Subject: FB Help Mail: 042 Gene data (problem or question)
comments: Hi,
As part of the TreeFam curation process, I looked for a fly
ortholog of APC subunit 13. One is described in PMID: 15060174.
However, its sequence appears to fall in exon 2 of CG6355 in a
different reading frame as that of CG6355 protein. In addition, the
N-terminal of CG6355 protein aligns poorly to orthologs in other
species. Is it possible that fly APC13 has been mistakenly included
in the 5' end of the downstream gene ? Or if the evidence for the
CG6355 structure is strong, is it possible to have another gene
nested in its 5' end ?
Thanks
Jean-Karim
realname: Jean-Karim Heriche
source: FB Help Mail:
Subject: Re: FB Help Mail: 042 Gene data (problem or question)
Dear Jean-Karim,
> As part of the TreeFam curation process, I looked for a fly ortholog
>of APC subunit 13. One is described in PMID: 15060174. However, its sequence
>appears to fall in exon 2 of CG6355 in a different reading frame as that of
>CG6355 protein. In addition, the N-terminal of CG6355 protein aligns poorly
>to orthologs in other species. Is it possible that fly APC13 has been
>mistakenly included in the 5' end of the downstream gene ? Or if the evidence
>for the CG6355 structure is strong, is it possible to have another gene
>nested in its 5' end ?
I think this must be a new gene for FlyBase. It looks like the second
situation you describe is the case: it is encoded within the 5' UTR of CG6355,
which means this transcript is dicistronic. Dicistronics are not particularly
rare, there are approximately 50 such pairs annotated in the genome at the
present time.
Thanks very much for bringing this to our attention. Anapc13 is so small, we
would not have noticed this error by simple inspection of the annotation.
Sincerely,
Lynn Crosby
FlyBase
> Jean-Karim