Hello,
among RefSeq annotations (hg19, from UCSC), one can find genes with several transcripts on different strands. One also finds genes with the same identifier but on different chromosomes. Here is an example combining the two (gene "OR4F29"):
wget --timestamping ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz
zcat refGene.txt.gz | grep "OR4F29"
587 NM_001005221 chr1 + 367658 368597 367658 368597 1 367658, 368597, 0 OR4F29 cmpl cmpl 0,
589 NM_001005221 chr1 - 621095 622034 621095 622034 1 621095, 622034, 0 OR4F29 cmpl cmpl 0,
1964 NM_001005221 chr5 + 180794287 180795226 180794287 180795226 1 180794287, 180795226, 0 OR4F29 cmpl cmpl 0,
Are these errors, knowing that Ensembl has only one transcript for this gene?
What do you do in such a case? Discard the genes? Use Ensembl instead?
Grab the sequence from NCBI. BLAT the sequence. Note the results:
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN
---------------------------------------------------------------------------------------------------
browser details NM_001005221.2 939 1 939 939 100.0% 1 - 621096 622034 939
browser details NM_001005221.2 939 1 939 939 100.0% 5 + 180794288 180795226 939
browser details NM_001005221.2 939 1 939 939 100.0% 1 + 367659 368597 939
(With lots more matches, but those are the three with 100% identity for the full length of the sequence).
There are multiple locations listed for this sequence because it appears at several loci in the genome.
David's last sentence is telling - this gene/transcript would be labeled as a likely repeat element, most probably a transcribed portion of an LTR or retro-element. Thus, I would do as Travis suggests and give such a gene some kind of alternate consideration/label.
I personally prefer the Ensembl approach in cases like this i.e. consider them as separate genes. Another option is to consider them as one gene but as sense/antisense representations of the gene. It depends a lot on preference and your own way of conceptualizing the genome/transcriptome. I would not discard any of the transcripts.
Trans-splicing can also cause some gene models to (legitimately) be annotated to both strands, such as the Drosophila Mod(mdg4) locus: http://genome.cshlp.org/content/13/10/2220.full
The first indication of a requirement for trans-splicing in the generation of Mod(mdg4) proteins came after the realization that the two DNA strands of the gene have coding capabilities and contain coding sequences present in mature mRNAs that are translated into functional proteins
@Casey thanks for this good reference! For the other users, the initial paper (Labrador et al, Nature 2001) can be found here http://www.nature.com/nature/journal/v409/n6823/full/4091000a0.html
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Ensembl has listed those three positions as separate genes - http://asia.ensembl.org/Homo_sapiens/Search/Details?species=Homo_sapiens;idx=Gene;end=3;q=OR4F29 - each with a single transcript of the exact same sequence. Personally I find RefSeq more... useful in this case