Home     Genomes     Genome Browser     Blat     Tables     Gene Sorter     PCR     FAQ     Help  
  Configure Image
  image width: text size:

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 Chromosome position in bases. (Clicks here zoom in 3x)
Chromosome Band Chromosome Bands Localized by FISH Mapping Clones
STS Markers STS Markers on Genetic (blue) and Radiation Hybrid (black) Maps
RGD QTL Quantitative Trait Locus (from RGD)
FISH Clones Clones Placed on Cytogenetic Map Using FISH
Recomb Rate Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default)
Map Contigs Physical Map Contigs
Assembly Assembly from Fragments
Gap Gap Locations
Coverage Clone Coverage
BAC End Pairs BAC End Pairs
Fosmid End Pairs Fosmid End Pairs
GC Percent GC Percent in 5-Base Windows
WSSD Duplication Sequence Identified as Duplicate by High-Depth Celera Reads
Short Match Perfect Matches to Short Sequence (AAAAA)
Restr Enzymes Restriction Enzymes from REBASE

 Genes and Gene Prediction Tracks    
Known Genes UCSC Known Genes (June, 05) Based on UniProt, RefSeq, and GenBank mRNA
CCDS Consensus CDS
RefSeq Genes RefSeq Genes
Other RefSeq Non-Human RefSeq Genes
MGC Genes Mammalian Gene Collection Full ORF mRNAs
Vega Genes Vega Annotations
Vega Pseudogenes Vega Annotated Pseudogenes and Immunoglobulin Segments
Ensembl Genes Ensembl Gene Predictions
AceView Genes AceView Gene Models With Alt-Splicing
ECgene Genes ECgene v1.2 Gene Predictions with Alt-Splicing
Twinscan Twinscan Gene Predictions Using Mouse/Human Homology
N-SCAN N-SCAN Gene Predictions
SGP Genes SGP Gene Predictions Using Mouse/Human Homology
Geneid Genes Geneid Gene Predictions
Genscan Genes Genscan Gene Predictions
Exoniphy Exoniphy Human/Mouse/Rat/Dog
Augustus Genes Augustus Gene Predictions
Retroposed Genes Retroposed Genes, Including Pseudogenes
Superfamily Superfamily/SCOP: Proteins Having Homologs with Known Structure/Function
Yale Pseudo Yale Pseudogenes.
EvoFold EvoFold Predictions of RNA Secondary Structure
sno/miRNA C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from Weber and Griffiths-Jones
T-ScanS miRNA TargetScanS miRNA Regulatory Sites
ExonWalk ExonWalk Alt-Splicing Transcripts

 mRNA and EST Tracks    
Human mRNAs Human mRNAs from GenBank
Spliced ESTs Human ESTs That Have Been Spliced
Human ESTs Human ESTs Including Unspliced
Other mRNAs Non-Human mRNAs from GenBank
Other ESTs Non-Human ESTs from GenBank
H-Inv H-Invitational Genes mRNA Alignments
TIGR Gene Index Alignment of TIGR Gene Index TCs Against the Human Genome
UniGene UniGene Alignments and SAGE Info
Gene Bounds Gene Boundaries as Defined by RNA and Spliced EST Clusters
Alt-Splicing Alternative Splicing from ESTs/mRNAs

 Expression and Regulation    
Gstone Arrays Gladstone microarray data including stem cell tissue
Allen Brain Allen Brain Atlas Probes
GNF Atlas 2 GNF Expression Atlas 2
GNF Ratio GNF Gene Expression Atlas Ratios Using Affymetrix GeneChips
Affy HuEx 1.0 Affymetrix Human Exon 1.0 Probe Sets
Affy U133 Alignments of Affymetrix Consensus/Exemplars from HG-U133
Affy GNF1H Alignments of Affymetrix Consensus/Exemplars from GNF1H
Affy U133Plus2 Alignments of Affymetrix Consensus/Exemplars from HG-U133 Plus 2.0
Affy U95 Alignments of Affymetrix Consensus/Exemplars from HG-U95
CpG Islands CpG Islands (Islands < 300 Bases are Light Green)
FirstEF FirstEF: First-Exon and Promoter Prediction
5x Reg Potential 5-Way Regulatory Potential - Human, Chimp, Dog, Mouse, Rat
TFBS Conserved HMR Conserved Transcription Factor Binding Sites
Affy Txn Phase2 Affymetrix Transcriptome Project Phase 2
SGMO/EIO CD34 HS Sangamo - Eur. Inst. Oncology DNase Hypersensitive Sites
NHGRI DNaseI-HS NHGRI DNaseI-Hypersensitive Sites

