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Configure Tracks on UCSC Genome Browser: Mouse Dec. 2011 (GRCm38/mm10)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   Hub: ENCODE DNA Trackhub    
ATAC-seq ATAC-seq
DNase-seq DNase-seq
Experiments by Ontology Experiments by Ontology
     unknown    
     stomach     stomach
     spleen     blood, bodily fluid, immune organ, spleen
     spinal cord     spinal cord
     small intestine     intestine, small intestine
     placenta     extraembryonic component, placenta
     musculature of body     musculature of body
     lymph node     blood, bodily fluid, lymph node
     lung     connective tissue, lung
     liver     endocrine gland, exocrine gland, liver
     limb     limb
     kidney     connective tissue, kidney
     intestine     intestine, large intestine
     heart     heart
     gonad     adipose tissue, connective tissue, gonad, ovary, testis
     eye     eye
     epithelium     epithelium, extraembryonic component
     endocrine gland     adrenal gland, endocrine gland, immune organ, thymus
     embryo     connective tissue, embryo, epithelium
     connective tissue     connective tissue
     breast     breast
     brain     brain
     bone marrow     bone element, bone marrow
     blood     blood, bodily fluid
     adipose tissue     adipose tissue, connective tissue
Histone ChIP-seq (by biosample) Histone ChIP-seq (by biosample)
     Histone ChIP-seq (by biosample) thymus     Histone ChIP-seq (by biosample) thymus
     Histone ChIP-seq (by biosample) testis     Histone ChIP-seq (by biosample) testis
     Histone ChIP-seq (by biosample) stomach     Histone ChIP-seq (by biosample) stomach
     Histone ChIP-seq (by biosample) splenic B cell     Histone ChIP-seq (by biosample) splenic B cell
     Histone ChIP-seq (by biosample) spleen     Histone ChIP-seq (by biosample) spleen
     Histone ChIP-seq (by biosample) small intestine     Histone ChIP-seq (by biosample) small intestine
     Histone ChIP-seq (by biosample) placenta     Histone ChIP-seq (by biosample) placenta
     Histone ChIP-seq (by biosample) olfactory bulb     Histone ChIP-seq (by biosample) olfactory bulb
     Histone ChIP-seq (by biosample) midbrain     Histone ChIP-seq (by biosample) midbrain
     Histone ChIP-seq (by biosample) MEL cell line     Histone ChIP-seq (by biosample) MEL cell line
     Histone ChIP-seq (by biosample) lung     Histone ChIP-seq (by biosample) lung
     Histone ChIP-seq (by biosample) liver     Histone ChIP-seq (by biosample) liver
     Histone ChIP-seq (by biosample) kidney     Histone ChIP-seq (by biosample) kidney
     Histone ChIP-seq (by biosample) intestine     Histone ChIP-seq (by biosample) intestine
     Histone ChIP-seq (by biosample) hindbrain     Histone ChIP-seq (by biosample) hindbrain
     Histone ChIP-seq (by biosample) heart     Histone ChIP-seq (by biosample) heart
     Histone ChIP-seq (by biosample) G1E-ER4     Histone ChIP-seq (by biosample) G1E-ER4
     Histone ChIP-seq (by biosample) G1E     Histone ChIP-seq (by biosample) G1E
     Histone ChIP-seq (by biosample) forebrain     Histone ChIP-seq (by biosample) forebrain
     Histone ChIP-seq (by biosample) embryonic ES-E14     Histone ChIP-seq (by biosample) embryonic ES-E14
     Histone ChIP-seq (by biosample) embryonic ES-Bruce4     Histone ChIP-seq (by biosample) embryonic ES-Bruce4
