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Configure Tracks on UCSC Genome Browser: Mouse Dec. 2011 (GRCm38/mm10)
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-   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 (CAGCAGCAGCAGCAGCAGCAGCAGCAG...)
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/ORFeome Genes MGC/ORFeome Full ORF mRNA Clones
     ORFeome Clones     ORFeome Collaboration Gene Clones
     MGC Genes     Mammalian Gene Collection Full ORF mRNAs
Old UCSC Genes Previous Version of UCSC Genes
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
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
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)
new EVA SNP Short Genetic Variants from European Variant Archive
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