[Pombelist] Annotated transcription start and termination sites for fission yeast.
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.
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
and view them in Artemis on your desktop (Artemis can be downloaded for
local use with a single click from here:
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.
More information about the Pombelist