     Histone ChIP-seq (by biosample) e3.5 day E14TG2a.4     Histone ChIP-seq (by biosample) e3.5 day E14TG2a.4
     Histone ChIP-seq (by biosample) e16.5 day stomach     Histone ChIP-seq (by biosample) e16.5 day stomach
     Histone ChIP-seq (by biosample) e16.5 day midbrain     Histone ChIP-seq (by biosample) e16.5 day midbrain
     Histone ChIP-seq (by biosample) e16.5 day lung     Histone ChIP-seq (by biosample) e16.5 day lung
     Histone ChIP-seq (by biosample) e16.5 day liver     Histone ChIP-seq (by biosample) e16.5 day liver
     Histone ChIP-seq (by biosample) e16.5 day kidney     Histone ChIP-seq (by biosample) e16.5 day kidney
     Histone ChIP-seq (by biosample) e16.5 day intestine     Histone ChIP-seq (by biosample) e16.5 day intestine
     Histone ChIP-seq (by biosample) e16.5 day hindbrain     Histone ChIP-seq (by biosample) e16.5 day hindbrain
     Histone ChIP-seq (by biosample) e16.5 day heart     Histone ChIP-seq (by biosample) e16.5 day heart
     Histone ChIP-seq (by biosample) e16.5 day forebrain     Histone ChIP-seq (by biosample) e16.5 day forebrain
     Histone ChIP-seq (by biosample) e15.5 day stomach     Histone ChIP-seq (by biosample) e15.5 day stomach
     Histone ChIP-seq (by biosample) e15.5 day neural tube     Histone ChIP-seq (by biosample) e15.5 day neural tube
     Histone ChIP-seq (by biosample) e15.5 day midbrain     Histone ChIP-seq (by biosample) e15.5 day midbrain
     Histone ChIP-seq (by biosample) e15.5 day lung     Histone ChIP-seq (by biosample) e15.5 day lung
     Histone ChIP-seq (by biosample) e15.5 day liver     Histone ChIP-seq (by biosample) e15.5 day liver
     Histone ChIP-seq (by biosample) e15.5 day limb     Histone ChIP-seq (by biosample) e15.5 day limb
     Histone ChIP-seq (by biosample) e15.5 day kidney     Histone ChIP-seq (by biosample) e15.5 day kidney
     Histone ChIP-seq (by biosample) e15.5 day intestine     Histone ChIP-seq (by biosample) e15.5 day intestine
     Histone ChIP-seq (by biosample) e15.5 day hindbrain     Histone ChIP-seq (by biosample) e15.5 day hindbrain
     Histone ChIP-seq (by biosample) e15.5 day heart     Histone ChIP-seq (by biosample) e15.5 day heart
     Histone ChIP-seq (by biosample) e15.5 day forebrain     Histone ChIP-seq (by biosample) e15.5 day forebrain
     Histone ChIP-seq (by biosample) e15.5 day embryonic facial prominence     Histone ChIP-seq (by biosample) e15.5 day embryonic facial prominence
     Histone ChIP-seq (by biosample) e14.5 day stomach     Histone ChIP-seq (by biosample) e14.5 day stomach
     Histone ChIP-seq (by biosample) e14.5 day neural tube     Histone ChIP-seq (by biosample) e14.5 day neural tube
     Histone ChIP-seq (by biosample) e14.5 day midbrain     Histone ChIP-seq (by biosample) e14.5 day midbrain
     Histone ChIP-seq (by biosample) e14.5 day megakaryocyte     Histone ChIP-seq (by biosample) e14.5 day megakaryocyte
     Histone ChIP-seq (by biosample) e14.5 day lung     Histone ChIP-seq (by biosample) e14.5 day lung
     Histone ChIP-seq (by biosample) e14.5 day liver     Histone ChIP-seq (by biosample) e14.5 day liver
     Histone ChIP-seq (by biosample) e14.5 day limb     Histone ChIP-seq (by biosample) e14.5 day limb
     Histone ChIP-seq (by biosample) e14.5 day kidney     Histone ChIP-seq (by biosample) e14.5 day kidney
