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?