Hello Jorje, What you are seeing are the results from two distinct data tracks along with data from a table (kgXref) that includes the maximum linked reference IDs from all public sources. There could be errors. The table is intended to be used as a resource, not as a final answer.
The actual tracks (UCSC Genes and RefSeq Genes, among others) are the mappings for the data that are based on target sequence homology to the reference genome. And although those two tracks may not always agree, as they are generated by different processes, they are a better source (as you state) for the correct genome position. If you want to use linked data, you may find the table kgAlias easier to use. It contains fewer types of linked information and so is less cluttered than the hgXref table. Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/17/10 2:07 AM, Jose Jorge Galan Retamal wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
