FlyBase is curating your Nov Development paper (actually I am checking
the curation done before Xmas).
Some ''homology'' questions:
If you can give me more data onall the matches to non-fly genes
ie the organism and the accession number of the matched sequence,
then I could improve the curation.
======
What is HN1 ?
AI124289
DE melanogaster cDNA 5' similar to HN1, mRNA sequence.
======
Is this one of the Ef1alphas ? and not one of those already in FB
AI124295
DE melanogaster cDNA 5' similar to eIF-1A, mRNA sequence.
FB knows of
Ef1α100E
======
1.69 was not in the Table, was this just an oversight ? It is
AI124285
======
What is VAP-33
AI124321
DE melanogaster cDNA 5' similar to VAP-33, mRNA sequence.
======
AI124338
DE melanogaster cDNA 5' similar to E(spl)m7/m8, mRNA sequence.
do you know if this is E(spl) (aka m8) (Genbank X16549, X16550, X16553)
or HLHm7 (Genbank U13069, X16553) ??
======
I cannot find an accession number for clone 1.39, clone 1.62, clone 2.1,
clone 2.40
I attach the annotation FB has now added to these records.
\*a is the FB gene symbol, \*g the accession number, \*d any functional
inference (on new genes only) \*J any structural inference (again on new
genes only), \*j similar genes in other species (on new genes only).
I would be grateful (very) if you could look this over and make sure I
have not made errors. We have given the new genes temporary symbols
anon-* where \* is your clone number.
====================================================================
Best wishes
Michael
Known genes:
\*a sta
\*g AI124333
\#
\*a HmgZ
\*g AI124283
\#
\*a Bsg25A
\*g AI124337
\#
\*a HmgD
\*g AI124252
\#
\*a αTub84B
\*g AI124284
\*g AI124313
\#
\*a E(spl)
\*g AI124338
\#
\*a nmo
\*g AI124322
\#
\*a N
\*g AI124254
\#
\*i EF-1αF
\*g AI124257
\#
\*a Gβ13F
\*g AI124260
\#
\*a Tis11
\*g AI124263
\#
\*a scrt
\*g AI124265
\#
\*a dally
\*g AI124335
\#
\*a Ef2b
\*g AI124274
\#
\*a Ef1α48D
\*g AI124325
\#
\*a HLHmγ
\*g AI124279
\#
\*a fs(1)h
\*g AI124291
\#
\*a Wnt4
\*g AI124296
\#
\*a ttk
\*g AI124297
\#
\*a Crc
\*g AI124298
\*g AI124304
\#
\*a awd
\*g AI124310
\#
\*a stg
\*g AI124307
\#
\*a pnut
\*g AI124305
\#
\*a Hsp83
\*g AI124331
\#
\*a EB1
\*g AI124315
\*g AI124330
\#
\*a RpS3A
\*g AI124312
\#
\*a Cys
\*g AI124316
\#
\*a msi
\*g AI124317
\#
\*a anon-1.1
\*g AI124249
\*d signal sequence receptor β \like
\#
\*a anon-1.11
\*g AI124251
\#
\*a anon-1.13
\*g AI124334
\#
\*a anon-1.14
\*g AI124255
\#
\*a anon-1.16
\*g AI124256
\#
\*a anon-1.18
\*d RNA helicase
\*g AI124258
\#
\*a anon-1.21
\*d pre-mRNA splicing helicase
\*g AI124259
\#
\*a anon-1.24
\*g AI124261
\#
\*a anon-1.25
\*g AI124262
\#
\*a anon-1.29
\*g AI124264
\#
\*a anon-1.3
\*g AI124250
\#
\*a anon-1.32
\*g AI124266
\#
\*a anon-1.34
\*g AI124267
\#
\*a anon-1.35
\*g AI124268
\#
\*a anon-1.37
\*g AI124269
\#
\*a anon-1.38
\*g AI124270
\#
\*a anon-1.39
\#
\*a anon-1.4
\*g AI124251
\#
\*a anon-1.40
\*g AI124271
\#
\*a anon-1.41
\*g AI124272
\#
\*a anon-1.43
\*g AI124273
\#
\*a anon-1.45
\*j species == Saccharomyces cerevisiae; gene == EMP24;  SGDID:L0000549 
\*d transport vesicle membrane protein \?
\*g AI124275
\#
\*a anon-1.46
\*g AI124276
\#
\*a anon-1.47
\*g AI124277
\#
\*a anon-1.48
\*j species == Saccharomyces cerevisiae; gene == SAR1;  SGDID:L0001801 
\*g AI124278
\*d GTP-binding protein \?