     Histone ChIP-seq (by biosample) e14.5 day intestine     Histone ChIP-seq (by biosample) e14.5 day intestine
     Histone ChIP-seq (by biosample) e14.5 day hindbrain     Histone ChIP-seq (by biosample) e14.5 day hindbrain
     Histone ChIP-seq (by biosample) e14.5 day heart     Histone ChIP-seq (by biosample) e14.5 day heart
     Histone ChIP-seq (by biosample) e14.5 day forebrain     Histone ChIP-seq (by biosample) e14.5 day forebrain
     Histone ChIP-seq (by biosample) e14.5 day erythroblast     Histone ChIP-seq (by biosample) e14.5 day erythroblast
     Histone ChIP-seq (by biosample) e14.5 day embryonic facial prominence     Histone ChIP-seq (by biosample) e14.5 day embryonic facial prominence
     Histone ChIP-seq (by biosample) e13.5 week embryonic fibroblast     Histone ChIP-seq (by biosample) e13.5 week embryonic fibroblast
     Histone ChIP-seq (by biosample) e13.5 day neural tube     Histone ChIP-seq (by biosample) e13.5 day neural tube
     Histone ChIP-seq (by biosample) e13.5 day midbrain     Histone ChIP-seq (by biosample) e13.5 day midbrain
     Histone ChIP-seq (by biosample) e13.5 day liver     Histone ChIP-seq (by biosample) e13.5 day liver
     Histone ChIP-seq (by biosample) e13.5 day limb     Histone ChIP-seq (by biosample) e13.5 day limb
     Histone ChIP-seq (by biosample) e13.5 day hindbrain     Histone ChIP-seq (by biosample) e13.5 day hindbrain
     Histone ChIP-seq (by biosample) e13.5 day heart     Histone ChIP-seq (by biosample) e13.5 day heart
     Histone ChIP-seq (by biosample) e13.5 day forebrain     Histone ChIP-seq (by biosample) e13.5 day forebrain
     Histone ChIP-seq (by biosample) e13.5 day embryonic facial prominence     Histone ChIP-seq (by biosample) e13.5 day embryonic facial prominence
     Histone ChIP-seq (by biosample) e12.5 day neural tube     Histone ChIP-seq (by biosample) e12.5 day neural tube
     Histone ChIP-seq (by biosample) e12.5 day midbrain     Histone ChIP-seq (by biosample) e12.5 day midbrain
     Histone ChIP-seq (by biosample) e12.5 day liver     Histone ChIP-seq (by biosample) e12.5 day liver
     Histone ChIP-seq (by biosample) e12.5 day limb     Histone ChIP-seq (by biosample) e12.5 day limb
     Histone ChIP-seq (by biosample) e12.5 day hindbrain     Histone ChIP-seq (by biosample) e12.5 day hindbrain
     Histone ChIP-seq (by biosample) e12.5 day heart     Histone ChIP-seq (by biosample) e12.5 day heart
     Histone ChIP-seq (by biosample) e12.5 day forebrain     Histone ChIP-seq (by biosample) e12.5 day forebrain
     Histone ChIP-seq (by biosample) e12.5 day embryonic facial prominence     Histone ChIP-seq (by biosample) e12.5 day embryonic facial prominence
     Histone ChIP-seq (by biosample) e11.5 day neural tube     Histone ChIP-seq (by biosample) e11.5 day neural tube
     Histone ChIP-seq (by biosample) e11.5 day midbrain     Histone ChIP-seq (by biosample) e11.5 day midbrain
     Histone ChIP-seq (by biosample) e11.5 day liver     Histone ChIP-seq (by biosample) e11.5 day liver
     Histone ChIP-seq (by biosample) e11.5 day limb     Histone ChIP-seq (by biosample) e11.5 day limb
     Histone ChIP-seq (by biosample) e11.5 day hindbrain     Histone ChIP-seq (by biosample) e11.5 day hindbrain
     Histone ChIP-seq (by biosample) e11.5 day heart     Histone ChIP-seq (by biosample) e11.5 day heart
     Histone ChIP-seq (by biosample) e11.5 day forebrain     Histone ChIP-seq (by biosample) e11.5 day forebrain
