[ensembl-dev] exon table does not map to dna table

[Joshua Bradley]

I am using the the latest release of the human genome,
homo_sapiens_core_76_38.

I am trying to map exons to their corresponding dna sequence. I'm running a
local instance of the sql tables to make things faster. My approach was to
take the seq_region_id in the exon table and use that to find the sequence
in the dna table. . The schema
<http://www.ensembl.org/info/docs/api/core/core_schema.html> online seems
to suggest that I can use the seq_region_id to do this but I am not getting
any results back from my sql queries.

I've verified what the schema says, that the seq_region table has a 1-1
mapping to the dna table by comparing counts between the two with the
following queries.

SELECT COUNT(*) FROM seq_region INNER JOIN dna ON
seq_region.seq_region_id=dna.seq_region_id;

SELECT COUNT(*) FROM dna;


This was to be expected, however when I try to do a join between the exon
table and dna table, I get a count of 0

SELECT COUNT(*) FROM exon INNER JOIN dna ON
exon.seq_region_id=dna.seq_region_id;

which tells me the seq_region_id is not a 1-1 mapping. I am able to use
biomart
<http://www.ensembl.org/biomart/martview/96b01e4e2043c838fc28f0969c5914a6?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.sequences.ensembl_gene_id%7Chsapiens_gene_ensembl.default.sequences.ensembl_transcript_id%7Chsapiens_gene_ensembl.default.sequences.gene_exon%7Chsapiens_gene_ensembl.default.sequences.ensembl_exon_id&FILTERS=hsapiens_gene_ensembl.default.filters.source.%22ensembl%22&VISIBLEPANEL=resultspanel>
(this
is a sample query) to get the exon-to-sequence mapping but I would like a
more automated approach. Can someone explain how biomart is able to do it?
It's possible I am interpreting the schema wrong. How does seq_region_id in
the exon table get mapped to seq_region_id in the dna table? I appreciate
any help.


Josh Bradley
Graduate Student
University of Maryland - College Park
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