Subject: Trf cluster
I would like to submit the following information regarding 2 genes of the
Trf cluster on the left arm of the 2nd chromosome at polytene band 28DE. An
entry for the Trf gene already exists in Flybase, so the info I am sending
concerns the 2 flanking genes.
The first Trf allele, PlacWTrf, arose in the enhancer-trap screen
carried out in the Jan lab at UCSF in the late 80's, and is characterized by
reporter gene expression in the embryonic CNS and spermatocytes in the adult
testis. Two phenotypes are associated with this mutation: leg-shaking in
ether-anesthetized adults and male-sterility. The 3 genes of the cluster lie
on one side of the transposon insertion, with Trf in the middle. The
insertion site is used as a point of reference for this locus, thus
providing the name Trf-proximal (Trfp) for the gene between the insertion
site and Trf. The gene most distal from the insertion site, Mcr, is named
based on protein sequence similarity.
Trfp:
Transcription of this gene has only been observed in the
spermatocytes of the adult testis. The cDNAs described below were obtained
from a testis library. Transcript is at least 950 nt based on the length of
the longest characterized cDNA, and an open reading frame (ORF) of 252
codons is found reading one strand of the sequence which is significantly
longer than any ORF on the other strand. The hypothetical translation of
this sequence yields an amino acid sequence, referred to as TRFP, with no
similarity to any in the protein databases.
Accession numbers
nucleotide: EMBL y10975
protein: SPTREMBL P91641
Macroglobulin-related protein (Mcr):
Transcribed in spermatocytes and in the embryonic PNS, cDNAs for
this gene have been obtained from both embryo and testis libraries, the
longest of which is 5.1 kb. The transcript detected on an embryo Northern is
8 kb, and the ORF of 1450 codons in the sequence of the longest cDNA extends
to the 5' end of the clone, indicating that there is likely to be more
protein sequence than that available in the characterized cDNAs. The
predicted amino acid sequence, referred to as MRP, is similar to the
mammalian serum proteinase-inhibitor, alpha-2-Macroglobulin, and contains a
complement-type repeat which is found in several of the complement proteins
of the mammalian immune system and the LDL receptor.
Nucleotide accession number: EMBL y11116
Based on the finding of the ORFs described above, both Trfp and Mcr
are transcribed towards the insertion site, while Trf is transcribed away.
Excision of the transposon along with 0.5 kb of flanking chromosomal
sequence is a larval-lethal mutation.
Reference:
Crowley TE, Hoey T, Liu JK, Jan YN, Jan L, Tjian R (1993) Nature  361:557-561 
Thanks,
Tom Crowley
>
Subject: Re: Trf cluster
Hi Tom,
Thanks for the information regarding the Trf cluster of genes.
The information has been curated as a personal communication from yourself
to FlyBase. All genetic and molecular data will be captured and available
in the public files within a few months.
Thanks again for taking the time to provide the data,
Eleanor Whitfield
FlyBase
>
Hi again,
Apologies for the multiple replies, Michael and I were working on your
message in different offices at the same time!
Anyway ....
Trf symbol is in FlyBase and will remain unchanged.
Mcr is the same as alpha-2-Mcr and anon-28DE so these two shall be
merged, but we cannot use Mcr as the gene symbol as it is already being
used for myosin rod protein. Do you have an alternative symbol we can
use?
Trfp is the same as l(2)28DE so the gene will be renamed to Trfp.
Thanks again,
Eleanor Whitfield
FlyBase
>
Subject: Mcr
Dear Eleanor:
Thanks for your response. Since the distal gene of the Trf cluster codes for
a protein with sequence similarity to both macroglobulin and some of the
complement proteins, it could be named: Mcr for Macroglobulin
complement-related. Hopefully this designation isn't already being used, if
it is let me know and we'll try again.
Tom