[BioC] question about TranscriptDb

[Matthew D. Wilkerson]

Hello,

I have a question about the gene_id attribute of 
TxDb.Hsapiens.UCSC.hg19.knownGene, version 2.80 (latest).

I noticed that some transcripts such as uc021ums.1, do not have an 
associated gene_id.

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
t=transcripts(txdb,columns=c("gene_id","tx_id","tx_name","cds_id","cds_name"))
t[ which(elementMetadata(t)[,"tx_name"]=="uc021ums.1"), ]

I understand that some ucsc genes might not have an entrez gene id 
associated.
I checked this locus and found that currently UCSC db does have this 
locus associated with LINGO3.

#hg19.knownGene.name	hg19.knownGene.chrom	hg19.knownGene.strand	hg19.knownGene.txStart	hg19.knownGene.txEnd	hg19.knownGene.cdsStart	hg19.knownGene.cdsEnd	hg19.knownGene.exonCount	hg19.knownGene.exonStarts	hg19.knownGene.exonEnds	hg19.knownGene.proteinID	hg19.knownGene.alignID	hg19.kgXref.kgID	hg19.kgXref.geneSymbol
uc021ums.1	chr19	-	2289996	2291775	2289996	2291775	1	2289996,	2291775,	P0C6S8	uc021ums.1	uc021ums.1	LINGO3


The kgXref table was last updated  2/5/12.


The bioconductor package was made on:
Creation time: 2012-09-10 12:56:25 -0700 (Mon, 10 Sep 2012)

If this date also refers to the date of download, then why is this 
transcript not affiliated with LINGO3?
If not, then what date does known gene refer to?


Thanks,
Matt

-- 
Matthew D. Wilkerson, Ph.D.
Lineberger Comprehensive Cancer Center
University of North Carolina at Chapel Hill
http://www.unc.edu/~mwilkers