Hi Vinayak, As you can see from the "Methods" section of the RefSeq Genes description page, the refSeq RNAs were aligned to against the human genome using blat.
This means that we obtain the refSeq RNAs from NCBI with out any coordinate data and then generate our own coordinate data by aligning the refSeq RNA sequence against the human genome using blat. NCBI may be aligning the RNAs with a different program (or different parameters) and that is why there are slight differences between UCSC's coordinates and NCBI's coordinates. Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Vinayak Kulkarni wrote: > Dear UCSC folks, > > I was looking at the gene SLC35D1, transcriptID : NM_015139.2 > > This is where UCSC says it maps on the genome : > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=146079382&o=67465014&t=67520080&g=refGene&i=NM_015139&c=chr1&l=67466148&r=67466208&db=hg19&pix=800 > > However the starts and stops on NCBI are a little different, > http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=23169 > > I wanted to know if there a difference in the way the alignments for UCSC > v/s NCBI work, or am I missing something? > > Thank you very much for your thoughts, > Have a good day, > Vinayak. > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
