The Case of the Vanishing Intron

Shahram Mori smori at
Fri Nov 11 23:26:38 EST 1994

Thierry Nouspikel (nouspike at wrote:
: Hello netters,

: Can anybody explain the folowing mystery ?

: Background
: =========
: - When studying my favorite gene in a patient, I discovered an aberrant 
:   plicing phenomenon, due to a cryptic acceptor site, 55nt downstream of the 
:   genuine one.
: - When PCRing cDNA in that region of the gene (RT-PCR), I got the expected 
:   290bp band  plus a non-stoichiometric amount of shorter (misspliced) product 
:   235bp long.
: - When PCRing genomic DNA , I got a single 605bp band.
:   Sequencing revealled there was a 315bp intron in it, with a poor acceptor 
:   site, explaining why a cryptic donor site is occasionnaly used.
: No problems so far...

: Puzzling observation
: =================
: I recently repeated this analysis with two new patients. In both cases RT-PCR 
: yielded a 290bp band and a small amount of 235bp misspliced product (as 
: expected).

: BUT with genomic PCR I got:
: - Two bands for patient #1: the expected 605bp band and ~290bp band !!
: - A single short band (~290bp) for patient #2 !!!

: Question
: =======
: Where did the intron go ??????

: Tentative answers
: ===============
: - The intron is absent in one allele of patient #1, and in both alleles of #2.
: BUT, if there is no intron why do I get aberrant splicing in patient #2 ?

:                                             Thierry Nouspikel

If we assume that there is a weak termination sequence present that in
case of patient # 1 is somehow alleviated by the loss of the intron. Maybe the
presence of intron made the the template somehow ustable for the polymerase?
e.g. maybe intron splicing is not ALWAYS the same in everybody and actually is
off by one or 2 nucleotides, releasing the unstability of the Pol on the
Shahram Mori					   _/\_
Program in Molecular Biology			  _\  /_
Dept. of chemistry and Biochemistry Box 3C	  \_  _/
NMSU  Las Cruces NM				    ||

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