     Histone ChIP-seq (by biosample) e11.5 day embryonic facial prominence     Histone ChIP-seq (by biosample) e11.5 day embryonic facial prominence
     Histone ChIP-seq (by biosample) e10.5 day midbrain     Histone ChIP-seq (by biosample) e10.5 day midbrain
     Histone ChIP-seq (by biosample) e10.5 day limb     Histone ChIP-seq (by biosample) e10.5 day limb
     Histone ChIP-seq (by biosample) e10.5 day hindbrain     Histone ChIP-seq (by biosample) e10.5 day hindbrain
     Histone ChIP-seq (by biosample) e10.5 day heart     Histone ChIP-seq (by biosample) e10.5 day heart
     Histone ChIP-seq (by biosample) e10.5 day forebrain     Histone ChIP-seq (by biosample) e10.5 day forebrain
     Histone ChIP-seq (by biosample) e10.5 day embryonic facial prominence     Histone ChIP-seq (by biosample) e10.5 day embryonic facial prominence
     Histone ChIP-seq (by biosample) cortical plate     Histone ChIP-seq (by biosample) cortical plate
     Histone ChIP-seq (by biosample) CH12.LX     Histone ChIP-seq (by biosample) CH12.LX
     Histone ChIP-seq (by biosample) cerebellum     Histone ChIP-seq (by biosample) cerebellum
     Histone ChIP-seq (by biosample) brown adipose tissue     Histone ChIP-seq (by biosample) brown adipose tissue
     Histone ChIP-seq (by biosample) bone marrow macrophage     Histone ChIP-seq (by biosample) bone marrow macrophage
     Histone ChIP-seq (by biosample) bone marrow     Histone ChIP-seq (by biosample) bone marrow
Histone ChIP-seq (by target) Histone ChIP-seq (by target)
     Histone ChIP-seq (by target) H3K9me3     Histone ChIP-seq (by target) H3K9me3
     Histone ChIP-seq (by target) H3K9ac     Histone ChIP-seq (by target) H3K9ac
     Histone ChIP-seq (by target) H3K79me2     Histone ChIP-seq (by target) H3K79me2
     Histone ChIP-seq (by target) H3K4me3     Histone ChIP-seq (by target) H3K4me3
     Histone ChIP-seq (by target) H3K4me2     Histone ChIP-seq (by target) H3K4me2
     Histone ChIP-seq (by target) H3K4me1     Histone ChIP-seq (by target) H3K4me1
     Histone ChIP-seq (by target) H3K36me3     Histone ChIP-seq (by target) H3K36me3
     Histone ChIP-seq (by target) H3K27me3     Histone ChIP-seq (by target) H3K27me3
     Histone ChIP-seq (by target) H3K27ac     Histone ChIP-seq (by target) H3K27ac
TF ChIP-seq (by biosample) TF ChIP-seq (by biosample)
     TF ChIP-seq (by biosample) thymus     TF ChIP-seq (by biosample) thymus
     TF ChIP-seq (by biosample) testis     TF ChIP-seq (by biosample) testis
     TF ChIP-seq (by biosample) stomach     TF ChIP-seq (by biosample) stomach
     TF ChIP-seq (by biosample) spleen     TF ChIP-seq (by biosample) spleen
     TF ChIP-seq (by biosample) small intestine     TF ChIP-seq (by biosample) small intestine
     TF ChIP-seq (by biosample) olfactory bulb     TF ChIP-seq (by biosample) olfactory bulb
     TF ChIP-seq (by biosample) myocyte     TF ChIP-seq (by biosample) myocyte
     TF ChIP-seq (by biosample) midbrain     TF ChIP-seq (by biosample) midbrain
     TF ChIP-seq (by biosample) MEL cell line     TF ChIP-seq (by biosample) MEL cell line
     TF ChIP-seq (by biosample) lung     TF ChIP-seq (by biosample) lung
     TF ChIP-seq (by biosample) liver     TF ChIP-seq (by biosample) liver
     TF ChIP-seq (by biosample) kidney     TF ChIP-seq (by biosample) kidney
