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Configure Tracks on UCSC Genome Browser: Mouse Jun. 2020 (GRCm39/mm39)
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-   PhyloCSF    
PhyloCSF Novel M27 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM27 Gene Set
PhyloCSF Novel M28 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM28 Gene Set
PhyloCSF Novel M29 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM29 Gene Set
PhyloCSF Novel M30 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM30 Gene Set
PhyloCSF Novel M31 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM31 Gene Set
PhyloCSF Novel M32 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM32 Gene Set
PhyloCSF Novel M33 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM33 Gene Set
PhyloCSF Novel M34 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM34 Gene Set
PhyloCSF Novel M35 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM35 Gene Set
PhyloCSF Novel M36 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM36 Gene Set
PhyloCSF Novel M37 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM37 Gene Set
PhyloCSF Novel vM26 PhyloCSF Candidate Coding Regions (PCCRs) Not In GENCODE vM26 Gene Set
Smoothed PhyloCSF Smoothed PhyloCSF
     PhyloCSF-3     Smoothed PhyloCSF Strand - Frame 3
     PhyloCSF-2     Smoothed PhyloCSF Strand - Frame 2
     PhyloCSF-1     Smoothed PhyloCSF Strand - Frame 1
     PhyloCSF+3     Smoothed PhyloCSF Strand + Frame 3
     PhyloCSF+2     Smoothed PhyloCSF Strand + Frame 2
     PhyloCSF+1     Smoothed PhyloCSF Strand + Frame 1
PhyloCSF Regions PhyloCSF approximate coding regions
     PhyloCSF-3Regns     PhyloCSF approximate coding regions, Strand -, Frame 3
     PhyloCSF-2Regns     PhyloCSF approximate coding regions, Strand -, Frame 2
     PhyloCSF-1Regns     PhyloCSF approximate coding regions, Strand -, Frame 1
     PhyloCSF+3Regns     PhyloCSF approximate coding regions, Strand +, Frame 3
     PhyloCSF+2Regns     PhyloCSF approximate coding regions, Strand +, Frame 2
     PhyloCSF+1Regns     PhyloCSF approximate coding regions, Strand +, Frame 1
Raw PhyloCSF Raw PhyloCSF
     PhyloCSFraw-3     Raw PhyloCSF Strand - Frame 3
     PhyloCSFraw-2     Raw PhyloCSF Strand - Frame 2
     PhyloCSFraw-1     Raw PhyloCSF Strand - Frame 1
     PhyloCSFraw+3     Raw PhyloCSF Strand + Frame 3
     PhyloCSFraw+2     Raw PhyloCSF Strand + Frame 2
     PhyloCSFraw+1     Raw PhyloCSF Strand + Frame 1
PhyloCSF Power Relative branch length of local alignment, a measure of PhyloCSF statistical power
Splice Predictions Splice Predictions
     SplicePred-     Splice Predictions For - Strand
     SplicePred+     Splice Predictions For + Strand
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Assembly Assembly from Fragments
Chromosome Band Chromosome Bands Based On Microscopy
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
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
Tandem Dups Paired identical sequences
UCSC liftOver mm10 UCSC liftOver alignments to mm10
-   Genes and Gene Predictions    
updated GENCODE VM37 GENCODE VM37
NCBI RefSeq RefSeq genes from NCBI
updated GENCODE Versions Container of all new and previous GENCODE releases
    new All GENCODE VM37     All GENCODE annotations from VM37 (Ensembl 114)
     All GENCODE VM36     All GENCODE annotations from VM36 (Ensembl 113)
     All GENCODE VM35     All GENCODE annotations from VM35 (Ensembl 112)
     All GENCODE VM34     All GENCODE annotations from VM34 (Ensembl 111)
     All GENCODE VM33     All GENCODE annotations from VM33 (Ensembl 110)
     All GENCODE VM32     All GENCODE annotations from VM32 (Ensembl 109)
     All GENCODE VM31     All GENCODE annotations from VM31 (Ensembl 108)
     All GENCODE VM30     All GENCODE annotations from VM30 (Ensembl 107)
     All GENCODE VM29     All GENCODE annotations from VM29 (Ensembl 106)
     All GENCODE VM28     All GENCODE annotations from VM28 (Ensembl 105)
     All GENCODE VM27     All GENCODE annotations from VM27 (Ensembl 104)
     All GENCODE VM26     All GENCODE annotations from VM26 (Ensembl 103)
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
GENCODE Archive GENCODE Archive
     GENCODE VM27     GENCODE VM27
     GENCODE VM30     GENCODE VM30
     GENCODE VM32     GENCODE VM32
     GENCODE VM33     GENCODE VM33
     GENCODE VM35     GENCODE VM35
Genscan Genes Genscan Gene Predictions
Other RefSeq Non-Mouse RefSeq Genes
Pfam in GENCODE Pfam Domains in GENCODE Genes
TOGA vs. hg38 TOGA annotations using human/hg38 as reference
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
UniProt UniProt SwissProt/TrEMBL Protein Annotations
-   RNA and Transcriptome    
RefSeq mRNAs RefSeq mRNAs mapped to this assembly
Mouse mRNAs Mouse mRNAs from GenBank
Mouse ESTs Mouse ESTs Including Unspliced
Other mRNAs Non-Mouse mRNAs from GenBank
-   Expression and Regulation    
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)
JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database
ReMap ChIP-seq ReMap Atlas of Regulatory Regions
updated VISTA Enhancers VISTA Enhancers
-   Comparative Genomics    
Conservation Vertebrate Multiz Alignment & Conservation (35 Species)
Chain/Net Chain and Net Alignments
-   Variation and Repeats    
RepeatMasker Repeating Elements by RepeatMasker
updated EVA SNP Short Genetic Variants from European Variant Archive
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust