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Configure Tracks on UCSC Genome Browser: Mouse Jun. 2020 (GRCm39/mm39)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   Hub: TAMI hub    
TAMI data A super-track of: Tissue-level transcriptome annotations for the BALB/c mouse
     Spleen transcriptome annotation     Spleen transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Kidney transcriptome annotation     Kidney transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Liver transcriptome annotation     Liver transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Lung transcriptome annotation     Lung transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Salivary Gland transcriptome annotation     Salivary Gland transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Stomach transcriptome annotation     Stomach transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Smooth Muscle transcriptome annotation     Smooth Muscle transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Heart transcriptome annotation     Heart transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Spinal Cord transcriptome annotation     Spinal Cord transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Eye transcriptome annotation     Eye transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Brain transcriptome annotation     Brain transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
     Testis transcriptome annotation     Testis transcriptome annotation. "+" transcripts in Blue, "-" transcripts in Red. Color Intensity based on relative expression within each gene
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Assembly Assembly from Fragments
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 VM36 GENCODE VM36
NCBI RefSeq RefSeq genes from NCBI
updated GENCODE Versions Container of all new and previous GENCODE releases
     All GENCODE VM26     All GENCODE annotations from VM26 (Ensembl 103)
     All GENCODE VM27     All GENCODE annotations from VM27 (Ensembl 104)
     All GENCODE VM28     All GENCODE annotations from VM28 (Ensembl 105)
     All GENCODE VM29     All GENCODE annotations from VM29 (Ensembl 106)
     All GENCODE VM30     All GENCODE annotations from VM30 (Ensembl 107)
     All GENCODE VM31     All GENCODE annotations from VM31 (Ensembl 108)
     All GENCODE VM32     All GENCODE annotations from VM32 (Ensembl 109)
     All GENCODE VM33     All GENCODE annotations from VM33 (Ensembl 110)
     All GENCODE VM34     All GENCODE annotations from VM34 (Ensembl 111)
     All GENCODE VM35     All GENCODE annotations from VM35 (Ensembl 112)
    new All GENCODE VM36     All GENCODE annotations from VM36 (Ensembl 113)
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CRISPR Targets CRISPR/Cas9 -NGG Targets, whole genome
GENCODE Archive GENCODE Archive
     GENCODE VM35     GENCODE VM35
     GENCODE VM33     GENCODE VM33
     GENCODE VM32     GENCODE VM32
     GENCODE VM30     GENCODE VM30
     GENCODE VM27     GENCODE VM27
Genscan Genes Genscan Gene Predictions
Other RefSeq Non-Mouse RefSeq Genes
Pfam in UCSC Gene Pfam Domains in UCSC 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
-   mRNA and EST    
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)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
     CpG Islands     CpG Islands (Islands < 300 Bases are Light Green)
JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database
ReMap ChIP-seq ReMap Atlas of Regulatory Regions
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
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
Time at end of doMiddle, next up cart write: 29 millis
 Time to write and close cart: 1 millis
 Overall total time: 95 millis