[BioSQL-l] Relationship between Gene CDS and mRNA Seqfeatures

[Nicholas Thrower]

Hello all,

I¹m new to this list so I hope this question hasn¹t been asked before. I
couldn¹t find an archive to search.

I have a biosql schema in oracle loaded with several genbank entries
including TAIR9. I would like some help determining the relationship between
mrna and cds features that belong to a single Gene entry.

My seqfeature table has the following entries.

OID         RANK    DISPLAY_NAME    ENT_OID     TYPE_TRM_OID
SOURCE_TRM_OID
666269  22747   Gene                       643516        626447
626431  
666270  22748   Mrna                       643516        626451
626431  
666271  22749   Mrna                       643516        626451
626431  
666272  22750   Cds                          643516        626455
626431  
666273  22751   Cds                          643516        626455
626431

I¹m trying to correlate CDS to mRNA so that I can display them. All of the
seqfeatures have the same exact locus_tag qualifier and I can¹t find any
other qualifiers noting this relationship. Do I need to make an assumption
based on seqfeature id, or rank in order to determine the relationship
between mRNA and CDS.

Here is an example from TAIR of what this data could look like.
http://arabidopsis.org/servlets/TairObject?id=134549&type=locus

How do I know which CDS and mRNA are paired together?

-Nick