Hello. Occasionally, a single mRNA transcript aligns well to multiple locations in the same genome. In the case of NM_001143883 (PPIAL4B), because it is a single transcript, you will only find one RefSeq record (http://www.ncbi.nlm.nih.gov/nuccore/NM_001143883?report=GenBank), but it aligns well to three different positions on the hg19 genome (chr1:144,363,462-144,362,246, chr1:147,954,635-147,955,419, chr1:149,553,003-149,553,787) so there are three separate entries for it in the refGene table. Two of those locations are on the minus strand and one is on the plus strand.
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 hujingchu Sent: Tuesday, June 26, 2012 11:53 PM To: [email protected] Subject: [Genome] transcript locate in plus and miplus simultaneously hi， i download the refgene track from UCSC, but i found some transcript located in plus and miplus chain simultaneously.the transcript id is :NM_001143883 . i am not sure why this would happen and theres only one transcript record in Ensemble, could you help me to figure out why the other two transcript were record in refGene. thank you very much~ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
