Hi Xue, Are you referring to the following paragraph from the methods section of the RefSeq Genes track (from which the refMrna.fa file is from)?
"RefSeq RNAs were aligned against the human genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept." Although only the single best alignment for each RefSeq entry is included in the track, RefSeq itself contains multiple entries for genes that have multiple known splice variants. So, the RefSeq Genes track does contain splice variants. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 10/3/11 9:19 AM, xue lin wrote: > Dear whom concerned, > Thank you for last time answering the question, and I still have a little > quesiton that I read the introduction of the refMrna.fa, there is no > redundancy in the file. Does it mean that there is no splicing sequences in > the mRNA refseq file? > Thank you very much. > All the best. > Xue > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
