Hello, This particular table is no longer created by the UCSC Genes process (previously called Known Genes). The table in the Human hg18 database is older and related to the track now named "Old UCSC Genes" that represents the prior Known Genes data. The most current mouse genome (mm9) only has the new UCSC Genes track and therefore no mrnaRefseq table as you noted. The prior mouse genome (mm8) does have the table. To find it in mm8, set the variables to the RefSeq Genes track, click on "describe table schema". The table will be in the list of "Connected Tables and Joining Fields". Many Known Genes tables will also be in the list, allowing you to link between the two tracks.****
The table mrnaRefSeq is a cross reference table between Refseq and mRNA IDs based on LocusLink from NCBI. The data can be retrieved there or instead you can use the UCSC Genes table kgXref in the mm9 genome. The kgXref uses multiple input sources to link together transcripts/genes using the methods as described in the UCSC Genes track's description. The refLink table does contain the locusLinkID for RefSeq sequences (however not all mRna sequences), but it may be helpful to know about. Also, comparing the content of the two tables (mrnaRefseq & kgXref) in a database that has both (human hg18 or mm8) would help you to determine if the kgXref table would meet your research needs. Thank you for your question, Jennifer Jackson UCSC Genome Bioinformatics Group Stefan Maas wrote: > Hello, > for the human genome annotation data, there is a table mrnaRefseq, which > links RNA accession numbers to Refseq IDs. I was looking for this table > for the mouse genome, but have not been able to locate it. Also, I was > not able to create such a table using the table browser. > Is there a mrnaRefseq table somewhere? > Thank you and best regards, > Stefan > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
