11-10-2018
Quote:
Originally Posted by
Don Cragun
may be classified as "intron",
may be classified as "exon"
may be classified as "splicing"
It certainly helps if one understands what this is all about and since it happens i have a biological researcher at home who explained it to me, here it is (errors/omissions are due to my limited understanding - i was told this is already the kindergarten version of what is really going on):
"exon", short for "expressed region", is a unit of a gene which codes something like a protein. Think of a "gene" as a text of describing something, then the "exon" would be one complete sentence of this text. When DNA is read (so that what it codes is actually produced) it is copied to "RNA"-pieces. This process is called RNA-splicing*) and these pieces contain always several whole such exons.
"intron", short for "intragenetic region" is (more or less meaningless) parts of the DNA between the exons. Think of it as some sort of punctuation and whitespace in the text. It is removed during RNA-splicing so that only the exons make it there.
*) RNA-splicing: the process of producing RNA from DNA works in several steps. First a complete DNA-piece is copied, including the introns. Then the real RNA is made from that ommitting the introns and only leaving the exons. This, in fact, is the "splicing".
In the human genome about 1% is exons (so this in fact makes up for the whole genetic information), about 25% is introns. The rest is intergenetic (that is: between genes and hence completely meaningless).
Thanks to my wife.
bakunin
Last edited by bakunin; 11-10-2018 at 05:05 AM..
This User Gave Thanks to bakunin For This Post:
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LEARN ABOUT DEBIAN
ace::sequence::gene
Ace::Sequence::Gene(3pm) User Contributed Perl Documentation Ace::Sequence::Gene(3pm)
NAME
Ace::Sequence::Gene - Simple "Gene" Object
SYNOPSIS
# open database connection and get an Ace::Object sequence
use Ace::Sequence;
# get a megabase from the middle of chromosome I
$seq = Ace::Sequence->new(-name => 'CHROMOSOME_I,
-db => $db,
-offset => 3_000_000,
-length => 1_000_000);
# get all the genes
@genes = $seq->genes;
# get the exons from the first one
@exons = $genes[0]->exons;
# get the introns
@introns = $genes[0]->introns
# get the CDSs (NOT IMPLEMENTED YET!)
@cds = $genes[0]->cds;
DESCRIPTION
Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds the ability
to retrieve the annotated introns and exons of the gene.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::Gene object directly. Instead, objects will be created in response to a genes() call to
an Ace::Sequence object.
OBJECT METHODS
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:
exons()
@exons = $gene->exons;
Return a list of Ace::Sequence::Feature objects corresponding to annotated exons.
introns()
@introns = $gene->introns;
Return a list of Ace::Sequence::Feature objects corresponding to annotated introns.
cds()
@cds = $gene->cds;
Return a list of Ace::Sequence::Feature objects corresponding to coding sequence. THIS IS NOT YET IMPLEMENTED.
relative()
$relative = $gene->relative;
$gene->relative(1);
This turns on and off relative coordinates. By default, the exons and intron features will be returned in the coordinate system used
by the gene. If relative() is set to a true value, then coordinates will be expressed as relative to the start of the gene. The first
exon will (usually) be 1.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF
AUTHOR
Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1999, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
POD ERRORS
Hey! The above document had some coding errors, which are explained below:
Around line 148:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-02-18 Ace::Sequence::Gene(3pm)