Subject: Helping FlyBase: ADRC-10143
Dear Bob,
We are currently curating the abstracts for the upcoming 42nd
(Washington, D.C.) Annual Drosophila Research Conference, for FlyBase.
I am writing in connection with your abstract:
'Drosophila ring finger protein dRoc1a is an essential component of an E3
ubiquitin ligase.'
You mention three genes that are new to FlyBase, Roc1a, Roc1b and
Roc2. Do you know which of the Genome Project CG annotations your
genes correspond to? All the CGs have corresponding gene records in
FlyBase already and we don't like to make duplicate records for what is
actually the same gene unless we can't avoid it. If your genes do not
correspond to CGs then perhaps you could tell me their map location, as
this is valuable information for the genome annotation project.
I am writing to you because the first author does not have an address
in FlyBase \- please feel free to pass my query on if there is someone
better placed to answer it.
Thank you for your help,
with best wishes,
Rachel.
Subject: Re: Helping FlyBase: ADRC-10143
Hi Rachel,
You came to the right place! I can help you out, but it will take a little
bit of explaining because of an error that I made and need to correct in
Genbank.
There is a RING domain protein that is part of the SCF ubiquitin ligase.
This protein goes by various names, including ROC1, RBX, and HRT1. As far
as we can tell, there are three of these genes in fly, and we are calling
them ROC1A, ROC1B, and ROC2 as per our abstract. 1A and 1B are very similar
to each other, and to a vertebrate gene called ROC1. There is also a
vertebrate gene called ROC2 that is most similar to a fly gene we now
therefore call ROC2.
Now the confusing part. Unfortunately, I submitted an entry to Genbank
before we realized that there was three genes. We had two in hand
(pre-genome days) that we original called ROC1 and ROC2, but that we now
call ROC1A and ROC1B, respectively, for the reasons I stated above.
Therefore the Genbank entry for fly ROC2 is what we are now calling ROC1B.
We changed because there was the vertebrate ROC2 gene that is most similar
to the new gene we found after the genome sequence came out. I will amend
the Genbank entry, and I also put a correction note on Gadfly.
Bottom line with respect to your question.
CG16982 is Roc1A
CG16988 is Roc1B, but is currently called ROC2 by Gadfly because of my
Genbank entry that I will correct.
ROC2 has no CG entry yet, probably because it has a huge intron in the
middle of a tiny ORF. We think it's a real gene though.
There is a related RING finger protein that is part of a different E3
ubiquitin ligase called APC11, and this is CG18042 (and the ORF is wrong in
the annotation.)
Sorry for the confusion. I hope this helps, and please be in touch if you
need more information.
Best wishes,
Bob
Bob Duronio
Department of Biology
CB#3280
307 Fordham Hall
S. Columbia Street
University of North Carolina
Chapel Hill, NC 27599