Hello, For the RefSeq track, if a transcript maps to more than one location within a close range of similarity, all qualifying locations are preserved. Instead, we recommend using the UCSC Genes track. Sorting out pseudogenes, genomic duplications, etc. are not a part of the RefSeq track process for the UCSC browser - we just align the data, but it is a part of the UCSC Genes process. The UCSC Genes track contains the RefSeq dataset as one of the input sources.
To see the difference, go to the human gateway page, enter the gene name DUX4 and submit. The list of results will show one location in the UCSC Genes track (plus other "like" transcripts at the other locations with distinct names) and multiple locations for the same transcript/same name in RefSeq track. The UCSC Genes and RefSeq Genes track descriptions offer many details for the methods used. For the RefSeq track, this section in particular is relevant to your query: -------------- Methods 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. ------------- I hope this helps to clarify the data, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- [email protected] wrote: > From: [email protected] > To: [email protected] > Sent: Wednesday, December 2, 2009 12:44:09 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Table browser > > I am trying to download a table with gene annotation information from > the table browser function. I'm using Hg18, RefSeq Genes track, genes > and gene prediction tracks group, refGene table, selected fields from > primary and related tables with a link to CCDS. The problem I'm > running into is the presence of chromosomes in the table that are > mapping to more than one chromosome, for example DUX4, which according > to the table maps to chr 4 and 10 yet when I search for this gene in > other databases it shows up only on chromosome 4. What is the reason > for the presence of this discrepancy and is there a way to filter out > erroneous chromosome mapping locations? > Regards, > > Jan Egan, PhD > Research Fellow > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
