> Hello, > > This is just nomenclature not being perfect, some schema's are used for many > datasets. For this case you are right, the sequence is the mRna for the > coding part of the gene - the protein. >
Just to clarify: Does the sequence also include the UTRs, that is, does it coincide exactly with the sequence represented by the exon positions in the knownGene tables? -Thanks Peter > Hope this helps, > Jennifer > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Dr. med. Peter Robinson" <[email protected]> wrote: > >> From: "Dr. med. Peter Robinson" <[email protected]> >> To: [email protected] >> Sent: Tuesday, September 29, 2009 1:47:07 PM GMT -08:00 US/Canada Pacific >> Subject: [Genome] Schema for knownGeneMrna >> >> Hi UCSC gurus, >> >> the description of the knownGeneMrna given via the web page >> http://genome.ucsc.edu/cgi-bin/hgTables appears to be wrong, in that >> the seq >> field is defined to hold a peptide sequence, whereas the table >> contains the >> mRNA (actually cDNA) sequences of the knownGenes. >> -cheers Peter >> >> >> >> Database: hg18 Primary Table: knownGeneMrna Row Count: 66,803 >> Format description: A predicted peptide - linked to a predicted gene. >> field example SQL type info description >> name uc001aaa.2 varchar(255) values Name of gene - same as >> in >> genePred >> seq gcagggctctcttgcttagagtggtgg... longblob Peptide sequence >> >> >> -- >> Dr. med. Peter Robinson >> Institut für Medizinische Genetik >> Charité - Universitätsmedizin Berlin >> Augustenburger Platz 1 >> 13353 Berlin >> Germany >> voice: 49-30-450569124 >> fax: 49-30-450569915 >> email: [email protected] >> http://compbio.charite.de/ >> http://www.human-phenotype-ontology.org >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > -- Dr. med. Peter Robinson Institut für Medizinische Genetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany voice: 49-30-450569124 fax: 49-30-450569915 email: [email protected] http://compbio.charite.de/ http://www.human-phenotype-ontology.org _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
