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Configure Tracks on UCSC Genome Browser: Rat Mar. 2012 (RGSC 5.0/rn5)
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Control track and group visibility more selectively below.
-   Mapping and Sequencing    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Gap Gap Locations
Assembly Assembly from Fragments
Chromosome Band Chromosome Bands Based On ISCN Lengths
GC Percent GC Percent in 5-Base Windows
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
-   Genes and Gene Predictions    
MGC Genes Mammalian Gene Collection Full ORF mRNAs
Other RefSeq Non-Rat RefSeq Genes
RefSeq Genes RefSeq Genes
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
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
Ensembl Genes Ensembl Genes
Genscan Genes Genscan Gene Predictions
-   mRNA and EST    
Rat mRNAs Rat mRNAs from GenBank
Spliced ESTs Rat ESTs That Have Been Spliced
Other mRNAs Non-Rat mRNAs from GenBank
Rat ESTs Rat ESTs Including Unspliced
-   Expression and Regulation    
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)
-   Comparative Genomics    
Conservation Multiz Alignment & Conservation (13 species)
Mouse Chain/Net Mouse (Dec. 2011 (GRCm38/mm10)), Chain and Net Alignments
Rhesus Chain/Net Rhesus (Oct. 2010 (BGI CR_1.0/rheMac3)), Chain and Net Alignments
Chimp Chain/Net Chimp (Feb. 2011 (CSAC 2.1.4/panTro4)), Chain and Net Alignments
-   Variation and Repeats    
RepeatMasker Repeating Elements by RepeatMasker
updated EVA SNP Short Genetic Variants from European Variant Archive
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust