RGD is pleased to announce that Rnor6.0 is now the default assembly for position data for all rat genes, QTLs, markers, variants and mapped strains! This change is denoted by the "Latest Assembly" entry on RGD report pages for rat which now lists "Rnor_6.0 - RGSC Genome Assembly v6.0", and by the fact that "Rnor 6.0" is in bold blue typeface in the Position table.
And speaking of the Position table, this section of all RGD gene pages has been enhanced with links to genome browsers right in the position table for easy access to that gene in the browser you most like to use, whether that's RGD's JBrowse, the UCSC browser or Ensembl. A link is also provided to NCBI's MapViewer for the cytogenetic map.
In keeping with RGD's switch from the legacy GBrowse browser to JBrowse, the "Model" section of the gene page now displays a snippet of JBrowse showing the intron/exon structures of all known and predicted transcripts for that gene on the 6.0 assembly. Rather than being a static image, this display is a functional segment of JBrowse giving the user the option of dragging the display within the box to view other genes in the genomic neighborhood. The "Full screen view" link opens the full Rnor6.0 JBrowse for that gene, giving a more complete view of that gene's genomic context including overlapping and nearby QTLs, strains, strain-specific variants and more.
Finally, links have been added from the nucleotide and protein sequence sections on RGD gene pages to NCBI's Sequence Viewer. Follow any of these links for a closer look at the sequence features for that nucleotide or protein sequence.
Click here to check out Aox3, the example gene shown here, or enter the symbol of your favorite gene in the Keyword search above to navigate to that page.