hi, i have a list of SNPs and their locations on hg18. i'd like to use ucsc data to find out for each SNP whether it falls in a known gene and if so in which of the following regions: 5'utr/coding sequence/intron/3'utr. if it does fall inside the coding sequence i would additionally like to know whether it is a synonymous SNP or not, and if not what is the resulting amino acid
i read through the mailing archives and understood its best to use refGene and refMrna for this task: for a given SNP coordinate i first check whether it falls inside any of refGene's transcription boundaries. if it does, i then determine in which region of the gene. if it falls inside one of the coding exons i then extract the relevant codon from refMrna - and here's where i'm stuck: according to the coordinates in refGene i might determine that the SNP is in e.g., the 5'utr but according to the coordinates in the CDS file it may turn out that it's actually in the coding sequence.and the other way around (plus other similar combinations of that problem concerning the 3'utr and intron regions). i understand that the genomic coordinates in refGene are the result of BLAT and those in the CDS file are local coordinates from NCBI. since the mapping of NCBI mRNAs to the genome is imperfect these location discrepancies occur. so, if my description is correct is there any solution to my problem? if i understood or am doing something wrong i would greatly appreciate your corrections. thank you very much for your time and help Nimrod Rubinstein The Department of Cell Research and Immunology Tel Aviv University _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
