Subject: EG vs CG: some more...
Hello Michael and all:
Here are some more cases you asked me to check:
1.  EG:34F3.1  \+  EG:34F3.2  > CG12467
Comment: reported by Michael
Takis : These genes are mere predictions. EDGP reported Genefinder
predictions as such; Celera reported (presumambly) Genie ones.
However,  EG:34F3.1  contains motif PS00012 (PHOSPHOPANTETHEINE), whereas
 EG:34F3.2  contains PF00169 (PH domain) and PF00784 (domain in myosin
and kinesin tails). Could the motifs in two genes be connected? (I
don't know)
2. CG11381 \+ CG14624 compared to  EG:BACR42I17.9 
Comment: reported by Michael
Takis : no evidence for either case. EDGP reports the longest gene.
EDGP reports one gene that constitutes the intact Genefinder
prediction. Celera reports two genes, presumambly two different
Genie/Genscan predictions. EDGP also misses one exon at the 5' of the
gene (reported by Celera).
3. CG18166 \+ CG18273 compared to  EG:171D11.6 
Comment: reported by Michael; Takis did the CLUSTAL analysis
Takis : Celera's genes are wrongly reported. EDGP followed the
predictions of Genscan and Genefinder as well as EST matches. Wherever
the two predictions didn't agree, EDGP adapted the longest exon, if was
agreeing with the EST hits. Based on that, the last exons were
discarded, since the EST matches support presence of genes on the other
strand.
Most curiously, gene CG18166 seems to be part of gene CG18273, as it is
shown in the alignment that is attached.
All the best,
t;)
\------------------------------------------------------------------------------
--
CLUSTAL W (1.7) multiple sequence alignment
>..............................................................................
.......
(truncatd part; Celera's genes do not match  EG:171D11.6 
>..............................................................................
.......
CG18166|FBan0018166|CT40990|FB
\----------------------------------------MVRRSQEPEK
CG18273|FBan0018273|CT41446|FB
\--------------------------------------------------
EG_171D11.6
REEQKKRNESESSEKTKAEPKVDHKKKNRDPETAKIQELEDNGKQRQPKL
CG18166|FBan0018166|CT40990|FB
LLEENNSKTVRPLVTRLNYRDANATRLLNVALTHRQRLHLDPDEIEFVLS
CG18273|FBan0018273|CT41446|FB
\----------------LNYRDANATRLLNVALTHRQRLHLDPDEIEFVLS
EG_171D11.6
IDENFRRICKIYIGHSLNYRDANATRLLNVALTHRQRLHLDPDEIEFVLS
CG18166|FBan0018166|CT40990|FB
SYWRQLNTDIEVGDTFASSALDCLEPAIKLILGYKTNEDFLLLLRRLSSQ
CG18273|FBan0018273|CT41446|FB
SYWRQLNTDIEVGDTFSSSALDCLEPAIKLIIGYKTNEDFLLLLHRLSSQ
EG_171D11.6
SYWRQLNTDIEVGDTFSSSALDCLEPAIKLIIGYKTNEDFLLLLHRLSSQ
CG18166|FBan0018166|CT40990|FB
VDMLDVDIKHLISHGGSWQHRQPDCNSTTQ--------------------
CG18273|FBan0018273|CT41446|FB
VEQMARPASQTEHTALQNVLTLLALFAKCSLSSVKGAMLNEHFEVISVSV
EG_171D11.6
VEQMARPASQTEHTALQNVLTLLALFAKCSLSSVKGAMLNEHFEVISVSV
\*: : .: . . :. .
CG18166|FBan0018166|CT40990|FB
\--------------------------------------------------
CG18273|FBan0018273|CT41446|FB
ALRLPEPKDLAYSGHALRLLEAQRNLAGNRTVPLTGESLDCLLSSMLDID
EG_171D11.6
ALRLPEPKDLAYSGHALRLLEAQRNLAGNRTVPLTGESLDCLLSSMLDID
CG18166|FBan0018166|CT40990|FB
\--------------------------------------------------
CG18273|FBan0018273|CT41446|FB
IKHLISHGGSWQQFVDLYSALTDNLIVLLKQHSNLMSDRAAQLSVLCQDL
EG_171D11.6
IKHLISHGGSWQQFVDLYSALTDNLIVLLKQHSNLMSDRAAQLSVLCQDL
CG18166|FBan0018166|CT40990|FB
\--------------------------------------------------
CG18273|FBan0018273|CT41446|FB
IQAVVGYRAERKQTQDISETELDGLADLGLKLATVMATVRATQALAVKRV
EG_171D11.6
IQAVVGYRAERKQTQDISETELDGLADLGLKLATVMATVRATQALAVKRV
CG18166|FBan0018166|CT40990|FB
\--------------------------------------------------
CG18273|FBan0018273|CT41446|FB
APFLLIFTIRQMVATERPTTLFEKIKVHIVRVCHELIGICDHRAGHFILR
EG_171D11.6
APFLLIFTIRQMVATERPTTLFEKVCFTLRERHWPSRSQNSSFAAFRRID
CG18166|FBan0018166|CT40990|FB \-----------------------------------
CG18273|FBan0018273|CT41446|FB SSNEAGARMYEGLVKDHEKYHKFRGKV--------
EG_171D11.6 QRFLFRVKKYMVLYSLRSNNCHFFILCVHVVYIFL
\------------------------------------------------------------------------------
--
Subject: Re: EG vs CG: some more...
Hi All,
In response to Takis mail I only have one thing to add:
>1.  EG:34F3.1  \+  EG:34F3.2  > CG12467
> Comment: reported by Michael
> Takis : These genes are mere predictions. EDGP reported Genefinder
> predictions as such; Celera reported (presumambly) Genie ones.
> However,  EG:34F3.1  contains motif PS00012 (PHOSPHOPANTETHEINE), whereas
>  EG:34F3.2  contains PF00169 (PH domain) and PF00784 (domain in myosin
> and kinesin tails). Could the motifs in two genes be connected? (I
> don't know)
In Swiss-prot there are no known genes that carry all three motifs mentioned
above (apart from TrEMBL entry Q9W5D0 for CG12467!). Myosin proteins can
carry ph domins so I suggest that this region remains annotated as two genes
and CDS feature for CG12467 be split into two potential reading frames.
thanks
Nellie