Hello Hui, Start coordinates in our database are 0-based, not 1-based. See this FAQ for an explanation:
http://genome.ucsc.edu/FAQ/FAQtracks#tracks1 If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/26/08 10:30 AM, Hui Liu wrote: > Hi all, > > I'm working on truncate 3'UTR from genome based on UCSC database, > and I have a question about exonStarts and exonEnds right now. > > Take NFKBIA for example: > > mrna_acce: NM_020529. > chrom: chr14 > strand: - > exonStarts: 34940466,34941350,34941727,34942106,34942646,34943374, > exonEnds: 34941017,34941620,34941816,34942317,34942755,34943711, > > But when I compare this information with NCBI, I found that all the exonStarts > are different. For NCBI, the exonStarts are: > 34940467,34941351,34941728,34942107,34942647,34943375, > http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=gene_table&list_uids=4792 > > > So every exonStarts in UCSC is 1nt smaller then NCBI while the exonEnds > is the same. I found same situation when I compared several positive strand > mRNA. > > So if I want to truncate a Exon from chromosome sequence, the start and stop > point should be "exonStarts+1 to exonEnds" or "exonStarts to exonEnds". > > If use "exonStarts to exonEnds", what I truncate will be different from NCBI > sequence. > > Thanks > > Hui > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
