Peng, It's deficult to trace where the Muc19/Smgc came from exactly. Considering it is sometimes cited in the literature as "Muc19/Smgc" (see links below), and NCBI says they are synonyms, it's difficult to conclude that this is an outright mistake. We are currently working on mm10 knownGenes and it is likely that the name of this will change to Smgc in a future release.
As you can see in the kgXref table below, "Muc19/Smgc" is based on the BC145136 transcript and was not assigned a RefSeq identifier at the time. mysql> select kgId, mRNA, geneSymbol, refseq from kgXref where geneSymbol like "%muc19%" or geneSymbol like "%Smgc%"; +------------+-----------+------------+-----------+ | kgId | mRNA | geneSymbol | refseq | +------------+-----------+------------+-----------+ | uc007xie.1 | NM_207243 | Muc19 | NM_207243 | | uc007xic.1 | NM_198927 | Smgc | NM_198927 | | uc011zxz.1 | AK132579 | Smgc | NM_198927 | | uc011zya.1 | BC055490 | Smgc | | | uc011zyb.1 | BC092073 | Smgc | NM_198927 | | uc011zxy.1 | BC145136 | Muc19/Smgc | | | uc011zyc.1 | BC069958 | Smgc | NM_198927 | | uc007xif.1 | BC038603 | Smgc | | | uc011zyd.1 | BC145136 | Smgc | NM_198927 | | uc007xid.1 | EU089958 | Muc19 | | +------------+-----------+------------+-----------+ You might find these helpful: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2664977/ http://www.ncbi.nlm.nih.gov/pubmed/15340121 http://www.wikigenes.org/e/gene/e/239611.html - Greg On 5/7/12 5:36 PM, Peng Yu wrote: > On Mon, May 7, 2012 at 7:22 PM, Greg Roe<[email protected]> wrote: >> Yes, on that second page, also click the RefSeq link: >> >> ==> RefSeq: NM_198927.3 > On the genbank, it says > > DEFINITION Mus musculus submandibular gland protein C (Smgc), mRNA. > > Also, the gene name is Smgc, Muc19 is a synonym. > /gene="Smgc" > /gene_synonym="2310010P21Rik; DXImx49e; Muc19; Sfc21" > > So the correct name should be Smgc. For the same reason, I think that > the official name of another Muc19 gene should also be Smgc. > > Mouse Gene Muc19 (uc007xid.1) Description and Page Index > Description: RecName: Full=Submandibular gland protein C; Flags: > Precursor; > Strand: + Genomic Size: 23110 Exon Count: 3 Coding Exon Count: 3 > > Have you got a chance to look my following question? I think that > there should be only one official gene symbol for transcripts at a > single locus. When there are two names referring to transcripts in the > same locus, it becomes confusing and probably should be fixed. > >> On the browser, I see several Muc19 UCSC knownGenes and several Smgc >> knowGenes. If the name Muc19/Smgc is correctly, why not these genes >> are not named as Muc19/Smgc? > >> On 5/7/12 5:11 PM, Peng Yu wrote: >> >> On Mon, May 7, 2012 at 6:04 PM, Greg Roe<[email protected]> wrote: >> >> Hi Peng, >> >> This is not a bug. If you click on the Muc19/smgc gene in the browser there >> is some information about it on the details page. If you scroll down the >> page and follow the RefSeq link, and then the RefSeq link on the subsequent >> page, you'll be brought to the correct place in Genbank. >> >> When I click the Muc19/smgc gene, I get to this page. >> >> http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc011zxy.1&hgg_prot=D7RV82&hgg_chrom=chr15&hgg_start=91668756&hgg_end=91681089&hgg_type=knownGene&db=mm9&hgsid=264444213 >> >> The link under "RefSeq Accession: NM_198927" is >> >> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=264444213&g=refGene&i=NM_198927&c=chr15&o=91668756&l=91668756&r=91681089&db=mm9 >> >> On this page, I see " >> RefSeq Gene Smgc >> RefSeq: NM_198927.3 Status: Provisional >> Description: Mus musculus submandibular gland protein C (Smgc), mRNA. >> CCDS: CCDS27762.1 >> Entrez Gene: 223809 >> PubMed on Gene: Smgc >> PubMed on Product: submandibular gland protein C precursor >> Stanford SOURCE: NM_198927" >> >> >> Would you please show me how you got to the Genbank page? >> >> Also, a quick Google search for "Muc19 smgc" turns up quite a few relevant >> pages on the topic. In summary, "[...] analyses indicate transcripts for >> Muc19 and Smgc (submandibular gland protein C) are splice variants of a >> larger gene, Muc19/Smgc." >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
