Gene or accession: CG5462
Missed gene
Comments: The CG5462 gene corresponds to the scibble gene described by Bilder
and Perrimon and to the vartul gene that we have independently isolated.
Bilder and Perrimon has identified a single transcript of 6.0 kb in size that
they have submitted to GenBank/EMBL/NCBI whereas our studies showed that this
gene encodes 3 transcripts of 7.2, 6.0 and 4.5 kb in size, respectively. The
7.2 (AC: AJ252084) and 6.0 transcripts differ by the length of their 3'UTR and
are made of 23 exons distributed over 53-kb genomic DNA. The Celera genomic
sequence is larger because it contains a Jocker repetitive element which is
missing in the genomic DNA sequence that we have analyzed. The 4.6 kb
transcript (AC: AJ271647) consists of 14 exons whose first 13 exons are
identical with those of the largest 7.2 and 6.0 kb transcripts. The largest
cDNAs contain an open reading frame of 5268 (without the termination codon)
encoding a protein of 1756 amino acids in length with an estimated molecular
mass!
of 190.382. This protein is designated as Vartul1. The alternatively spliced
4.6 kb mRNA encodes the Vartul2 protein containing 1247 amino acids with an
estimated molecular mass of 136.436. Both Vartul1 and Vartul2 share identical
sequence over the first 1143 amino acids but differ by their C-extremity. Both
proteins are recognised by affinity-purified antibodies raised against an
N-terminal synthetic peptide and display a size of ~220K and ~140k on Western
blots of Drosophila protein extracts. The N-terminal domain of both proteins
contains 16 contiguous LRRs with a repeating 23-residue consensus sequence.
Four PDZ domains are present in Vartul1 whereas only the first two PDZ domains
are including in Vartul2. The highest sequence identity of Vartul1 is to the
putative human protein KIAA0147 (AC: D63481).
The following ESTs belongs to Vartul transcripts (7.2, 6.0, and 4.6-kb
transcripts): LD28165,LD11253,LD43114,LD43989,LD15830,LD16092,LD13923,
GH23755,and GH27616 (we have not sequenced these ESTs. GM12994, SD05339,
LD37377, and CK00392 belong to the 7.2 and 6.0-kb class of transcripts (we
have not sequences the 3' end of these ESTs). However we have sequenced
completely LD26440, LD22510 and LD32992. These three ESTs belong to the 6.0-kb
class of transcript with a short 3'UTR. The EST SD05630 3' sequence
corresponds to the 3' end of the 7.2-kb transcript. The ESTs LD15830 and
GM13360 belong to the 4.5-kb alternatively spliced transcript (we have
completely sequences LD15830).
For determining the exon-intron borders, I have aligned the three size-classes
of transcripts with the Celera genomic sequences deposited in Dec. 1999
(AC013024 and AC012994) but have not yet made the alignment with the new
contig. Theere are some sequence divergences reflecting the different
libraries that we have used. Most of the divergences reflect silent
substitution or lead to conservative amino acid substitution.