Hello, Nadia. The reason for the difference in length between the two sequences is because JAM3 in the RefSeq Genes track corresponds to NM_032801.4 as you correctly pointed out. JAM3 in the UCSC Genes track (uc001qhb.1) corresponds to NM_032801.3. You should use NM_032801.4 which is the most current revision.
It is also worth noting that we are currently in the process of updating the UCSC Genes track. It is not on the public site yet, but you can view it on our preview server at http://genome-preview.ucsc.edu/. If you search JAM3 on the preview server, you will notice that the UCSC Genes track now references uc001qhb.2 which corresponds to NM_032801.4. Please keep in mind this track has not yet been reviewed by the quality assurance team and may undergo some changes. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Nadia Awni Fayad Akawi Sent: Wednesday, October 26, 2011 1:35 AM To: [email protected] Subject: [Genome] JAM3 gene Dear Sir/Madam, Human Feb. 2009 (GRCh37/hg19) Assembly chr11:133,938,820-134,021,649 JAM3 Why JAM3 Refseq NM_032801.4<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucl eotide&term=NM_032801&doptcmdl=GenBank&tool=genome.ucsc.edu> is shorter than the UCSC seq uc001qhb.1 ? and which one should we use for nomenclature of SNPs and mutations? Thanks for help Best Regards, Nadia Akawi, PhD Student United Arab Emirates University Faculty of Medicine & Health Sciences Department of Pathology UAE, Al-Ain Tel.+971 3 7137639 Fax.+971 3 7671966 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
