mRNA without main open reading frame?

chai_z at chai_z at
Wed Jun 23 19:39:55 EST 1993

I have recently cloned out an abalone cDNA which was detected by an oligo 
from a lambda gt10 library. After sequenced, the cDNA was found having a 
region with 78.571% homology with the probe (22/28) and a poly(A) tail. 
Unfortunately, the rest of the sequence did not show any good similarity or 
the features of the target gene. What I could not understand was that no main 
open reading frame was found in the sequence (there were too many stop codens),
Based on the cDNA sequence, 3 PCRs were carried out using genomic DNA and 
3 expected sizes of products were amplified. One of the genomic PCR product was
sequenced. The sequence confirmed the reality of the cDNA sequence. But, the
genomic DNA sequence had a 18bp gap and 6 single base replacements when
compared with the cDNA sequence, which made the genomic shorter than its cDNA.

My questions are:

	A. Is it normal to have unfunctional messanger RNA present in vivo?

	B. Is it possible that during the transcription an additional sequence
would be added into the transcript (It's commonly known that splicing deletes
some introns and as a result the RNA is shorter than its gene in that case) ?

	C. Is it possible that the genomic sequence I obtained was a different
gene in the same family of the sequenced cDNA? If so, why did not I pcr out the 
right one or why the pcr did not give me multi-bands (more than 1 species with
various sizes)?

Any comments and ideas are appreciated


Zhonglin Chai
CSIRO, Parkville

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