Hello, Sunita, UCSC gets the cytoBand map coordinates from NCBI and then the transcripts are aligned to underlying reference genome assembly. I see that when you visit the DAPK1 gene at ncbi by following the link you sent, it does indeed say 9q34.1. However, if you click on the Mapviewer link on the same line as the cytoBand indication, you go their page:
http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&chr=9&MAPS=genec,ugHs,genes-r&cmd=focus&fill=80&query=uid%28-2146582277%29&QSTR=1612[gene_id] which shows a map and this: Region Displayed: 9q21.32-9q22.2 Ensembl also has this gene on 9q21. I believe you should inquire at NCBI about the difference. I did not look further at the two other example. good luck and best wishes, --b0b kuhn ucsc genome bioinformatics group On 2/14/2012 12:22 PM, Setlur, Sunita R.,Ph.D. wrote: > Hello, > > I noticed that the cytoband locations of several genes differ between NCBI and > UCSC. Is there a way to convert one to the other? Following is an example - > NCBI: http://www.ncbi.nlm.nih.gov/gene/1612. The NCBI cytoband location for > this > gene is 9q31.4, while it is 9q21.33 in UCSC. Two additional examples are MSH3 > and DHFR. Note, the build is 37. > Thanks for your help with this. > > Best, > Sunita > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
