Pseudogenes/Sequences with introns

Keith Robison robison at nucleus.harvard.edu
Wed Jan 25 00:15:35 EST 1995


Ram Samudrala (ram at mbisgi.umd.edu) wrote:
: I did a literature search on pseudogenes and from the abstracts all
: the pseudogenes seem to be intron-less.  I am looking for pseudogenes
: that might have arisen out of gene duplication events as opposed to
: retroviral insertion.  (Or does the definition of a pseudogene apply
: only to a retroviral insertion?)

No, there are examples of pseudogenes which contain
intron.  If I remember correctly, Chimpanzee (Pan troglodytes sp?)
triose phosphate isomerase is one example (don't ask why I know this :-)

: Also, how does one find the locations of introns in a DNA sequence?  I
: use entrez primarily to retrieve nucleotide sequences and it's not
: obvious where the exon/intron splicing occurs since it doesn't say!


GOOD LUCK!

The Entrez data model does not explicitly include introns.  The
GenBank flatfile format does, and so Entrez records may import
those features, but people weren't terribly consistent about
annotating them anyway.  You can infer the presence of introns
by looking for multi-part coding regions (CDS in the flatfile,
cd_region in the ASN.1 and probably the report format). 
_It is perfectly legal for an intronless gene to be specified
in segments_, and there are examples, but in general if it
is in segments it has introns.

Starting with Entrez, your best bet is probably to search for
the keyword "exon" and go from there.  Also, pseudo is 
a word which is frequently spelled incorrectly -- try
searching also for psuedo (probably the most common error)
and other single transposition mutants.

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 





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