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Configure Tracks on UCSC Genome Browser: Mouse July 2007 (NCBI37/mm9)
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-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
STS Markers STS Markers on Genetic and Radiation Hybrid Maps
Assembly Assembly from Fragments
BAC End Pairs BAC End Pairs
Chromosome Band Chromosome Bands Based On Microscopy
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
GRC Incident GRC Incident Database
Map Contigs Physical Map Contigs
Mappability Mappability or Uniqueness of Reference Genome from ENCODE
MGI QTL Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
-   Genes and Gene Predictions    
UCSC Genes UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics)
updated Ensembl Genes Ensembl Genes
Human Proteins Human Proteins Mapped by Chained tBLASTn
RefSeq Genes RefSeq Genes
Other RefSeq Non-Mouse RefSeq Genes
AceView Genes AceView Gene Models With Alt-Splicing
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CCDS Consensus CDS
CRISPR... CRISPR/Cas9 Sp. Pyog. target sites
     CRISPR Regions     Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 200 bp)
     CRISPR Targets     CRISPR/Cas9 -NGG Targets
Exoniphy Exoniphy Mouse/Rat/Human/Dog
Gene Trap International Gene Trap Consortium Sequence Tag Alignments
Geneid Genes Geneid Gene Predictions
Genscan Genes Genscan Gene Predictions
IKMC Genes International Knockout Mouse Consortium Genes
miRNA MicroRNAs from miRBase
N-SCAN N-SCAN Gene Predictions
NIA Gene Index NIA Mouse Gene Index
Old UCSC Genes Previous Version of UCSC Genes
ORFeome Clones ORFeome Collaboration Gene Clones
Pfam in UCSC Gene Pfam Domains in UCSC Genes
SGP Genes SGP Gene Predictions Using Mouse/Human Homology
Transcriptome TROMER Transcriptome database
tRNA Genes Transfer RNA Genes Identified with tRNAscan-SE
UCSC Alt Events Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
Vega Genes Vega Annotations
Yale Pseudo60 Yale Pseudogenes based on Ensembl Release 60
-   Literature    
Publications Publications: Sequences in Scientific Articles
Web Sequences DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research
-   mRNA and EST    
Spliced ESTs Mouse ESTs That Have Been Spliced
Mouse mRNAs Mouse mRNAs from GenBank
Mouse ESTs Mouse ESTs Including Unspliced
Other mRNAs Non-Mouse mRNAs from GenBank
PolyA-Seq Poly(A)-sequencing from Merck Research Laboratories
SIB Alt-Splicing Alternative Splicing Graph from Swiss Institute of Bioinformatics
-   Phenotype and Allele    
MGI Allele Jackson Laboratory / Mouse Genome Informatics Allele
MGI Gene Trap Jackson Laboratory / Mouse Genome Informatics DNA and RNA Gene Traps
MGI Phenotype Jackson Laboratory / Mouse Genome Informatics Phenotype
MGI RepTranscrpt Jackson Laboratory / Mouse Genome Informatics Representative Transcript
-   Expression and Regulation    
Affy Exon... Affymetrix All Exon Microarrays
     Affy Exon Probes     Affymetrix Exon Array 1.0: Probesets
     Affy Exon Tissues     Affymetrix Exon Array 1.0: Normal Tissues
Affy GNF1M Alignments of Probes from Affymetrix GNF1M Chip
Affy MOE430 Alignments of Affymetrix Consensus Sequences from Mouse MOE430 (A and B)
Affy U74 Alignments of Affymetrix Consensus Sequences from MG-U74 v2 (A,B, and C)
Allen Brain Allen Brain Atlas Probes
Caltech Histone Histone Modifications by ChIP-seq from ENCODE/Caltech
Caltech RNA-seq RNA-seq from ENCODE/Caltech
Caltech TFBS Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech
CpG Islands... CpG Islands (Islands < 300 Bases are Light Green)
     CpG Islands     CpG Islands (Islands < 300 Bases are Light Green)
     Unmasked CpG     CpG Islands on All Sequence (Islands < 300 Bases are Light Green)
CSHL Long RNA-seq Long RNA-seq from ENCODE/Cold Spring Harbor Lab
FaceBase 24STypes FaceBase 24 Sample Types Averaged
FSU Repli-chip Replication Timing by Repli-chip from ENCODE/FSU
GNF Atlas 2 GNF Expression Atlas 2
GNF U74A GNF Expression Atlas on Mouse Affymetrix U74A Chip
GNF U74B GNF Expression Atlas on Mouse Affymetrix U74B Chip
GNF U74C GNF Expression Atlas on Mouse Affymetrix U74C Chip
LICR Histone Histone Mods by ChIP-seq from ENCODE/LICR
