Worm Breeder's Gazette 11(1): 44

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Does the ama-1 Transcript have an Unusual 5' End?

David Bird and Mark Wilson

Figure 1

[See Figure 1]
Bold sequence is contiguous in the genome (lower case=intron).  The 
open characters show sequence, which, although at the 5' end of the 
message, does not occur within at least 3 kb upstream of ama-1.The 
absence of splice signals suggest that this 29 bp sequence is not an 
ama-1 exon.  
Our initial assumption was that this short extension was a cloning 
artifact.  However, a data base search revealed that these 29 bp are 
identical with residues 951-980 of dpy-13, and encode a helix to non-
helix transition near the carboxyl terminus of this collagen.  Since 
ama-1 and dpy-13 are very close on LGIV (dpy-13 is 11 kb 5' from ama-1)
, we speculate that the ligation of a stretch of RNA from the 
abundantly expressed dpy-13 to the ama-1 transcript occured in vivo, 
although we hesitate to propose a mechanism.  Currently we are using 
primer extension and PCR approaches to assess how common this event 
might be.

Figure 1