Home
Genomes
Genome Browser
Blat
Tables
Gene Sorter
PCR
FAQ
Help
Configure Image
image width:
text size:
tiny
small
medium
large
huge
Display chromosome ideogram above main graphic
Show light blue vertical guidelines
Display labels to the left of items in tracks
Display description above each track
Show track controls under main graphic
Configure Tracks
Control tracks in all groups here:
Control track visibility more selectively below.
Mapping and Sequencing Tracks
Base Position
hide
dense
full
Chromosome position in bases. (Clicks here zoom in 3x)
Chromosome Band
hide
dense
squish
pack
full
Chromosome Bands Localized by FISH Mapping Clones
STS Markers
hide
dense
squish
pack
full
STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
RGD QTL
hide
dense
squish
pack
full
Quantitative Trait Locus (from RGD)
FISH Clones
hide
dense
squish
pack
full
Clones Placed on Cytogenetic Map Using FISH
Recomb Rate
hide
dense
squish
pack
full
Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default)
Map Contigs
hide
dense
full
Physical Map Contigs
Assembly
hide
dense
squish
pack
full
Assembly from Fragments
Gap
hide
dense
squish
pack
full
Gap Locations
Coverage
hide
dense
full
Clone Coverage
BAC End Pairs
hide
dense
squish
pack
full
BAC End Pairs
Fosmid End Pairs
hide
dense
squish
pack
full
Fosmid End Pairs
GC Percent
hide
dense
full
GC Percent in 5-Base Windows
WSSD Duplication
hide
dense
squish
pack
full
Sequence Identified as Duplicate by High-Depth Celera Reads
Short Match
hide
dense
squish
pack
full
Perfect Matches to Short Sequence (AAAAA)
Restr Enzymes
hide
dense
squish
pack
full
Restriction Enzymes from REBASE
Genes and Gene Prediction Tracks
Known Genes
hide
dense
squish
pack
full
UCSC Known Genes (June, 05) Based on UniProt, RefSeq, and GenBank mRNA
CCDS
hide
dense
squish
pack
full
Consensus CDS
RefSeq Genes
hide
dense
squish
pack
full
RefSeq Genes
Other RefSeq
hide
dense
squish
pack
full
Non-Human RefSeq Genes
MGC Genes
hide
dense
squish
pack
full
Mammalian Gene Collection Full ORF mRNAs
Vega Genes
hide
dense
squish
pack
full
Vega Annotations
Vega Pseudogenes
hide
dense
squish
pack
full
Vega Annotated Pseudogenes and Immunoglobulin Segments
Ensembl Genes
hide
dense
squish
pack
full
Ensembl Gene Predictions
AceView Genes
hide
dense
squish
pack
full
AceView Gene Models With Alt-Splicing
ECgene Genes
hide
dense
squish
pack
full
ECgene v1.2 Gene Predictions with Alt-Splicing
Twinscan
hide
dense
squish
pack
full
Twinscan Gene Predictions Using Mouse/Human Homology
N-SCAN
hide
dense
squish
pack
full
N-SCAN Gene Predictions
SGP Genes
hide
dense
squish
pack
full
SGP Gene Predictions Using Mouse/Human Homology
Geneid Genes
hide
dense
squish
pack
full
Geneid Gene Predictions
Genscan Genes
hide
dense
squish
pack
full
Genscan Gene Predictions
Exoniphy
hide
dense
squish
pack
full
Exoniphy Human/Mouse/Rat/Dog
Augustus Genes
hide
dense
squish
pack
full
Augustus Gene Predictions
Retroposed Genes
hide
dense
squish
pack
full
Retroposed Genes, Including Pseudogenes
Superfamily
hide
dense
squish
pack
full
Superfamily/SCOP: Proteins Having Homologs with Known Structure/Function
Yale Pseudo
hide
dense
squish
pack
full
Yale Pseudogenes.