 Comparative Genomics    
Conservation Hu/Chimp/Mouse/Rat/Dog/Chick/Fugu/Zfish Multiz Alignments & Conservation
Most Conserved PhastCons Conserved Elements, Hu/Chimp/Mouse/Rat/Dog/Chick/Fugu/Zfish
Fugu Blat Fugu (Aug. 2002/fr1) Translated Blat Alignments
Fugu Chain Fugu (Aug. 2002/fr1) Chained Alignments
Fugu Net Fugu (Aug. 2002/fr1) Alignment Net
Tetraodon Ecores Human(hg17)/Tetraodon (Feb. 2004/tetNig1) Evolutionary Conserved Regions
Tetraodon Chain Tetraodon (Feb. 2004/tetNig1) Chained Alignments
Tetraodon Net Tetraodon (Feb. 2004/tetNig1) Alignment Net
Zebrafish Chain Zebrafish (June 2004/danRer2) Chained Alignments
Zebrafish Net Zebrafish (June 2004/danRer2) Alignment Net
X. tropicalis Chain X. tropicalis (Oct. 2004/xenTro1) Chained Alignments
X. tropicalis Net X. tropicalis (Oct. 2004/xenTro1) Alignment Net
Chicken Chain Chicken (Feb. 2004/galGal2) Chained Alignments
Chicken Net Chicken (Feb. 2004/galGal2) Alignment Net
Opossum Chain Opossum (Oct. 2004/monDom1) Chained Alignments
Opossum Net Opossum (Oct. 2004/monDom1) Alignment Net
Rat Chain Rat (June 2003/rn3) Chained Alignments
Rat Net Rat (June 2003/rn3) Alignment Net
Mouse Chain Mouse (Aug. 2005/mm7) Chained Alignments
Mouse Net Mouse (Aug. 2005/mm7) Alignment Net
Cow Chain Cow (Sep. 2004/bosTau1) Chained Alignments
Cow Net Cow (Sep. 2004/bosTau1) Alignment Net
Cow BAC Ends Cow (Sep. 2004/bosTau1) BAC Ends (BLASTn)
Cow Synteny Cow Synteny Using RH Mapping
Dog Chain Dog (July 2004/canFam1) Chained Alignments
Dog Net Dog (July 2004/canFam1) Alignment Net
Rhesus Chain Rhesus (Jan. 2005/rheMac1) Chained Alignments
Rhesus Net Rhesus (Jan. 2005/rheMac1) Alignment Net
Chimp Chain Chimp (Nov. 2003/panTro1) Chained Alignments
Chimp Net Chimp (Nov. 2003/panTro1) Alignment Net

 Variation and Repeats    
SNPs Simple Nucleotide Polymorphisms (SNPs)
Tajima's D SNPs Tajima's D SNPs
Tajima's D Tajima's D
Recomb Hotspots Recombination Hotspots from SNP Genotyping
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
RepeatMasker Repeating Elements by RepeatMasker
Simple Repeats Simple Tandem Repeats by TRF
Self Chain Human Chained Self Alignments

 ENCODE Regions and Genes    
ENCODE Regions Encyclopedia of DNA Elements (ENCODE) Regions
Gencode Genes Gencode Gene Annotations
Gencode Introns Gencode Intron Validation
EGASP Full ENCODE Gene Prediction Workshop (EGASP) All ENCODE Regions
EGASP Partial ENCODE Gene Prediction Workshop (EGASP) for Partial ENCODE Regions
EGASP Update ENCODE Gene Prediction Workshop (EGASP) Updates
GIS PET RNA Genome Institute of Singapore PET of PolyA+ RNA
Known+Pred RNA Known and Predicted RNA Transcription in the ENCODE Regions
TBA23 EvoFold EvoFold Predictions of RNA Secondary Structure Using TBA23

