[ensembl-dev] RNA Edits

[Michael Schuster]

Dear Trevor,

The basis of all sequences in Ensembl is the genome sequence assembly.  
Exon sequences are just regions read off the genome sequence,  
transcript sequences are concatenations of exon sequences and coding  
sequences are characterised by a start and end exon in the transcript,  
as well as a start and end position in the respective exon.  
Translation sequences are the translation of the coding sequence,  
taking the codon table attribute, which is set for the sequence region  
into account.

We use sequence edits to modify sequences that we read off the genome  
sequence. We can set transcript and translation exceptions, as  
transcript and translation attributes, where the sequence of a gene  
product does not match the genome sequence. This allows us to model  
real biology. As an example, for some human proteins the initiation  
methionine is not paired with an ATG codon. In such a case we can  
override the start codon to translate into a methionine.

Biological RNA editing occurs after the transcription and again we can  
model this by setting transcript exceptions to override regins of the  
sequence.

The sequence edits are tied to a particular sequence region.

In the case you are pointing out, we are reusing these rna_edit  
attributes for small-scale sequence variations between the reference  
assembly and an LRG sequence. Ideally, we would introduce another  
attribute type dna_edit for LRG cases, as it is really the genome  
sequence and not a transcript that gets modified here.

Best regards,
Michael Schuster



On 22 Mar 2012, at 17:54, PATERSON Trevor wrote:

> Hi
>
> Is there any documentation to help me understand what is going on  
> with the 'RNA Edits' that are cached on construction of a  
> SequenceAdaptor in the PerlAPI?
>
> The only doumentation that I can find  about RNA Edits is in an  
> apparently out of date file on the ftp server...
> ftp://ftp.ensembl.org/pub/ensembl/misc-scripts/attribute_types/attrib_type.txt
> which cryptically says for this attribute type:
> # Drosophila. Sometimes sequences have been manually altered to  
> remove one base, and this alters the whole translation
> 145	_rna_edit	rna_edit	RNA edit
> Is there better documentation on the various attribute types  
> somewhere?
> Also
> How are RNA Edits related to LRGs? ( are they LRGs? in humans they  
> are on the same coordinate system...)
> Under what circumstances are sequences retrieved by the  
> SequenceAdaptor 'RNA Editted' according to the cached information?
>
> I am guessing that the RNA Edits are just an edge-case that have  
> been levered in to the schema, I only became aware of them when I  
> started looking into using LRGs.
>
> Thanks
>
> trevor
>
>
> Trevor Paterson PhD
> trevor.paterson at roslin.ed.ac.uk
>
> Bioinformatics
> The Roslin Institute
> Royal (Dick) School of Veterinary Studies
> University of Edinburgh
> Easter Bush
> Midlothian
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> Scotland UK
>
> phone +44 (0)131 651 9157
>
> http://bioinformatics.roslin.ed.ac.uk/
>
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--
Michael Schuster, Ph.D.
Ensembl Genome Browser Project
Vertebrate Genomics Team
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD
United Kingdom

http://www.ensembl.org/