     TF ChIP-seq (by biosample) intestine     TF ChIP-seq (by biosample) intestine
     TF ChIP-seq (by biosample) hindbrain     TF ChIP-seq (by biosample) hindbrain
     TF ChIP-seq (by biosample) heart     TF ChIP-seq (by biosample) heart
     TF ChIP-seq (by biosample) G1E-ER4     TF ChIP-seq (by biosample) G1E-ER4
     TF ChIP-seq (by biosample) G1E     TF ChIP-seq (by biosample) G1E
     TF ChIP-seq (by biosample) forebrain     TF ChIP-seq (by biosample) forebrain
     TF ChIP-seq (by biosample) embryonic ES-E14     TF ChIP-seq (by biosample) embryonic ES-E14
     TF ChIP-seq (by biosample) embryonic ES-Bruce4     TF ChIP-seq (by biosample) embryonic ES-Bruce4
     TF ChIP-seq (by biosample) e3.5 day E14TG2a.4     TF ChIP-seq (by biosample) e3.5 day E14TG2a.4
     TF ChIP-seq (by biosample) e14.5 day megakaryocyte     TF ChIP-seq (by biosample) e14.5 day megakaryocyte
     TF ChIP-seq (by biosample) e14.5 day lung     TF ChIP-seq (by biosample) e14.5 day lung
     TF ChIP-seq (by biosample) e14.5 day liver     TF ChIP-seq (by biosample) e14.5 day liver
     TF ChIP-seq (by biosample) e14.5 day erythroblast     TF ChIP-seq (by biosample) e14.5 day erythroblast
     TF ChIP-seq (by biosample) e13.5 week embryonic fibroblast     TF ChIP-seq (by biosample) e13.5 week embryonic fibroblast
     TF ChIP-seq (by biosample) cortical plate     TF ChIP-seq (by biosample) cortical plate
     TF ChIP-seq (by biosample) CH12.LX     TF ChIP-seq (by biosample) CH12.LX
     TF ChIP-seq (by biosample) cerebellum     TF ChIP-seq (by biosample) cerebellum
     TF ChIP-seq (by biosample) bone marrow macrophage     TF ChIP-seq (by biosample) bone marrow macrophage
     TF ChIP-seq (by biosample) bone marrow     TF ChIP-seq (by biosample) bone marrow
TF ChIP-seq (by target) TF ChIP-seq (by target)
     TF ChIP-seq (by target) ZNF384     TF ChIP-seq (by target) ZNF384
     TF ChIP-seq (by target) ZMIZ1     TF ChIP-seq (by target) ZMIZ1
     TF ChIP-seq (by target) ZKSCAN1     TF ChIP-seq (by target) ZKSCAN1
     TF ChIP-seq (by target) USF2     TF ChIP-seq (by target) USF2
     TF ChIP-seq (by target) USF1     TF ChIP-seq (by target) USF1
     TF ChIP-seq (by target) TCF12     TF ChIP-seq (by target) TCF12
     TF ChIP-seq (by target) TBP     TF ChIP-seq (by target) TBP
     TF ChIP-seq (by target) TAL1     TF ChIP-seq (by target) TAL1
     TF ChIP-seq (by target) SMC3     TF ChIP-seq (by target) SMC3
     TF ChIP-seq (by target) SIN3A     TF ChIP-seq (by target) SIN3A
     TF ChIP-seq (by target) RCOR1     TF ChIP-seq (by target) RCOR1
     TF ChIP-seq (by target) POU5F1     TF ChIP-seq (by target) POU5F1
     TF ChIP-seq (by target) POLR2AphosphoS5     TF ChIP-seq (by target) POLR2AphosphoS5
     TF ChIP-seq (by target) POLR2AphosphoS2     TF ChIP-seq (by target) POLR2AphosphoS2
     TF ChIP-seq (by target) POLR2A     TF ChIP-seq (by target) POLR2A
     TF ChIP-seq (by target) PAX5     TF ChIP-seq (by target) PAX5
     TF ChIP-seq (by target) NRF1     TF ChIP-seq (by target) NRF1
     TF ChIP-seq (by target) NANOG     TF ChIP-seq (by target) NANOG
     TF ChIP-seq (by target) MYC     TF ChIP-seq (by target) MYC
     TF ChIP-seq (by target) MYB     TF ChIP-seq (by target) MYB
     TF ChIP-seq (by target) MXI1     TF ChIP-seq (by target) MXI1
     TF ChIP-seq (by target) MEF2A     TF ChIP-seq (by target) MEF2A
