Track Descriptions & Citations

Tracks Built into this Server

Mouse Synteny Block

This track shows the Mouse Synteny Blocks, as calculated by the Mercator program developed by Colin Dewey at UW Madison. Hovering over a feature provides additional annotation including the synteny ID which is identical between syntenic rat-human-mouse blocks and the actual position of the synteny block in the mouse genome. Synteny blocks are color-coded based on their original chromosome number using the UCSC color scheme.

Mouse Orthologs

This track shows the orthologous mouse genes for the RGD rat genes as defined by the ortholog mapping maintained at RGD. Hovering over a feature provides additional annotation including the gene name, gene type, description, the original position of the gene within the mouse genome, and synteny ID indicating the synteny block that gene belongs to. In addition the NCBI, RGD, MGI IDs are provided as links to the appropriate gene report pages. Mouse genes are colored based on their mouse chromosome number using the UCSC color scheme. These genes are highlighted with a blue background if they have an ortholog which is currently off-screen.

RGD Genes

This track shows the RGD curated genes. Hovering over a feature provides additional annotation including the EntrezGeneID, name, RGD description (where available), and RGD ID. In addition, for RGD genes which encompass a feature in the NIH Mammalian Gene Collection (MGC) program, the MGC clone ID is provided, and for genes which encompass a feature in the Image Consortium Collection (a public cDNA collection), the IMAGE clone ID is provided as a link to the IMAGE consortium query pages. Additional links are provided to the RGD Gene Report, and EntrezGene record. If there are multiple transcripts for a particular gene, this track shows the longest transcript. Also, if there are more than one longest transcripts, the one that has highest number of exon is shown. The arrow indicates the direction of transcription. Rat genes are colored based on their chromosome number using the UCSC color scheme. These genes are highlighted with a blue background if they have an ortholog which is currently off-screen.

Human Orthologs

This track shows the orthologous human genes for the RGD rat genes as defined by the ortholog mapping maintained at RGD. Hovering over a feature provides additional annotation including the gene name, gene type, description, the original position of the gene within the human genome, and synteny ID indicating the synteny block that gene belongs to. In addition the NCBI, RGD, HGNC, HPRD IDs are provided as links to the appropriate gene report pages. Human genes are colored based on their human chromosome number using the UCSC color scheme. These genes are highlighted with a blue background if they have an ortholog which is currently off-screen.

Human Synteny Block

This track shows the Human Synteny Blocks, as calculated by the Mercator program developed by Colin Dewey at UW Madison. Hovering over a feature provides additional annotation including the synteny ID which is identical between syntenic rat-human-mouse blocks and the actual position of the synteny block in the human genome. Synteny blocks are color-coded based on their original chromosome number using the UCSC color scheme.

Rat Synteny Block

This track shows the Rat Synteny Blocks, as calculated by the Mercator program developed by Colin Dewey at UW Madison. Hovering over a feature provides additional annotation including the synteny ID which is identical between syntenic rat-human-mouse blocks and the actual position of the synteny block in the rat genome. Synteny blocks are color-coded based on their chromosome number using the UCSC color scheme.

Entrez Transcripts

This track shows the EntrezGene transcripts derived from GenBank. For genes with multiple transcripts, each transcript will be shown in the track. Hovering over a feature provides additional annotation including the appropriate gene name, EntrezGene ID (links to the EntrezGene Report page), GI number (which will differ for each transcript; links to the EntrezGene transcript record), and RGD ID (links to the RGD Gene Report page). Clicking on a feature links to the EnterezGene transcript record. The arrow indicates the direction of transcription.

Entrez Pseudogenes

This track shows pseudogenes labeled as such at GenBank. Hovering over a feature provides additional annotation including the EntrezGeneID, Name, Description, and Source. Clicking on a features links to the appropriate EntrezGene record.

GenBank tRNAs

This track shows tRNAs labeled as such at GenBank. Hovering over a feature provides additional annotation including the Name, Aminoacid, Description, and Source.

CNVs

Copy Number Variants (CNVs) identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute's CNV pages.
CNVs are colored based on type as following:

Type	Color
Collapse	Purple
Overprediction	Yellow
Loss	Blue
Loss+Collapse	Dark blue
Loss+Overprediction	Light blue
Gain	Red
Gain+Collapse	Dark red
Gain+Overprediction	Light red

Misassemblies

Putative mis-assemblies in the reference genome identified through computational approaches as described and published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the Misassembly ID, Method (Whole Genome Shotgun mapping, Nimblegen RN34 Whole Genome Tiling Array, Affymetrix RaEx Rat Exon Array, Optical_mapping), Type, and Source. Clicking on a feature or selecting the Misassembly ID links to the Hubrecht Institute's misassembly pages.
Misassemblies are colored based on type as following:

Type	Color
Collapse	Purple
Overprediction	Yellow
Loss	Blue
Loss+Collapse	Dark blue
Loss+Overprediction	Light blue
Gain	Red
Gain+Collapse	Dark red
Gain+Overprediction	Light red

PGA

This track includes the genomic locations of the PhysGen PGA mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.

DNA/GC Content

At most resolutions this shows the %GC content of DNA; at high resolution it shows the nucleotides (for both sense and antisense strand) of a given region.

Contigs

This track shows the contigs which comprise the rat genome assembly, as defined at GenBank. Hovering over a feature provides additional annotation including the contig name, genomic coordinates, description and strain. Clicking on a feature or selecting the contig name links to the NCBI Contig report.

Human Alignment NET

This UCSC derived track shows the best human/rat chain for every part of the rat genome. It is useful for finding orthologous regions and for studying genome rearrangement. The human sequence used in this annotation is from the Mar. 2006 (hg18) assembly. Clicking on this track links to the UCSC Genome Browser, with the entire segment of the net alignment in view. Hovering over the feature provides additional annotation including the coordinates in both the rat (Base Position) and human (Matched Region) genomes spanned by the alignment net.

