howe at DARWIN.UCSC.EDU
Wed Nov 15 12:46:55 EST 1995
if your sequence does contain an ORF interrupted by an intron, you're
in luck. In yeast pre-mRNAs, introns are generally located close to
the 5' end of the gene, are usually short (averaging between 250-350nt)
and are flanked by very well conserved consensus sequences
(5'exon:GUAUGU-------UACUAAC---yAG:3'exon, where everything between the
colons are intron sequence and the UACUAAC is the branchpoint sequence
and y=pyrimidine). Of course, there are exceptions to these rules, but
if you can find these signals within your sequence, you're probably
looking at an intron.
As for more detailed information on the structure of interruptd genes
in yeast, check out the following:
Pikielny and Rosbash (1985) Cell 41:119-126
Rymond and Rosbash (1992) The Molecular and Cellular Biology of the
yeast Saccharomyces cerevisiae: Gene expression pp143-192
Ruby and Abelson (1991) Trends in Genetics 7:79-85
Hope this helps.
"The onions expressed here are my own"
On 14 Nov 1995, Dean Danner Lab
> Date: 14 Nov 1995 18:21:01 GMT
> From: Dean Danner Lab <djdlab at bimcore.emory.edu>
> To: yeast at net.bio.net
> Subject: Yeast Introns??
> I have recently cloned a PCR product obtained using yeast genomic DNA
> as the template. The product was produced using degenerate primers,
> designed to match sequences conserved across species in a particular
> protein. Some of the sequence seems to match well with the expected
> translated product, however, the clone does not appear to have a single
> ORF (i.e., when translated in the 3 frames suggested by the assumed
> orientation of the original primers, none of the 3 frames are a complete
> One of the possibilities is that this is, indeed, the gene I'm looking for,
> but it contains at least one intron.
> I don't know much about introns in yeast nuclear genes. Basically I want
> to know how to spot an intron from the primary sequence and where to find
> basic info on yeast nuclear genomic introns and splicing.
> I will post a summary of the best help I have received in response.
> Brett Burkholder
> Emory University
> Genetics and Molecular Medicine
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