     TF ChIP-seq (by target) MAZ     TF ChIP-seq (by target) MAZ
     TF ChIP-seq (by target) MAX     TF ChIP-seq (by target) MAX
     TF ChIP-seq (by target) MAFK     TF ChIP-seq (by target) MAFK
     TF ChIP-seq (by target) JUND     TF ChIP-seq (by target) JUND
     TF ChIP-seq (by target) JUN     TF ChIP-seq (by target) JUN
     TF ChIP-seq (by target) HCFC1     TF ChIP-seq (by target) HCFC1
     TF ChIP-seq (by target) GATA4     TF ChIP-seq (by target) GATA4
     TF ChIP-seq (by target) GATA2     TF ChIP-seq (by target) GATA2
     TF ChIP-seq (by target) GATA1     TF ChIP-seq (by target) GATA1
     TF ChIP-seq (by target) GABPA     TF ChIP-seq (by target) GABPA
     TF ChIP-seq (by target) FLI1     TF ChIP-seq (by target) FLI1
     TF ChIP-seq (by target) ETS1     TF ChIP-seq (by target) ETS1
     TF ChIP-seq (by target) EP300     TF ChIP-seq (by target) EP300
     TF ChIP-seq (by target) ELF1     TF ChIP-seq (by target) ELF1
     TF ChIP-seq (by target) E2F4     TF ChIP-seq (by target) E2F4
     TF ChIP-seq (by target) CTCF     TF ChIP-seq (by target) CTCF
     TF ChIP-seq (by target) CHD2     TF ChIP-seq (by target) CHD2
     TF ChIP-seq (by target) CEBPB     TF ChIP-seq (by target) CEBPB
     TF ChIP-seq (by target) BHLHE40     TF ChIP-seq (by target) BHLHE40
whole-genome shotgun bisulfite sequencing whole-genome shotgun bisulfite sequencing
-   Hub: Umap and Bismap mappability    
Umap Single-read and multi-read mappability by Umap
     Umap S100     Single-read mappability with 100-mers
     Umap M100     Multi-read mappability with 100-mers
     Umap S50     Single-read mappability with 50-mers
     Umap M50     Multi-read mappability with 50-mers
     Umap S36     Single-read mappability with 36-mers
     Umap M36     Multi-read mappability with 36-mers
     Umap S24     Single-read mappability with 24-mers
     Umap M24     Multi-read mappability with 24-mers
Bismap Single-read and multi-read mappability after bisulfite conversion
     Bismap S100 -     Single-read mappability with 100-mers after bisulfite conversion (reverse strand)
     Bismap S100 +     Single-read mappability with 100-mers after bisulfite conversion (forward strand)
     Bismap M100     Multi-read mappability with 100-mers after bisulfite conversion
     Bismap S50 -     Single-read mappability with 50-mers after bisulfite conversion (reverse strand)
     Bismap S50 +     Single-read mappability with 50-mers after bisulfite conversion (forward strand)
     Bismap M50     Multi-read mappability with 50-mers after bisulfite conversion
     Bismap S36 -     Single-read mappability with 36-mers after bisulfite conversion (reverse strand)
     Bismap S36 +     Single-read mappability with 36-mers after bisulfite conversion (forward strand)
     Bismap M36     Multi-read mappability with 36-mers after bisulfite conversion
     Bismap S24 -     Single-read mappability with 24-mers after bisulfite conversion (reverse strand)
     Bismap S24 +     Single-read mappability with 24-mers after bisulfite conversion (forward strand)
     Bismap M24     Multi-read mappability with 24-mers after bisulfite conversion
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
p14 Fix Patches Reference Assembly Fix Patch Sequence Alignments
All Gaps All gaps of unknown nucleotides (N's), including AGP annotated gaps
p14 Alt Haplotypes Reference Assembly Alternate Haplotype Sequence Alignments
