microsatellites - Di-nucleotide and Tri-nucleotide Repeats |
| NumtS Sequence |
| Mouse NumtS mitochondrial sequence |
| Segmental Dups |
| Duplications of >1000 Bases of Non-RepeatMasked Sequence |
| Simple Repeats |
| Simple Tandem Repeats by TRF |
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