[Genome] Exon conservation

[Ann Zweig]

Hello Isabelle,

Sorry that you are continuing to have difficulty with this.  Let's try one more 
thing.  Take, for example, this location on human chromosome 1: 
chr1:157,236,032-157,291,851.  In this location, there are 7 Ensembl Genes.

If you load my Session, we can ensure that we are viewing the exact same thing. 
  To load my Session, press the 'Session' link in the top blue navigation bar. 
Then under Load Settings, enter

user: MLQ
session name: ensemblExons

When you follow the link back to the Genome Browser, you will see 5 tracks 
loaded in the latest human browser:

1. A Custom Track made from the exons of the Ensembl Genes.
2. The Ensembl Gene track.
3. The Conservation track (with only mouse and chimp lines displayed).
4. The Mouse Net track.
5. The Chimp Net track.

This particular configuration of the browser will give you an overview of how 
conserved these particular human Ensembl Exons are in the mouse and chimp.  In 
this particular part of chr1, there is good conservation in some of these exons 
and not-so-good conservation in others.

Click on a blue or gray mini-button to the left of a track to read more about 
how the track was crated and what the data mean.

Note that if you hold your mouse over an item in either of the two Net tracks, 
you will see what the orthologous location is in that assembly. In this case, 
this location in human maps to chromosome 1 in both mouse and chimp.

That explains how to visualize the data.  If you do not have a large area to 
review, then this is probably the best method to use.  If, however, you are 
looking at the entire genome, you would probably rather get data in an output 
file.

After you create the Custom Track containing the Exons, you will intersect it 
first with the mouse Net track, then separately, with the chimp Net.  If you are 
having difficulty creating a custom track using the table browser, read this 
User's guide: 
http://genome.cse.ucsc.edu/goldenPath/help/hgTablesHelp.html#CustomTrack

The output you pasted in below looks like part of your exon Custom Track.
 > -----------------------
 > track name="tb_ensGene" description="table browser query on ensGene"
 > visibility=2 url=
 > chrX	119906996	119909329	ENST00000328078	0	+
 > 119907073	119908750	0	1	2333,	0,
 > -----------------------

You will now need to intersect this Custom Track with the mouse Net track.  If 
you need help on intersections, see this page: 
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection

By performing this intersection, you will find those areas in mouse that are 
orthologous to the human Ensembl Gene Exons.

If, after reading this and the two help pages, you still don't understand, 
please feel free to write back to the genome list.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




Isabelle Dupanloup wrote:
> Hello there,
> 
> I'm trying to get some info about exon conservation in mammals (genome
> scale).
> For example, I would like to know if exons annotated by ENSEMBL in the
> human genome are present in the genome of mouse, chimp, etc.
> 
> One of your colleagues (Heather) suggested me to use the table browser
> to generate a custom track that contains exons 
> from gene annotations. Then to use the table browser to intersect the
> exons with the Mouse/Chimp chain (from the conservation track).
> 
> This is what I did (see screen shots attached). But the output does not
> contain anything about exon conservation:
> 
> -----------------------
> track name="tb_ensGene" description="table browser query on ensGene"
> visibility=2 url= 
> chrX	119906996	119909329	ENST00000328078	0	+
> 119907073	119908750	0	1	2333,	0,
> -----------------------
> 
> Could you help me to solve that problem ?
> 
> For me what could be nice is to get orthologous positions of human exons
> in the mouse/chimp genome (if they exist) and an indication of the
> absence of the human exons in the mouse/chimp genome (if they are not
> found in these genomes).
> 
> I hope my msg is clear enough.
> 
> Thank you very much in advance for your help and your great UCSC tool !
> 
> Best, Isabelle
> 
> -------------------
> Isabelle Dupanloup PhD
> Computational and Molecular Population Genetics Group
> Baltzerstrasse 6
> 3012 Bern
> Switzerland
> Tel: +41 31 631 45 49
> Fax: +41 31 631 48 88
> 
> 
> ------------------------------------------------------------------------
> 
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