Hi Jessilyn, The accession number for the transcript at this location is NM_010637. Search for "KLF4" from the Genome Browser Gateway (assuming you are using the mm9 assembly) and click submit, then click on the link under RefSeq Genes: Klf4 at chr4:55540009-55545347 - (NM_010637) Krueppel-like factor 4. Clicking on the blue highlighted item "Klf4" within the browser display will take you to the following item description page: http://genome.ucsc.edu/cgi-bin/hgc?db=mm9&g=refGene&i=NM_010637. From here, click on the "NM_010637.3" link, which will direct you to the correct GenBank page: http://www.ncbi.nlm.nih.gov/nuccore/NM_010637?report=GenBank.
The Table Browser can be used to download the gene sequence (http://genome.ucsc.edu/cgi-bin/hgTables). Please see this previously answered question for more details: https://lists.soe.ucsc.edu/pipermail/genome/2012-January/028092.html Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 4/5/2012 12:25 PM, Jessilyn Dunn wrote: > Hello, > I have a question about comparing a gene's location between the UCSC genome > browser and NCBI Genbank. It seems that the genes have different loci in > the two different databases. The gene in particular I am looking at is > Klf4. In the UCSC genome browser its location is defined > as chr4:55,540,009-55,545,347 while in the NCBI Genbank looking at Klf4 > (RefSeq NC_000070.6) its location is defined as chr4:55,527,137-55,532,475. > I am wondering why there is a deviation? Also, is there a way to view the > gene sequence in a highlighted region of the UCSC browser? > > Thank you for your assistance! > Jessilyn > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
