Configure Image
 
Image width:pixels
Label area width:characters
Text size:
Font:
Style:
Tooltip text size:
Maximum track load time: seconds
Display chromosome ideogram above main graphic
Show light blue vertical guidelines, or light red vertical window separators in multi-region view
Display labels to the left of items in tracks
Display description above each track
Show track controls under main graphic
Next/previous item navigation
Next/previous exon navigation
Show exon numbers
Show move left/right limit buttons under image
Enable highlight with drag-and-select (if unchecked, drag-and-select always zooms to selection)
Enable pop-up when clicking items

Configure Tracks on UCSC Genome Browser: Mouse Dec. 2011 (GRCm38/mm10)
  Tracks:    Groups:
Control track and group visibility more selectively below.
+   Hub: Jones_ChIP    
-   Hub: mSS_KJlab_ChIPseq    
mSS_Brd9_peak mSS Brd9 peaks
mSS_Brg1_peak mSS Brg1 peaks
mSS_Dpf2_peak mSS Dpf2 peaks
mSS_fusion_peak mSS fusion peaks
mSS_H2AK119ub_peak mSS H2AK119ub peaks
mSS_H3K27ac_peak mSS H3K27ac peaks
mSS_H3K27me3_peak mSS H3K27me3 peaks
mSS_H3K36me3_peak mSS H3K36me3 peaks
mSS_H3K4me1_peak mSS H3K4me1 peaks
mSS_H3K4me3_peak mSS H3K4me3 peaks
mSS_merged_Brd9 merged fusion binding
mSS_merged_Brg1 merged Brg1 binding
mSS_merged_Dpf2 merged Dpf2 binding
mSS_merged_fusion merged fusion binding
mSS_merged_H2AK119ub merged H2AK119ub binding
mSS_merged_H3K27ac merged H3K27ac binding
mSS_merged_H3K27me3 merged H3K27me3 binding
mSS_merged_H3K36me3 merged H3K36me3 binding
mSS_merged_H3K4me1 merged H3K4me1 binding
mSS_merged_H3K4me3 merged H3K4me3 binding
mSS_merged_Pbrm1 merged Pbrm1 binding
mSS_Pbrm1_peak mSS Pbrm1 peaks
-   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/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    
-   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