Dear all, I am trying to retrieve human mrna genomic intervals from the UCSC table browser (whole genome). I have noticed that the same mrna can be located on different genomic regions depending on the search you perform on the table browser. Two examples:
*The AK310762 mrna* *Search 1:* clade: Mammal genome: Human assembly: GRCh37 group: All Tables database: hg19 table: kgXref region: position AK310762 *results in: * SIZE IDENTITY CHROMOSOME STRAND START END cDNA START END TOTAL ------------------------------------------------------------------------------ 1352 100.0% 19 + 47105328 47113252 AK310762 23 1374 1375 <http://genome.ucsc.edu/cgi-bin/hgTables?position=chr19:47105328-47113252&all_mrna=pack&hgsid=152164491> *Search 2:* clade: Mammal genome: Human assembly: GRCh37 group: All Tables database: hg19 table: kgXref region: genome output format: select fields from primary and related tables selected fields: hg19.kgXref.mRNA hg19.refGene.chrom hg19.refGene.strand hg19.refGene.txStart hg19.refGene.txEnd *the AK310762 mrna **appears in the output as:* hg19.kgXref.mRNA hg19.refGene.chrom hg19.refGene.strand hg19.refGene.txStart hg19.refGene.txEnd AK310762 chr14 + 90863326 90874617 *The CR607619 mrna* *Search 1:* clade: Mammal genome: Human assembly: GRCh37 group: All Tables database: hg19 table: kgXref region: position CR607619 *results in: * SIZE IDENTITY CHROMOSOME STRAND START END cDNA START END TOTAL ------------------------------------------------------------------------------ 1342 100.0% 7 - 5566815 5568363 CR607619 1 1342 1343 <http://genome.ucsc.edu/cgi-bin/hgTables?position=chr7:5566815-5568363&all_mrna=pack&hgsid=152164491> *Search 2:* clade: Mammal genome: Human assembly: GRCh37 group: All Tables database: hg19 table: kgXref region: genome output format: select fields from primary and related tables selected fields: hg19.kgXref.mRNA hg19.refGene.chrom hg19.refGene.strand hg19.refGene.txStart hg19.refGene.txEnd *the CR607619* *mrna **appears in the output as:* hg19.kgXref.mRNA hg19.refGene.chrom hg19.refGene.strand hg19.refGene.txStart hg19.refGene.txEnd CR607619 chr17 - 79476998 79479827 I have checked the actual locations for both AK310762 and CR607619 mRNAs in the UCSC Genome browser. It seems that the actual positions for both mRNAs are those obtained in Searches 1. Therefore, it seems that there is a problem in linking the tables kgXref and refGene. I would be very grateful if someone could check this question and propose any solution for it. Best wishes, Jorge _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