Mouse Alignment NET

This UCSC derived track shows the best mouse/rat chain for every part of the rat genome. It is useful for finding orthologous regions and for studying genome rearrangement. The mouse sequence used in this annotation is from the July 2007 (mm9) assembly. Clicking on this track links to the UCSC Genome Browser, with the entire segment of the net alignment in view. Hovering over the feature provides additional annotation including the alignment file used to create the track and the coordinates in both the rat (Base Position) and mouse (Matched Region) genomes spanned by the alignment net.

Ensembl SNPs

Single Nucleotide Polymorphisms (SNPs) extracted from Ensembl SNP. IDs beginning with rs are SNPs from NCBI dbSNP. SNPs that are discovered by Ensembl from resequencing and comparing reads to the genome assembly have Ensembl SNP IDs beginning with ENSRNOSNP. Clicking on the SNP links to the Ensembl SNP Report pages. Hovering over the SNP provides additional annotation including:

• Map weight - the number of times a SNP maps to the genome contig (range 1-10)
  
  • 1 = hit genome once, annotated on NT_ contigs
  • 2 = hit genome twice, annotated on NT_ contigs with warning
  • 3 = hit genome 3-9 times, not annotated
  • 10 = hit 10+ times on genome, not annotated
• Alleles - the alleles observed for the SNP and submitted to Ensembl
• Ambiguity Code - the IUPAC nucleotide ambiguity code representing the polymorphism as identified by Ensembl
• Strain - the strains in which the SNP was identified
• Type - the genomic location of the SNP as defined at Ensembl. Defined as: Flanking to a transcript (within 5,000 bp upstream or downstream from the transcript); in a UTR; intronic; or in a coding sequence. Coding SNPs are divided into those annotated by Ensembl as being synonymous (does not change the amino acid/peptide) or non-synonymous (changes the amino acid/peptide).

Ensembl SNPs are colored as following:

Ensembl SNP Type	Color
Intergenic	Grey
Intronic	Red
Upstream	Pink
Downstream	Orange
Synonymous Coding	Purple
Non Synonymous Coding	Yellow
Splice-site	Black
3Prime UTR	Dark blue
5Prime UTR	Light blue
Stop gained	Light yellow
Stop Lost	Dark yellow
Other	Brown

dbSNPs

Single Nucleotide Polymorphisms (SNPs) extracted from NCBI dbSNP. Clicking on the SNP links to the dbSNP SNP Report pages. Hovering over the SNP provides additional annotation including:

• Map weight - the number of times a SNP maps to the genome contig (range 1-10)
  
  • 1 = hit genome once, annotated on NT_ contigs
  • 2 = hit genome twice, annotated on NT_ contigs with warning
  • 3 = hit genome 3-9 times, not annotated
  • 10 = hit 10+ times on genome, not annotated
• Type - the genomic location of the SNP as defined at dbSNP. Defined as: Coding nonsynonymous (changes the amino acid/peptide); Coding synonymous (does not change the amino acid/peptide); in untranslated region; intronic (except first 2 and last 2 bases); in Splice-site (in first two or last two bases of intron); in locus region (not assigned to a gene but can be in an untranscribed region of a gene; may be in regulatory region).

dbSNPs are colored as following:

dbSNP Type	Color
Locus-region	Grey
Intron	Red
5Upstream	Pink
3Downstream	Orange
Synonymous Coding	Purple
Non Synonymous Coding	Yellow
Splice-site	Black
mRNA-UTR	Blue
3UTR	Dark blue
5UTR	Light blue
Other	Brown

miRNAs

This track shows rat microRNAs (miRNAs) derived from the Sanger Institute's miRBase. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.

RGD QTLs

This track shows RGD Rat Quantitative Trait Loci (QTL). In some cases the boundaries of the QTL have been estimated as explained in QTLs Readme file. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.

EST

This track shows Rat Expressed Sequence Tags (EST). Hovering over a feature provides additional annotation including the EST ID, which links to the Report page at NCBI. Clicking on a feature links to the same NCBI report page. The arrow indicates the direction of transcription.

MGC mRNAs

This track shows the location of rat mRNAs verified and available from the NIH Mammalian Gene Collection (MGC). The MGC program is a multi-institutional effort to identify and sequence cDNA clones containing a full-length open reading frame for human, mouse, and rat genes. Hovering over a feature provides additional annotation including the clone ID. Clicking on a features links to the EntrezGene mRNA record.

GENSCAN predictions

This track shows predictions from the GENSCAN program written by Chris Burge. The predictions are based on transcriptional, translational, and donor/acceptor splicing signals, as well as the length and compositional distributions of exons, introns and intergenic regions.

Ensembl Genes

This track shows the gene calls from Ensembl. Clicking on a feature links to the appropriate Ensembl Transcript Report using the ID starting with ENSRNOT. The arrow indicates the direction of transcription.

UniSTS

This track shows Sequence Tagged Sites (STS) derived from UniSTS. These markers have been mapped using either genetic (Rat FHH x ACI F2 Intercross Genetic Map, Rat SHRSP x BN F2 Intercross Genetic Map) or radiation hybridization (RH Map 2.2) mapping techniques. Hovering over a feature provides additional annotation including the UniSTS ID and name. Clicking on a feature or selecting the UniSTS ID links to the UniSTS marker report page at NCBI.

RGD SSLPs

Rat Simple Sequence Length Polymorphisms (microsatellite markers). Each marker is linked to its report page in RGD.

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Generic genome browser version 1.7