biocommons/uta

Mismatch of genomic and transcript positions

lacek opened this issue · 0 comments

lacek commented

I am trying to use transcript positions provided by UTA to convert cDNA positions to genomic positions.
I got a wrong result when working on the transcript NM_006331.7 where genomic and transcript positions are inconsistent.

By executing the query:

SELECT ord, tx_start_i, tx_end_i, alt_start_i, alt_end_i
FROM tx_exon_aln_v
WHERE tx_ac = 'NM_006331.7'
AND alt_aln_method = 'splign'
AND alt_ac = 'NC_000012.11'
ORDER BY ord;

The following results are returned:

ord tx_start_i tx_end_i alt_start_i alt_end_i
0 0 311 7079943 7080253
1 311 413 7083500 7083602
2 413 555 7083713 7083855
3 555 614 7084251 7084310
4 614 764 7084390 7084540
5 764 1072 7084857 7085165

In the first exon, tx_end_i - tx_start_i = 311bp but alt_end_i - alt_start_i = 310bp. I wonder if there is something wrong with the data. Or am I just querying improperly?