Configure Image - Genome Browser V478
 
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: Hub (Histone ChIP-seq ENCSR058DOA)    
H3K27ac histone of liver ENCSR058DOA H3K27ac histone Histone ChIP-seq of Mus musculus strain B6NCrl mixed sex embryo (11.5 days) liver tissue - ENCSR058DOA
-   Hub: Hub (ATAC-seq ENCSR785NEL)    
ATAC-seq of liver ENCSR785NEL ATAC-seq of Mus musculus strain B6NCrl mixed sex embryo (11.5 days) liver tissue - ENCSR785NEL
-   Hub: Track Collections    
fetal liver attic and h3k27ac New Collection description
-   Custom Tracks    
BG252_BG296_BG296r_Fli1_HE BG252_BG296_BG296r_Fli1_HE
BG83_5307_3_CTCF BG83_5307_3_CTCF
CTCF_GSM1023420_Rag1-_Pro_B CTCF_GSM1023420_Rag1-_Pro_B
D340003_Pu1 D340003_Pu1
GSE21614_Spi1_BCells GSE21614_Spi1_BCells
GSM1409207_Cebpa GSM1409207_Cebpa
GSM539537_8_Sfpi1 GSM539537_8_Sfpi1
GSM552238_Lyl1 GSM552238_Lyl1
GSM936199_200_Ikzf1 GSM936199_200_Ikzf1
GSM989017_Cebpb GSM989017_Cebpb
TG10_B020004_Stat5 TG10_B020004_Stat5
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Chromosome Band Chromosome Bands Based On Microscopy
p14 Fix Patches Reference Assembly Fix Patch Sequence Alignments
Assembly Assembly from Fragments
Gap Gap Locations
Short Match Perfect Matches to Short Sequence ()
Restr Enzymes Restriction Enzymes from REBASE
All Gaps All gaps of unknown nucleotides (N's), including AGP annotated gaps
p14 Alt Haplotypes Reference Assembly Alternate Haplotype Sequence Alignments
Clone Ends Mapping of clone libraries end placements
Contigs Contig fragments used in the assembly
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)***
UCSC liftOver mm39 UCSC liftOver alignments to mm39
-   Genes and Gene Predictions    
updated NCBI RefSeq RefSeq genes from NCBI
GENCODE Versions Container of all new and previous GENCODE releases
     All GENCODE VM25     All GENCODE annotations from VM25 (Ensembl 100)
     All GENCODE VM24     All GENCODE annotations from VM24 (Ensembl 99)
     All GENCODE VM22     All GENCODE annotations from VM22 (Ensembl 97)
     All GENCODE VM18     All GENCODE annotations from VM18 (Ensembl 93)
     All GENCODE VM16     All GENCODE annotations from VM16 (Ensembl 91)
     All GENCODE VM14     All GENCODE annotations from VM14 (Ensembl 89)
     GENCODE VM11 (Ensembl 86)     Gene Annotations from ENCODE/GENCODE Version M11 (Ensembl 86)
     GENCODE VM9 (Ensembl 84)     Gene Annotations from ENCODE/GENCODE Version M9 (Ensembl 84)
     TransMap Ensembl     TransMap Ensembl and GENCODE Mappings Version 5
     TransMap RefGene     TransMap RefSeq Gene Mappings Version 5
     TransMap RNA     TransMap GenBank RNA Mappings Version 5
     TransMap ESTs     TransMap EST Mappings Version 5
GENCODE VM23 GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
CCDS Consensus CDS
Other RefSeq Non-Mouse RefSeq Genes
     MGC Genes     Mammalian Gene Collection Full ORF mRNAs
     ORFeome Clones     ORFeome Collaboration Gene Clones
SGP Genes SGP Gene Predictions Using Mouse/Human Homology
Geneid Genes Geneid Gene Predictions
Genscan Genes Genscan Gene Predictions
tRNA Genes Transfer RNA Genes Identified with tRNAscan-SE
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CRISPR 10K CRISPR/Cas9 Sp. Pyog. target sites (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
     CRISPR Targets 10K     CRISPR/Cas9 -NGG Targets (exons +/- 10,000 bp)
MGC/ORFeome Genes MGC/ORFeome Full ORF mRNA Clones
Old UCSC Genes Previous Version of UCSC Genes