LICR RNA-seq RNA-seq from ENCODE/LICR
LICR TFBS Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR
NHGRI BiP ENCODE NHGRI Elnitski Bidirectional Promoters
NKI Nuc Lamina... NKI Nuclear Lamina Associated Domains (LaminB1 DamID)
     mouse LaminB1 ESC     NKI LaminB1 (DamID of LaminB1 in mouse Embryonic Stem cells, log2-ratio)
     mouse LaminB1 NPC     NKI LaminB1 (DamID of LaminB1 in mouse Neural Progenitor cells, log2-ratio)
     mouse LaminB1 AC     NKI LaminB1 (DamID of LaminB1 in mouse Astrocytes, log2-ratio)
     mouse LaminB1 MEF     NKI LaminB1 (DamID of LaminB1 in mouse Embryonic Fibroblasts, log2-ratio)
ORegAnno Regulatory elements from ORegAnno
PSU DNaseI HS DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU
PSU Histone Histone Modifications by ChIP-seq from ENCODE/PSU
PSU RNA-seq RNA-seq from ENCODE/PSU
PSU TFBS Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU
REST Repressor Element 1-Silencing Transcription Factor (REST) binding sites
Stan/Yale Histone Histone Modifications by ChIP-seq from ENCODE/SYDH
Stan/Yale RNA-seq RNA-seq from ENCODE/Stanford/Yale
Stan/Yale TFBS Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale
TS miRNA sites TargetScan miRNA Regulatory Sites
UW DNaseI DGF DNaseI Digital Genomic Footprinting from ENCODE/University of Washington
UW DNaseI HS DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington
UW RNA-seq RNA-seq from ENCODE/UW
-   Comparative Genomics    
Conservation 30-Way Multiz Alignment & Conservation
GERP GERP scores for mammalian alignments
Rat Chain/Net Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments
Guinea pig Chain/Net Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments
Rabbit Chain/Net Rabbit (Apr. 2009 (Broad/oryCun2)), Chain and Net Alignments
Marmoset Chain/Net Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments
Rhesus Chain/Net Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments
Orangutan Chain/Net Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments
Chimp Chain/Net Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments
Human Chain/Net Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments
Panda Chain/Net Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments
Dog Chain/Net Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments
Cat Chain/Net Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments
Horse Chain/Net Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments
Sheep Chain/Net Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments
bosTau6 Chain/Net Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments
Pig Chain/Net Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments
Elephant Chain/Net Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments
Opossum Chain/Net Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments
Platypus Chain/Net Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments
Lizard Chain/Net Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments
Turkey Chain/Net Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments
Chicken Chain/Net Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments
X. tropicalis Chain/Net X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments
Zebrafish Chain/Net Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments
Stickleback Chain/Net Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments
Medaka Chain/Net Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments
Fugu Chain/Net Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments
Tetraodon Chain/Net Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments
Lamprey Chain/Net Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments
Lancelet Chain/Net Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments
-   Variation and Repeats    
SNPs (128) Simple Nucleotide Polymorphisms (dbSNP build 128)
RepeatMasker Repeating Elements by RepeatMasker
Agilent CGH Agilent CGH Microarray probesets
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
NumtS Sequence Mouse NumtS mitochondrial sequence
Segmental Dups Duplications of >1000 Bases of Non-RepeatMasked Sequence
Simple Repeats Simple Tandem Repeats by TRF