 ENCODE Transcript Levels    
Affy RNA Affymetrix PolyA+ RNA and Transfrags
BU First Exon Boston University First Exon Activity
Riken CAGE Riken CAGE - Predicted Gene Start Sites
Stanf Promoter Stanford Promoter Activity
Stanf RTPCR Stanford Endogenous Transcript Levels in HCT116 Cells
Yale MAS RNA Yale Maskless Array Synthesizer, RNA Transcript Map
Yale MAS TAR Yale Maskless Array Synthesizer, RNA Transcriptionally Active Regions
Yale RNA Yale RNA Transcript Map (Neutrophil, Placenta and NB4 cells)
Yale TAR Yale RNA Transcriptionally Active Regions (TARs)

 ENCODE Chromatin Immunoprecipitation    
Affy pVal Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) P-Value
Affy Sites Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) Sites
Affy Strict pVal Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) Strict P-Value
Affy Strict Sig Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) Strict Signal
Affy Strict Sites Affymetrix ChIP/Chip (retinoic acid-treated HL-60 cells) Strict Sites
GIS p53 5FU HCT116 Genome Institute of Singapore ChIP-PET: p53 Ab on 5FU treated HCT116 cells
GIS STAT1 HeLa Genome Institute of Singapore ChIP-PET: STAT1 Ab on (+/-)gIF HeLa cells
LI ChIP Various Ludwig Institute/UCSD ChIP/Chip: Pol2 8WG16, TAF1, H3ac, H3K4me2, H3K27me3 antibodies
LI gIF ChIP Ludwig Institute/UCSD ChIP/Chip - Gamma Interferon Experiments
LI Ng gIF ChIP Ludwig Institute/UCSD ChIP/Chip NimbleGen - Gamma Interferon Experiments
LI Ng TAF1 IMR90 Ludwig Institute NimbleGen ChIP/Chip: TAF1 antibody, IMR90 cells
LI Ng Validation Ludwig Institute ChIP/Chip Validation: IMR90 cells
Sanger ChIP Sanger ChIP/Chip (histones H3,H4 ab in GM06990, K562 and HeLa cells)
Sanger ChIP Hits Sanger ChIP/Chip Hits and Peak Centers
Stanf ChIP Stanford ChIP/chip (HCT116, Jurkat, K562 cells; Sp1, Sp3 ChIP)
Stanf ChIP Score Stanford ChIP/chip Smoothed Score
UCD Ng ChIP UC Davis ChIP/Chip NimbleGen (E2F1, Myc ab, HeLa Cells)
UT-Austin ChIP University of Texas, Austin ChIP/Chip
Uppsala ChIP University of Uppsala, Sweden ChIP/Chip
Yale ChIP pVal Yale ChIP/Chip (STAT1 ab, HeLa cells) P-Value
Yale ChIP Sig Yale ChIP/Chip (STAT1 ab, HeLa cells) Signal
Yale ChIP Sites Yale ChIP/Chip (STAT1 ab, HeLa cells) Binding Sites

 ENCODE Chromosome, Chromatin and DNA Structure    
BU ORChID Boston University ORChID (OH Radical Cleavage Intensity Database)
NHGRI DNaseI-HS NHGRI DNaseI-Hypersensitive Sites
Stanf Meth Stanford Methylation Digest: Be2C, CRL1690, HCT116, HT1080, HepG2, JEG3, Snu182, U87
Stanf Meth Score Stanford Methylation Digest Smoothed Score
UNC FAIRE UNC FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
UVa DNA Rep University of Virginia Temporal Profiling of DNA Replication
UVa DNA Rep Seg University of Virginia DNA Replication Temporal Segmentation
UVa DNA Rep Ori University of Virginia DNA Replication Origins
UVa DNA Rep TR50 University of Virginia DNA Smoothed Timing at 50% Replication
UW/Reg DNaseI Sens ENCODE UW/Regulome Mean DNaseI Sensitivity
UW/Reg DNaseI HSs ENCODE UW/Regulome DNaseI Hypersensitive Sites/Scores
UW/Reg Q/A ENCODE UW/Regulome Plate Quality Score

 ENCODE Variation    
NHGRI DIPs NHGRI Deletion/Insertion Polymorphisms in ENCODE regions
HapMap Coverage ENCODE HapMap (16c.1) Resequencing Coverage
Sanger Assoc Sanger Genotype-Expression Association
HapMap SNPs ENCODE HapMap (16c.1) Allele Frequencies