Assembly Assembly from Fragments
Chromosome Band Chromosome Bands Based On Microscopy
Clone Ends Mapping of clone libraries end placements
Contigs Contig fragments used in the assembly
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
GRC Incident GRC Incident Database
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
MGI QTL Mouse Genome Informatics Quantitative Trait Loci ***Lifted from NCBI 37 (mm9)***
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
UCSC liftOver mm39 UCSC liftOver alignments to mm39
-   Genes and Gene Predictions    
GENCODE VM23 GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
NCBI RefSeq RefSeq genes from NCBI
GENCODE Versions Container of all new and previous GENCODE releases
     GENCODE VM9 (Ensembl 84)     Gene Annotations from ENCODE/GENCODE Version M9 (Ensembl 84)
     GENCODE VM11 (Ensembl 86)     Gene Annotations from ENCODE/GENCODE Version M11 (Ensembl 86)
     All GENCODE VM14     All GENCODE annotations from VM14 (Ensembl 89)
     All GENCODE VM16     All GENCODE annotations from VM16 (Ensembl 91)
     All GENCODE VM18     All GENCODE annotations from VM18 (Ensembl 93)
     All GENCODE VM22     All GENCODE annotations from VM22 (Ensembl 97)
     All GENCODE VM24     All GENCODE annotations from VM24 (Ensembl 99)
     All GENCODE VM25     All GENCODE annotations from VM25 (Ensembl 100)
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CCDS Consensus CDS
CRISPR 10K CRISPR/Cas9 Sp. Pyog. target sites (exons +/- 10,000 bp)
     CRISPR Targets 10K     CRISPR/Cas9 -NGG Targets (exons +/- 10,000 bp)
     CRISPR Regions 10K     Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 10,000 bp)
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
Geneid Genes Geneid Gene Predictions
Genscan Genes Genscan Gene Predictions
MGC Genes Mammalian Gene Collection Full ORF mRNAs
Old UCSC Genes Previous Version of UCSC Genes
ORFeome Clones ORFeome Collaboration Gene Clones
Other RefSeq Non-Mouse RefSeq Genes
Pfam in UCSC Gene Pfam Domains in UCSC Genes
RetroGenes V6 Retroposed Genes V6, Including Pseudogenes
SGP Genes SGP Gene Predictions Using Mouse/Human Homology
TOGA vs. hg38 TOGA annotations using human/hg38 as reference
TransMap V5 TransMap Alignments Version 5
     TransMap ESTs     TransMap EST Mappings Version 5
     TransMap RNA     TransMap GenBank RNA Mappings Version 5
     TransMap RefGene     TransMap RefSeq Gene Mappings Version 5
     TransMap Ensembl     TransMap Ensembl and GENCODE Mappings Version 5
tRNA Genes Transfer RNA Genes Identified with tRNAscan-SE
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
UniProt UniProt SwissProt/TrEMBL Protein Annotations
-   Literature    
Lens Patents Lens PatSeq Patent Document Sequences
UniProt Variants UniProt/SwissProt Amino Acid Substitutions
-   mRNA and EST    
Mouse ESTs Mouse ESTs Including Unspliced
Mouse mRNAs Mouse mRNAs from GenBank
Other mRNAs Non-Mouse mRNAs from GenBank
-   Expression and Regulation    
ENCODE cCREs ENCODE Candidate Cis-Regulatory Elements (cCREs) combined from all cell types
Tabula Muris Single Cell FACS RNA-Seq of 44,779 cells from Tabula Muris
     Splice Sites     Tabula Muris single cell RNA-Seq splice sites
     Genome Coverage     Tabula Muris single cell RNA-Seq genome coverage
     Cell expression     Single Cell RNA-Seq Gene Expression from Tabula Muris
