Worm Breeder's Gazette 11(4): 43
These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.
We have been using the 55 kb unc-22 sequence (G. Benian et al,
Nature 342 (1989) 45-50, and this WBG) to test the gm automated DNA
sequence analysis program (WBG Jan. 1990). One of the initial test
runs on the complete sequence predicted ten short exons between
positions 16700 and 22000, which together encoded an amino-acid
sequence containing twitchin-like repeats. Five of these exons were
shown to be true unc-22 exons by PCR sequencing of unc-22 cDNA. At
analysis stringencies similar to those that give good results for the
myosin sequences, gm predicts numerous minor splicing alternatives for
unc-22. A typical 'best' prediction, run in 17 minutes on a
workstation, predicts 15 of the 20 unc-22 exons located 3' of position
15000 correctly, predicts one of the two boundaries of another 2 exons
correctly, and predicts 6 spurious exons.
A spinoff of these tests has been the prediction of several new
genes in the unc-22 sequence. two of which have now been confirmed by
cDNA analysis. The extents and orientations of three genes predicted
in the unc-22 sequence are shown in Fig. 1.
[See Figure 1]
Only the 3' end of the predicted female-specific ('fem-sp') gene is
contained within the unc-22 sequence. The amino acid sequence of this
fragment is highly similar to that of the mouse interleukin-1
precursor (PIR ICMS1); however, more of the sequence is needed to see
whether this is significant. A partial cDNA overlapping this
prediction has been isolated. The predicted 'serine-rich' gene is
embedded entirely within the 7.4 kb intron of unc-22. By using
selected fragments from the first 24 kb of unc-22 as probes against
Northerns, at least two male-specific messages have been detected;
probably one of these messages in encoded by spe-17 (more in the next
WBG). Neither of these messages, however, seems to be from the
predicted serine-rich gene. A number of ORFs over 100 bases in length
contained within the sequence have no known function; one or more of
these may encode male-specific transcripts.
The predicted 'transporter' gene is the best characterized of the
predictions shown in Fig. 1. A partial cDNA overlapping this
prediction has been isolated. An amino-acid sequence derived from the
cDNA data and the gm run is shown in Fig. 2, together with an
alignment with a mammalian glucose transporter protein generated by
fasta (W. Pearson and D. Lipmann, PNAS 85 (1987) 2444-2448). The
predicted protein is also significantly similar to other mammalian
glucose and ion transporters.
[See Figure 2]
The predicted protein has four highly hydrophobic regions, and is
expected from the Garnier rules to be composed primarily of alpha
helix, suggesting that it is an integral membrane protein. We suspect
that this gene encodes a glucose transporter, or a closely related
protein. D. Baillie has located at least three other potential
integral membrane protein genes between unc-22 and dpy-20 (S. Prasad
and D. Baillie, Genomics 5 (1989)185-198), one of which appears to be
the Na+/H+ antiporter gene (this WBG).