EvoFold
hide
dense
squish
pack
full
EvoFold Predictions of RNA Secondary Structure
sno/miRNA
hide
dense
squish
pack
full
C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from Weber and Griffiths-Jones
T-ScanS miRNA
hide
dense
squish
pack
full
TargetScanS miRNA Regulatory Sites
ExonWalk
hide
dense
squish
pack
full
ExonWalk Alt-Splicing Transcripts
mRNA and EST Tracks
Human mRNAs
hide
dense
squish
pack
full
Human mRNAs from GenBank
Spliced ESTs
hide
dense
squish
pack
full
Human ESTs That Have Been Spliced
Human ESTs
hide
dense
squish
pack
full
Human ESTs Including Unspliced
Other mRNAs
hide
dense
squish
pack
full
Non-Human mRNAs from GenBank
Other ESTs
hide
dense
squish
pack
full
Non-Human ESTs from GenBank
H-Inv
hide
dense
squish
pack
full
H-Invitational Genes mRNA Alignments
TIGR Gene Index
hide
dense
squish
pack
full
Alignment of TIGR Gene Index TCs Against the Human Genome
UniGene
hide
dense
squish
pack
full
UniGene Alignments and SAGE Info
Gene Bounds
hide
dense
squish
pack
full
Gene Boundaries as Defined by RNA and Spliced EST Clusters
Alt-Splicing
hide
dense
squish
pack
full
Alternative Splicing from ESTs/mRNAs
Expression and Regulation
Gstone Arrays
hide
dense
squish
pack
full
Gladstone microarray data including stem cell tissue
Allen Brain
hide
dense
squish
pack
full
Allen Brain Atlas Probes
GNF Atlas 2
hide
dense
squish
pack
full
GNF Expression Atlas 2
GNF Ratio
hide
dense
full
GNF Gene Expression Atlas Ratios Using Affymetrix GeneChips
Affy HuEx 1.0
hide
dense
squish
pack
full
Affymetrix Human Exon 1.0 Probe Sets
Affy U133
hide
dense
squish
pack
full
Alignments of Affymetrix Consensus/Exemplars from HG-U133
Affy GNF1H
hide
dense
squish
pack
full
Alignments of Affymetrix Consensus/Exemplars from GNF1H
Affy U133Plus2
hide
dense
squish
pack
full
Alignments of Affymetrix Consensus/Exemplars from HG-U133 Plus 2.0
Affy U95
hide
dense
squish
pack
full
Alignments of Affymetrix Consensus/Exemplars from HG-U95
CpG Islands
hide
dense
squish
pack
full
CpG Islands (Islands < 300 Bases are Light Green)
FirstEF
hide
dense
squish
pack
full
FirstEF: First-Exon and Promoter Prediction
5x Reg Potential
hide
dense
full
5-Way Regulatory Potential - Human, Chimp, Dog, Mouse, Rat
TFBS Conserved
hide
dense
squish
pack
full
HMR Conserved Transcription Factor Binding Sites
Affy Txn Phase2
hide
dense
full
Affymetrix Transcriptome Project Phase 2
SGMO/EIO CD34 HS
hide
dense
squish
pack
full
Sangamo - Eur. Inst. Oncology DNase Hypersensitive Sites
NHGRI DNaseI-HS
hide
dense
squish
pack
full
NHGRI DNaseI-Hypersensitive Sites
Comparative Genomics
Conservation
hide
dense
squish
pack
full
Hu/Chimp/Mouse/Rat/Dog/Chick/Fugu/Zfish Multiz Alignments & Conservation
Most Conserved
hide
dense
squish
pack
full
PhastCons Conserved Elements, Hu/Chimp/Mouse/Rat/Dog/Chick/Fugu/Zfish
Fugu Blat
hide
dense
squish
pack
full
Fugu (Aug. 2002/fr1) Translated Blat Alignments
Fugu Chain
hide
dense
squish
pack
full
Fugu (Aug. 2002/fr1) Chained Alignments
Fugu Net
hide
dense
full
Fugu (Aug. 2002/fr1) Alignment Net
Tetraodon Ecores
hide
dense
squish
pack
full
Human(hg17)/Tetraodon (Feb. 2004/tetNig1) Evolutionary Conserved Regions
Tetraodon Chain
hide
dense
squish
pack
full
Tetraodon (Feb. 2004/tetNig1) Chained Alignments
Tetraodon Net
hide
dense
full
Tetraodon (Feb. 2004/tetNig1) Alignment Net
Zebrafish Chain
hide
dense
squish
pack
full
Zebrafish (June 2004/danRer2) Chained Alignments
Zebrafish Net
hide
dense
full
Zebrafish (June 2004/danRer2) Alignment Net
X. tropicalis Chain
hide
dense
squish
pack
full
X. tropicalis (Oct. 2004/xenTro1) Chained Alignments
