Subject:  Re: Symbol change for Ninjurin A
Dear Andrea,
OK! If you like Nij A so much, let's have it. I grant the corresponding
permission for the change of symbol from Nin A to Nij A.
Luis Garcia-Alonso
Instituto de Neurociencias CSIC-UMH
Andrea Page-McCaw wrote:
> Dear Dr. Garcia-Alonso,
> Of your symbol suggestions, I would favor NijA, as it is closer to the
> full length gene name and the vertebrate name.  It avoids the
> double-entendre of NinjA while still being pronouncable.  Is that one
> that you would consider?
> Andrea
Subject:  Ninjurin A symbol
Dear David,
We corresponded a month ago about the name and symbol of Ninjurin A.
In the interim, I have persuaded Luis Garcia-Alonso to change the
symbol of Ninjurin A to NijA (from NinA).  He has sent you an email
about this today to give his permission.  Is this all that is required
for the symbol change?
Thank you for your help.
Best wishes,
Andrea
Subject:  Symbol change for Ninjurin A
Dear Dr. Page-McCaw,
I do not like the suggestion of using NnjA, since NnjB and NnjC will be
unpronounciable. The obvious symbol NinjA, which would match the
vertebrate symbols for Ninj 1 and Ninj 2, has an obvious and cheap
double meaning. On the other hand, NijA sounds similar to NinjA. NirA
seems a reasonable alternative although it is far away from the
vertebrate symbol. I would consider accepting this last abreviation
instead of NinA if you wish.
Sincerely,
Luis Garcia-Alonso
Andrea Page-McCaw wrote:
> Dear Dr. Garcia-Alonso,
>
> I am a new Drosophila investigator and Flybase has suggested that I
> contact you.  I pulled the gene CG6449 out of a yeast two-hybrid
> screen, and we are now writing a manuscript about our work.  Because
> of your Genbank entries, you have naming precedent for both the gene
> name (Ninjurin A) and the symbol (NinA).  I am very happy with this
> gene name but I have a concern about the gene symbol.  Specifically, I
> am concerned that it can be easily confused with the gene NinaA.
>
> I am wondering if you would be willing to change the symbol to NnjA.
> Like NinA, this has the advantage of being a name that can be
> pronounced when spoken ("Ninj-A" or "Ninja"), but it might alleviate
> confusion with NinaA.  I would also be happy to consider other symbol
> names if NnjA does not appeal to you.
>
> If you are agreeable to this, Flybase can change the gene symbol only
> with your express permission.  Would you consider contacting Flybase
> to allow them to make the change?  I have corresponded with David
> Sutherland there ..
>
> If we can resolve this, sooner is better.  According to the references
> listed at Flybase, the gene CG6449 has only been mentioned twice in
> publications, once by its CG number, the other time as "Ninjurin", and
> both were only in passing.  Our publication might be the first study
> of the gene in the literature, and I am obligated to use the
> Flybase-accepted nomenclature.  If we use NinA, changing the name
> after our publication will cause too much confusion (and may not be
> allowed).
>
> I realize that nomenclature issues can be tricky and political, and so
> I would like to emphasize that I happily accept your gene name
> Ninjurin A.  I am just trying to spare the fly world a little
> confusion with the abbreviation.
>
> Thank you for your consideration.
>
> Andrea Page-McCaw, PhD
Wed, 11 Jan 2006  14:58:02  \-0500  ( 19:58  GMT)
Dear David,
Thank you for your reply.  I will try to persuade Garcia-Alonso to
change the NinA name, but we'll see how it goes.
It is ironic that Flybase is sticking to the NinA name but not the
isoform names that Garcia-Alonso used.  I am perfectly happy to switch
to Flybase's A,B,C nomenclature for those, but I think it's really
confusing that A is not alpha, etc.  I recognize that Flybase is not in
the habbit of matching transcript suffixes to previously described
names, but isn't this the kind of nomenclature confusion that Flybase
wants to avoid?  Would it be possible for Flybase to change the names
of the isoforms so they matched Garcia-Alonso's, ie, RA=alpha, RB=beta,
RC=gamma?  Since there are no publications on this topic, confusion
could be avoided by acting now.  (Curating the different symbols,
although helpful, won't make it straightforward for people because of
the inherent confusion of A being gamma not alpha.)
Thanks again for your help,
Andrea
>
Subject:  Re: nomenclature
Dear Andrea,
The 'ninA' symbol and the name 'ninjurin A' were used by
Lara and Garcia-Alonso in GenBank submissions dated Jan 2002:
AJ428205
AJ428206
AJ428207
...  thus establishing precedence for this symbol and name.
I'm afraid we can only change name or symbol if you can persuade
these authors to send us an E.mail agreeing to your proposed
changes.
FlyBase makes no attempt to match the \-RA, \-RB (etc.)
transcript and protein suffixes to previously described
symbols.  However, we can capture alternative symbols
as synonyms.
We will go ahead and curate the alpha, beta and gamma
synonyms for the ninA isoforms.  Then, if you prefer
to use that convention, it will be straightforward
for people to associate your symbols with ours.
gamma = RA, PA
alpha = RB, PB
beta  = RC, PC
(Correct?)
Best,
David Sutherland & Lynn Crosby for FlyBase
Subject:  nomenclature
Dear Flybase,
I am expecting to submit a manuscript soon about CG6449.  I have two
nomenclature questions.
The first is about the Flybase name for this gene, NinjurinA (NinA).
This gene has been reported only twice in the literature, once in
passing when "CG6449" was mentioned as an upstream gene of tna
(Guitierrez et al, 2003); the other time "Ninjurin" was mentioned once
in the text as a gene identified by microarrays (no follow up was
reported; Boutros et al, 2002).  So my first question is, is NinA a
permanent designation for this gene, even though it has never appeared
in the literature?  (I am guessing that the A is to differentiate it
from 2 other Dmel genes that also contain Ninjurin domains, but these
still have CG designations, so the A is confusing.)  I would prefer to
follow the lead of Boutros et al and call it Ninjurin (Ninj).
The second question is about splice form nomenclature.  When we first
started working on this gene years ago, there were 3 splice forms in
genbank \-- alpha, beta, and gamma.  So we have been using that
nomenclature. But now I see the official Flybase nomenclature is A,B,
and C.  But the worst part is that A is not alpha, etc.  Can these two
splice-form nomenclatures be reconciled before I publish, to avoid
confusion?
Thanks for your help.
Andrea Page-McCaw, PhD