Hi Qi, From looking at your example coordinates, I think the RefSeq data you downloaded was for the GRCh37/hg19 assembly. On that assembly, the SGIP1 RefSeq Gene is at postion:
chr1:66,999,825-67,210,768 (note that the first coordinate is one higher than the coordinate listed in the table. See: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1) I hope this explains what you are seeing. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/23/10 16:01, Qi Ma wrote: > Dear representative, > > I am confused about the REfseq data table I downloaded from UCSC genome > browser Tables, because I found I can not match the coordination of > gene transcription starting site and ending site with the visualized > coordination of the same gene's. > For example, in the accessory file of the human Refseq genomes 18, the first > gene(SGIP1), the transcript starting site and end site are (66999824, > 67210768). > But when I use visualization way of showing the coordination of gene(SGIP1), > it shows the transcript starting site and end site are (66770000, 66900000). > Maybe I made a mistake, and could you give me an explanation?Thanks. > > Best wishes > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
