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