\#
\*a anon-1.52
\*g AI124280
\#
\*a anon-1.53
\*g AI124281
\#
\*a anon-1.56
\*g AI124282
\*d ribosomal-protein-S8 \like
\#
\*a anon-1.62
\#
\*a anon-1.66
\*j species == Saccharomyces cerevisiae; gene == CDC47;  SGDID:L0002760 
\*g AI124336
\#
\*a anon-1.69
\*g AI124285
\#
\*a anon-1.72
\*g AI124286
\#
\*a anon-1.74
\*g AI124287
\#
\*a anon-1.75
\*g AI124288
\#
\*a anon-1.76
\*g AI124289
\#
\*a anon-1.78
\*g AI124339
\#
\*a anon-1.79
\*g AI124290
\#
\*a anon-1.80
\*d calponin \?
\*g AI124340
\#
\*a anon-1.82
\*g AI124292
\#
\*a anon-1.83
\*g AI124293
\#
\*a anon-2.1
\#
\*a anon-2.12
\*g AI124299
\#
\*a anon-2.13
\*g AI124300
\#
\*a anon-2.14
\*g AI124301
\#
\*a anon-2.15
\*F methionine--tRNA ligase == EC 6.1.1.10 \?
\*g AI124302
\#
\*a anon-2.16
\*g AI124303
\#
\*a anon-2.19
\*g AI124306
\#
\*a anon-2.2
\*g AI124294
\#
\*a anon-2.23
\*g AI124308
\#
\*a anon-2.24
\*g AI124309
\*d cyclin \?
\#
\*a anon-2.28
\*g AI124311
\#
\*a anon-2.3
\*g AI124295
\#
\*a anon-2.31
\*g AI124314
\#
\*a anon-2.38
\*g AI124318
\#
\*a anon-2.39
\*g AI124319
\#
\*a anon-2.40
\#
\*a anon-2.41
\*g AI124320
\#
\*a anon-2.42
\*g AI124321
\#
\*a anon-2.44
\*g AI124323
\#
\*a anon-2.45
\*g AI124324
\#
\*a anon-2.47
\*g AI124326
\#
\*a anon-2.48
\*g AI124327
\*J Zinc finger protein.
\#
\*a anon-2.49
\*g AI124328
\#
\*a anon-2.51
\*g AI124329
\#
\*a anon-2.54
\*g AI124332
\#
>
Dear Michael,
	I have three large folders with a section on each one of these
homologies.  Each section contains BLAST results, some medline abstracts,
and a copy of at least one relevant paper.  Is this information of any use
to flybase?
	 Also, please note that in Table 2, those genes given in italics
are neither homologous to nor like the named Drosophila gene, they are
identical to the named Drosophila gene (the DNA sequence match is
perfect).
 	 In reply to your questions:
1. HN-1 is a mouse gene mapped to chromosome 11.  It is expressed at
highest levels in hemopoietic and brain tissues.  The numbers associated
with this sequence on the NCBI blast search are gi 1864165 or U90123.  The
paper describing HN1 is Tang et al (1997) Mammalian Genome 8, 165.  (We
did not note matches to other ESTs for which there was no biologically
useful data.  This clone is one of the most marginally informative
homologies that we noted.)
2. eIF 1A is a translation initiation factor.  It used to be called
eIF-4C.  There is no flybase entry for this gene.  I think the Ef1alphas
you refer to are translation elongation factors. (Fly base is using the
old nomenclature, and still and calls the initiation factors it has
entries for eIF-4B etc.  Probably they should give both current and old
names for all of these from now on.  Your having the same problem I had:
too many proteins with similar names.)  Using BLAST we got matches to
genes in Eukaryotes and Prokaryotes and Phage, but not in Drosophila.  The
numbers associated with the human homologue are gi 306725 or L18960 or sp
P47813.  The numbers associated with the S. cerevisiae homologue are
Accession # 729814 or gi 533534 or sp P38912.  A paper describing the
Yeast protein is Wei et al (1995) J. Biol. Chem. 270, 22788-22794.
3. Clone 1.69 is actually one of the ribosomal RNAs.  Two clones of the 99
clones that we performed in situs on gave no expression above background.
Cone 1.69 was one of these clones.  By chance, the probe was the correct
strand to hybridize with the endogenous RNA, but we got no signal.  I
guess that the fast majority of the RNA is too crosslinked to the ribosome
to be accessible.  Since this is a technical artifact, I would prefer that
you omit this ''result''  from Flybase.  In the Table legend, we did note
that two clones which gave no detectable expression were not included in
the Table.