Pfam in UCSC Gene Pfam Domains in UCSC Genes
RetroGenes V6 Retroposed Genes V6, Including Pseudogenes
TOGA vs. hg38 TOGA annotations using human/hg38 as reference
TransMap V5 TransMap Alignments Version 5
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 mRNAs Mouse mRNAs from GenBank
Mouse ESTs Mouse ESTs Including Unspliced
Other mRNAs Non-Mouse mRNAs from GenBank
-   Expression and Regulation    
     Cell expression     Single Cell RNA-Seq Gene Expression from Tabula Muris
ENCODE cCREs ENCODE Candidate Cis-Regulatory Elements (cCREs) combined from all cell types
     Genome Coverage     Tabula Muris single cell RNA-Seq genome coverage
     Splice Sites     Tabula Muris single cell RNA-Seq splice sites
Tabula Muris Single Cell FACS RNA-Seq of 44,779 cells from Tabula Muris
     TSS peaks     FANTOM5: DPI peak, robust set
     Total counts     Total counts of CAGE reads
     Max counts     Max counts of CAGE reads
     TSS activity (read counts)     TSS activity per sample (read counts)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
     TSS activity (TPM)     TSS activity per sample (TPM)
     Chromatin State     Chromatin state of embryonic tissue (12 tissues, 8 ages) from ENCODE 3 (UCSD/Ren)
     CpG Islands     CpG Islands (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
EPDnew Promoters Promoters from EPDnew
FaceBase 24STypes FaceBase 24 Sample Types Averaged
FANTOM5 FANTOM5: Mapped transcription start sites (TSS) and their usage
     Histone Modifications     Histone modifications in embryonic tissue (8 marks, 12 tissues, 8 ages) from ChIP-seq by ENCODE 3 (UCSD/Ren)
JASPAR Transcription Factors JASPAR Transcription Factor Binding Site Database
     Open Chromatin     Open chromatin in embryonic tissue (12 tissues, 8 ages) from ATAC-seq by ENCODE 3 (UCSD/Ren)
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    
     All SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142)
Common SNPs(142) Simple Nucleotide Polymorphisms (dbSNP 142) Found in >= 1% of Samples
     Mult. SNPs(142)     Simple Nucleotide Polymorphisms (dbSNP 142) That Map to Multiple Genomic Loci
     All SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138)
     Common SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138) Found in >= 1% of Samples
     Mult. SNPs(138)     Simple Nucleotide Polymorphisms (dbSNP 138) That Map to Multiple Genomic Loci
     All SNPs(137)     Simple Nucleotide Polymorphisms (dbSNP 137)
     Common SNPs(137)     Simple Nucleotide Polymorphisms (dbSNP 137) Found in >= 1% of Samples
     Mult. SNPs(137)     Simple Nucleotide Polymorphisms (dbSNP 137) That Map to Multiple Genomic Loci
     Alignment     Alternate mouse strains, alignments to reference genome
     Alternate strains     Alternate mouse strains, mapped to their corresponding reference genome location
Alternate strains Alternate mouse strain sequences
Mouse SNPs Annotated SNPs from mouse strain comparison analysis
dbSNP Archive dbSNP Track Archive
EVA SNP Short Genetic Variants from European Variant Archive
RepeatMasker Viz. Detailed Visualization of RepeatMasker Annotations
WM + SDust Genomic Intervals Masked by WindowMasker + SDust
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
RepeatMasker Repeating Elements by RepeatMasker
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Simple Repeats Simple Tandem Repeats by TRF
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats