Dear all, I have downloaded the upstream1000.maf.gz file for the hg19 build using the following URL:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/maf/ This file contains the upstream region of RefSeq genes with annotated 5'UTRs. I find some inconsistency in this file in comparison to the UCSC genome browser annotation: ######################################## refseq-acc: NM_000586 => extract of the upstream1000.maf file: ... r txupstream 1000 NM_000586 s hg19.chr4 67775626 1000 - 191154276 AGGACTCTCT-CTGAGACAGG... ... ----------------------- But the genome browser find this gene in the following location: NM_000586 at chr4:123372630-123377650 ######################################## refseq-acc: NM_000162 => extract of the upstream1000.maf file: ... r txupstream 1000 NM_000162 s hg19.chr7 114908641 1000 - 159138663 acctctgag... ... ----------------------- But the genome browser find this gene in the following location: NM_000162 at chr7:44183870-44229022 ######################################## Did I miss something? Could you please explain me that problem? Martin Haubrock. -- Department of Bioinformatics (UMG) University Medicine Göttingen, Goldschmidtstr. 1, 37075 Göttingen _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