4. VAP-33 is a VAMP binding protein from aplysia that is required for
Neurotransmitter release.  (VAMP is an integral membrane protein that is
something to do with synaptic vesicle fusion.) VAP-33Us numbers are:
Accession 136258 or g1362584.  A reference is Skehel et al (1995) Science
269 1580-1583.  There is also a S. cerevisiae homologue (Accession 731508
or sp P40075)  that is a suppressor of a choline sensitive mutant.
5. Clone 1.71 is E(spl) m7/m8 - aka m8 - Genbank X19553, not the other
gene you mentioned.
6. The four clones without accession numbers did not give readable DNA
sequence.  Unfortunately, we never got the time to go back and redo these,
so it is possible that we are missing a couple of homologies from our
table.
	I have looked at the data you sent.  I have only one correction
anon 1.11   The accession number is wrong it should be AI124253, not
AI124251
Thanks for the time you have taken
Mark
>
Subject: Re: Help FlyBase please
Dear Michael,
I have tried to give you as many Swiss Prot numbers as possible. These are
sp numbers.  I am not sure what data bases the other numbers are from.
All are protein sequences except for clone 1.56, which are DNA sequences.
1.1 Signal sequence receptor beta. There are many matches.  Here are 3.
sp P23438  Canis f.  Signal sequence receptor beta
sp P43308  Human Signal sequence receptor beta
gi 1086874  C. elegans cDNA yk67f10.3
1.18 	RNA helicase. There are many matches.  Here are 3.
sp P53131 Yeast putative ATP dependent helicase
sp P24384 Yeast pre mRNA splicing factor
gi 2407195 (AF017153) M. musculus putative ATP dependent helicase
1.21	premRNA splicing helicase
sp P32639 Yeast pre mRNA splicing helicase BRR2
1.45	Emp24 Protein transport
gi 1223892 (U418805) putative T1/ST2 receptor
sp P49020  Cricetulus griseus COP coated vesicle membrane protein P24
gi 2275635 (AF014940) C. elegans ho,ologue of EMP24/GP25L
1.48 SAR-1 G protein. There are many matches.  Here are 3.
sp P36536 Mouse SARA GTP binding
sp P20606 Yeast SAR1 GTP binding
sp O01474 or Q01474 Arabidopsis
1.56 ribosomal protein S8. There are many matches.  Here are 3.  These are
DNA sequences.
emb X73829 MMRPS8  M. musculus
gb U40799 CELF42C5 C. elegans cosmid
emb X67247 HSRPS8  Human
1.66	CDC47/MCM2.    There are many matches.  Here are 4
sp P33993  Human DNA replication licensing factor
sp P38132  Yeast cell division control protein
gi 1469526  XMCM7
pir JC4580   mouse cell division protein
1.76	HNI
gi 1864165 or U90123  mouse
1.80	Calponin.    There are many matches.  Here are 4
sp P51911  Human Calponin H1
sp O08092  Pig Calponin H1
sp O08091  Mouse Calponin H1
sp O08090  Rat Calponin H1
2.3 eIF 1A translation initiation factor (AKA eIF-4C). There are many
matches.  Here are 3.
sp P47813 Human eIF 1A
sp P38912 S. cerevisiae eIF 1A
sp P47815 Wheat eIF 1A
2.15	Met t-RNA synthetase. There are many matches.  Here are 3.
sp P00958  Yeast Met tRNA synthetase
sp P00959  E. coli Met tRNA synthetase
pir JC5224  Human methionine tRNA ligase
2.24 	cyclin G2
gi 2228813 (AF005885) cyclin G2 M. musculus
sp P51959  Human G2/mitotic specific cyclin G1
sp P39950  Rat G2/mitotic specific cyclin G1
2.33 and 2.52   EB1. There are many matches.  Here are 3.
pir I52726  Human EB1
gi 1256434 (U51196)  M. musculus EB1 homologue
sp P40013 Yeast 38.4 KD hypothetical protein
2.42	VAP-33
pir A57245  VAP-33
sp P40075 S. cerevisiae
gi 2394471 (AF024499) C. elegans homologue VAP-33
2.48 	A zinc finger. There are many matches.  Here are 3.
sp P51523  Human zinc finger
sp P17141  Mouse zinc finger ZFP-37
sp P18727  Xenopus gastrula zinc finger protein XLCGF26
Thanks again
Mark