X. tropicalis Net
hide
dense
full
X. tropicalis (Oct. 2004/xenTro1) Alignment Net
Chicken Chain
hide
dense
squish
pack
full
Chicken (Feb. 2004/galGal2) Chained Alignments
Chicken Net
hide
dense
full
Chicken (Feb. 2004/galGal2) Alignment Net
Opossum Chain
hide
dense
squish
pack
full
Opossum (Oct. 2004/monDom1) Chained Alignments
Opossum Net
hide
dense
full
Opossum (Oct. 2004/monDom1) Alignment Net
Rat Chain
hide
dense
squish
pack
full
Rat (June 2003/rn3) Chained Alignments
Rat Net
hide
dense
full
Rat (June 2003/rn3) Alignment Net
Mouse Chain
hide
dense
squish
pack
full
Mouse (Aug. 2005/mm7) Chained Alignments
Mouse Net
hide
dense
full
Mouse (Aug. 2005/mm7) Alignment Net
Cow Chain
hide
dense
squish
pack
full
Cow (Sep. 2004/bosTau1) Chained Alignments
Cow Net
hide
dense
full
Cow (Sep. 2004/bosTau1) Alignment Net
Cow BAC Ends
hide
dense
squish
pack
full
Cow (Sep. 2004/bosTau1) BAC Ends (BLASTn)
Cow Synteny
hide
dense
squish
pack
full
Cow Synteny Using RH Mapping
Dog Chain
hide
dense
squish
pack
full
Dog (July 2004/canFam1) Chained Alignments
Dog Net
hide
dense
full
Dog (July 2004/canFam1) Alignment Net
Rhesus Chain
hide
dense
squish
pack
full
Rhesus (Jan. 2005/rheMac1) Chained Alignments
Rhesus Net
hide
dense
full
Rhesus (Jan. 2005/rheMac1) Alignment Net
Chimp Chain
hide
dense
squish
pack
full
Chimp (Nov. 2003/panTro1) Chained Alignments
Chimp Net
hide
dense
full
Chimp (Nov. 2003/panTro1) Alignment Net
Variation and Repeats
SNPs
hide
dense
squish
pack
full
Simple Nucleotide Polymorphisms (SNPs)
Tajima's D SNPs
hide
dense
squish
pack
full
Tajima's D SNPs
Tajima's D
hide
dense
full
Tajima's D
Recomb Hotspots
hide
dense
squish
pack
full
Recombination Hotspots from SNP Genotyping
Segmental Dups
hide
dense
squish
pack
full
Duplications of >1000 Bases of Non-RepeatMasked Sequence
RepeatMasker
hide
dense
full
Repeating Elements by RepeatMasker
Simple Repeats
hide
dense
squish
pack
full
Simple Tandem Repeats by TRF
Self Chain
hide
dense
squish
pack
full
Human Chained Self Alignments
ENCODE Regions and Genes
ENCODE Regions
hide
dense
squish
pack
full
Encyclopedia of DNA Elements (ENCODE) Regions
Gencode Genes
hide
dense
squish
pack
full
Gencode Gene Annotations
Gencode Introns
hide
dense
squish
pack
full
Gencode Intron Validation
EGASP Full
hide
dense
squish
pack
full
ENCODE Gene Prediction Workshop (EGASP) All ENCODE Regions
EGASP Partial
hide
dense
squish
pack
full
ENCODE Gene Prediction Workshop (EGASP) for Partial ENCODE Regions
EGASP Update
hide
dense
squish
pack
full
ENCODE Gene Prediction Workshop (EGASP) Updates
GIS PET RNA
hide
dense
squish
pack
full
Genome Institute of Singapore PET of PolyA+ RNA
Known+Pred RNA
hide
dense
squish
pack
full
Known and Predicted RNA Transcription in the ENCODE Regions
TBA23 EvoFold
hide
dense
squish
pack
full
EvoFold Predictions of RNA Secondary Structure Using TBA23
ENCODE Transcript Levels
Affy RNA
hide
dense
full
Affymetrix PolyA+ RNA and Transfrags
BU First Exon
hide
dense
squish
pack
full
Boston University First Exon Activity
Riken CAGE
hide
dense
full
Riken CAGE - Predicted Gene Start Sites
Stanf Promoter
hide
dense
squish
pack
full
Stanford Promoter Activity
Stanf RTPCR
hide
dense
squish
pack
full
Stanford Endogenous Transcript Levels in HCT116 Cells
Yale MAS RNA
hide
dense
full
Yale Maskless Array Synthesizer, RNA Transcript Map
Yale MAS TAR
hide
dense
squish
pack
full
Yale Maskless Array Synthesizer, RNA Transcriptionally Active Regions
Yale RNA
hide
dense
full
Yale RNA Transcript Map (Neutrophil, Placenta and NB4 cells)
Yale TAR
hide
dense
squish
pack
full
