[ensembl-dev] Getting antisense transcript of gene using sql / biomart

[Henrikki Almusa]

Hi all,

I'm delving into the antisense transcript world. I've found two slightly 
different descriptions for this.

First from
http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html

Gene
Antisense. Has transcripts that overlap any coding exon of a locus on 
the opposite strand, or for published instances of antisense regulation 
of a coding gene.
Transcript
Antisense. Transcripts that overlap any coding exon of a locus on the 
opposite strand, or for published instances of antisense regulation of a 
coding gene.

Second from:
http://www.gencodegenes.org/gencode_biotypes.html
antisense Transcript believed to be an antisense product used in the 
regulation of the gene to which it belongs.

Now the second implies that gene connected to antisense transcript would 
be the gene that it blocks. But this conflicts which the other pages 
description.

So onto the main thing. I was asked to get a list of exons which have 
antisense transcript. Output would have gene name, transcript name, 
antisense transcript name and exon name and coordinates. I wrote 
following sql to retrieve this, but it does not give me the gene which 
is "blocked" but the "gene" of antisense transcript. Any help in getting 
the blocked transcript as well.

SELECT g.stable_id gene, tr.stable_id transcript, e.stable_id exon, 
e.seq_region_start, e.seq_region_end, ext.rank
FROM transcript tr
   JOIN exon_transcript ext USING(transcript_id)
   JOIN exon e USING(exon_id)
   JOIN gene g USING(gene_id)
   JOIN seq_region sr ON e.seq_region_id=sr.seq_region_id
   JOIN coord_system coord USING (coord_system_id)
WHERE coord.version = 'GRCh37' AND tr.biotype = 'antisense'

Thanks,
-- 
Henrikki Almusa
Bioinformatician
Institute for Molecular Medicine Finland FIMM

-- 
Henrikki Almusa