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Locus_genomic_seq and Locus_other_seq

Keith Bradnam krb at sanger.ac.uk
Tue Oct 30 09:38:25 EST 2001

On 30 Oct 2001, Marc Logghe wrote:

> Hi,
> In 'old' scripts I used the Locus tag to get information about the locus
> corresponding to a gene. This tag appeared to be broken in recent releases
> of Acedb. When I looked at the class map I saw two new (?) tags:
> Locus_genomic_seq and Locus_other_seq. Can anybody tell me what the
> difference is between those 2 or show me where to find this information.
> I tried eg F08B6.4a and F08B6.4b and I only get something with
> Locus_other_seq for the b splice variant.

Hu Marc,

The change was made to allow WormBase (the C. elegans genomic database) to
be slightly more clever in how it makes connections between Genes (locus
names) and sequences.

The WormBase database contains sequences of the 3,200 or so clones that
comprise the genome sequence.  It also contains details of a lot of other
sequences that have been submitted to EMBL (e.g. genes sequenced outside
of the genome project).

Because these 'other' sequences often have mapping information or have
been associated with a classical gene we use the 'Locus_genomic_seq' and
'Locus_other_seq' tags to distinguish between the two.  The corresponding
tags in the Locus class are 'Genomic_sequence' and 'Other_sequence'.

E.g. the Locus daf-2 has a connection to the genomic sequence Y55D5A.5
(a predicted gene in the clone 'Y55D5A') but it also has a connection to
the two EMBL sequences 'EMBL:AF012437.1' and 'EMBL:AF012437.2'.

Hope this helps,


~  Keith Bradnam - WormBase group: http://wormbase.sanger.ac.uk/
~  The Sanger Centre, Wellcome Trust Genome Campus
~  Hinxton, Cambridge, CB10 1SA, UK.  Tel (01223) 497516

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