Yale RNA Transcriptionally Active Regions (TARs)
ENCODE Chromatin Immunoprecipitation
Affy pVal
hide
dense
full
Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) P-Value
Affy Sites
hide
dense
squish
pack
full
Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) Sites
Affy Strict pVal
hide
dense
full
Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) Strict P-Value
Affy Strict Sig
hide
dense
full
Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) Strict Signal
Affy Strict Sites
hide
dense
squish
pack
full
Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) Strict Sites
GIS p53 5FU HCT116
hide
dense
squish
pack
full
Genome Institute of Singapore ChIP-PET: p53 Ab on 5FU treated HCT116 cells
GIS STAT1 HeLa
hide
dense
squish
pack
full
Genome Institute of Singapore ChIP-PET: STAT1 Ab on (+/-)gIF HeLa cells
LI ChIP Various
hide
dense
full
Ludwig Institute/UCSD ChIP/Chip: Pol2 8WG16, TAF1, H3ac, H3K4me2, H3K27me3 antibodies
LI gIF ChIP
hide
dense
full
Ludwig Institute/UCSD ChIP/Chip - Gamma Interferon Experiments
LI Ng gIF ChIP
hide
dense
full
Ludwig Institute/UCSD ChIP/Chip NimbleGen - Gamma Interferon Experiments
LI Ng TAF1 IMR90
hide
dense
full
Ludwig Institute NimbleGen ChIP/Chip: TAF1 antibody, IMR90 cells
LI Ng Validation
hide
dense
full
Ludwig Institute ChIP/Chip Validation: IMR90 cells
Sanger ChIP
hide
dense
full
Sanger ChIP/Chip (histones H3,H4 ab in GM06990, K562 and HeLa cells)
Sanger ChIP Hits
hide
dense
full
Sanger ChIP/Chip Hits and Peak Centers
Stanf ChIP
hide
dense
full
Stanford ChIP/chip (HCT116, Jurkat, K562 cells; Sp1, Sp3 ChIP)
Stanf ChIP Score
hide
dense
full
Stanford ChIP/chip Smoothed Score
UCD Ng ChIP
hide
dense
full
UC Davis ChIP/Chip NimbleGen (E2F1, Myc ab, HeLa Cells)
UT-Austin ChIP
hide
dense
full
University of Texas, Austin ChIP/Chip
Uppsala ChIP
hide
dense
full
University of Uppsala, Sweden ChIP/Chip
Yale ChIP pVal
hide
dense
full
Yale ChIP/Chip (STAT1 ab, HeLa cells) P-Value
Yale ChIP Sig
hide
dense
full
Yale ChIP/Chip (STAT1 ab, HeLa cells) Signal
Yale ChIP Sites
hide
dense
squish
pack
full
Yale ChIP/Chip (STAT1 ab, HeLa cells) Binding Sites
ENCODE Chromosome, Chromatin and DNA Structure
BU ORChID
hide
dense
full
Boston University ORChID (OH Radical Cleavage Intensity Database)
NHGRI DNaseI-HS
hide
dense
squish
pack
full
NHGRI DNaseI-Hypersensitive Sites
Stanf Meth
hide
dense
full
Stanford Methylation Digest: Be2C, CRL1690, HCT116, HT1080, HepG2, JEG3, Snu182, U87
Stanf Meth Score
hide
dense
full
Stanford Methylation Digest Smoothed Score
UNC FAIRE
hide
dense
full
UNC FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
UVa DNA Rep
hide
dense
squish
pack
full
University of Virginia Temporal Profiling of DNA Replication
UVa DNA Rep Seg
hide
dense
squish
pack
full
University of Virginia DNA Replication Temporal Segmentation
UVa DNA Rep Ori
hide
dense
squish
pack
full
University of Virginia DNA Replication Origins
UVa DNA Rep TR50
hide
dense
full
University of Virginia DNA Smoothed Timing at 50% Replication
UW/Reg DNaseI Sens
hide
dense
full
ENCODE UW/Regulome Mean DNaseI Sensitivity
UW/Reg DNaseI HSs
hide
dense
full
ENCODE UW/Regulome DNaseI Hypersensitive Sites/Scores
UW/Reg Q/A
hide
dense
squish
pack
full
ENCODE UW/Regulome Plate Quality Score
ENCODE Variation
NHGRI DIPs
hide
dense
squish
pack
full
NHGRI Deletion/Insertion Polymorphisms in ENCODE regions
HapMap Coverage
hide
dense
full
ENCODE HapMap (16c.1) Resequencing Coverage
Sanger Assoc
hide
dense
squish
pack
full
Sanger Genotype-Expression Association
HapMap SNPs
hide
dense
squish
pack
full
ENCODE HapMap (16c.1) Allele Frequencies