[Pombelist] Annotated transcription start and termination sites for fission yeast.

Val Wood val at sanger.ac.uk
Fri Feb 4 12:08:34 GMT 2011


A set of genome wide transcription start and termination sites manually 
annotated  by  Lantermann et. al in  PMID: 20118936, based on 
transcriptome data from Dutrow et. al.  PMID: 18641648 have been used to 
create 5' and 3'UTR features for the reference genome, for genes with no 
previously annotated transcript from another source.

This increases the number of manually annotated UTRs from
298 to 3605 for 5'
778 to 3693 for 3'

Because it appears that transcription start and end can be  fuzzy,  
these features should be considered as an "indicator" of the likely 
extent of  transcription. We will continue to revise the reference 
transcript set as updates are reported, to represent the longest 
discrete transcript for a region as the consensus.

Data Access
You can access the transcription start and end from individual  GeneDB 
gene pages for genes of interest using the sequence viewers GBrowse or 
Artemis. The links to these 2 browsers are to the right and left of the 
"context map" on the "Location" section of the gene page.
(Artemis tips: Use the "Artemis applet" option selected;  If you are 
interested in a specific gene, reduce the upstream and downstream range 
of   to 1000 before clicking "submit"; the page will take a few seconds 
to render the first time in a session)

You can download this data as part of the complete annotation in the 
"rich EMBL files"  from here
ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/ (the files 
chromosome*.contig)
and view them in Artemis on your desktop (Artemis can be downloaded for 
local use with a single click from here: 
http://www.sanger.ac.uk/resources/software/artemis/)

Hosting Further Transcriptome Datasets
Clearly, as more transcriptome data becomes available the community will 
require access to the different datasets, in addition to the consensus 
transcripts. We intend to provide this in the future  through  the new 
PomBase using the Ensembl viewer.






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