Section 3: Gene Annotation
Recent work in genomics has revealed a number of new mechanisms by which
DNA can be transcribed, new ways in which functional products can be
assembled from mRNA transcripts and new ways in which mature RNAs can be
translated into protein. There has been extensive discussion of how best
to define the gene in the light of these phenomena, about the significance
of 'gene counts' under various definitions of the gene and about how
valuable the traditional notion of the gene remains when annotating genomes
for the purposes of contemporary genomics. We aim to compare some of these
ideas to the views of a wide range of working biologists.
To keep the questionnaire short, we are asking each person about only six
of these phenomena. However, if you request the background information
package at the end of the questionnaire, you will receive details on all
: Some of the terms used to describe the following six cases might be unfamiliar to
you or have changed their meaning to accommodate to newly detected complexities of gene
expression. There will be a link to a
at the end of each page of all following
cases, opening in a separate window.
: Some of these phenomena may be unfamiliar to you if they do not occur in the
systems with which you work, but your 'at first glance' response is nevertheless very relevant
and useful to us. Most of the phenomena we mention are now documented in mammalian genomes.
: In the diagrams below italic upper-case letters (
A, B, C...
) are used as theoretically
neutral labels for sections of DNA sequence. If upper-case letters are used to mark part of
a RNA transcript, they refer to the DNA sequence from which that transcript was derived.