CpG Islands CpG Islands (Islands < 300 Bases are Light Green)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
     CpG Islands     CpG Islands (Islands < 300 Bases are Light Green)
ENC+EPD Enhc-Gene Enhancer-gene map from ENCODE 3 (UCSD/Ren) with promoters from EPDnew
ENCODE Regulation Integrated Regulation from ENCODE
     Open Chromatin     Open chromatin in embryonic tissue (12 tissues, 8 ages) from ATAC-seq by ENCODE 3 (UCSD/Ren)
     Histone Modifications     Histone modifications in embryonic tissue (8 marks, 12 tissues, 8 ages) from ChIP-seq by ENCODE 3 (UCSD/Ren)
     Chromatin State     Chromatin state of embryonic tissue (12 tissues, 8 ages) from ENCODE 3 (UCSD/Ren)
EPDnew Promoters Promoters from EPDnew
FaceBase 24STypes FaceBase 24 Sample Types Averaged
new FANTOM5 FANTOM5: Mapped transcription start sites (TSS) and their usage
     TSS activity (TPM)     TSS activity per sample (TPM)
     TSS activity (read counts)     TSS activity per sample (read counts)
     Max counts     Max counts of CAGE reads
     Total counts     Total counts of CAGE reads
     TSS peaks     FANTOM5: DPI peak, robust set
updated JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database
ORegAnno Regulatory elements from ORegAnno
qPCR Primers Mouse (mm10) Whole Transcriptome qPCR Primers
RefSeq Func Elems NCBI RefSeq Functional Elements
ReMap ChIP-seq ReMap Atlas of Regulatory Regions
VISTA Enhancers VISTA Enhancers
-   Comparative Genomics    
Conservation Vertebrate Multiz Alignment & Conservation (60 Species)
ClinVar Lift Human ClinVar variants lifted to Mouse
Euarch Chain/Net Euarchontoglire Genomes, Chain and Net Alignments
Glires Chain/Net Glires Genomes, Chain and Net Alignments
Placental Chain/Net Placental Genomes, Chain and Net Alignments
Vertebrate Chain/Net Vertebrate Genomes, Chain and Net Alignments
-   Variation and Repeats    
Common SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples
RepeatMasker Repeating Elements by RepeatMasker
Alternate strains Alternate mouse strain sequences
     Alternate strains     Alternate mouse strains, mapped to their corresponding reference genome location
     Alignment     Alternate mouse strains, alignments to reference genome
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Mouse SNPs Annotated SNPs from mouse strain comparison analysis
dbSNP Archive dbSNP Track Archive
     Mult. SNPs(137)     Simple Nucleotide Polymorphisms (dbSNP 137) That Map to Multiple Genomic Loci
     Common SNPs(137)     Simple Nucleotide Polymorphisms (dbSNP 137) Found in >= 1% of Samples
     All SNPs(137)     Simple Nucleotide Polymorphisms (dbSNP 137)
     Mult. SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci
     Common SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples
     All SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138)
     Mult. SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci
     All SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142)
EVA SNP Release 3 Short Genetic Variants from European Variant Archive Release 3
EVA SNP Release 4 Short Genetic Variants from European Variant Archive Release 4
EVA SNP Release 5 Short Genetic Variants from European Variant Archive Release 5
RepeatMasker Viz. Detailed Visualization of RepeatMasker Annotations
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust