[Pombelist] Import of the fission yeast revisions from the Broad Institute comparative genome paper into GeneDB

Val Wood val at sanger.ac.uk
Sat Apr 23 16:00:37 BST 2011


The changes reported in PMID:21511999 are visible in GeneDB.

Gene Structure Changes
We have imported 306 of the  gene structure changes. Some reported 
changes were rejected because :
i) The change was already incorporated
ii) The gene is known to be frame-shifted (the correct, albeit gene 
structure is currently represented) the confirmed  frame-shifts  will be 
fixed in the next round of sequence changes.
iii) A different start site was reported, but homology or experimental 
evidence supports the existing coding sequence start site (if this was 
inconclusive I used the Broad start site)
iv) The existing structure was already experimentally supported (in 
these cases alternative transcript features will be created once we move 
to the new PomBase)

Most of the changes are small, alterations to gene structures and 
include mainly:
i) Additional in-frame introns
ii) Use  of an alternative starting methionine
iii) Use of an alternative, but  proximal acceptor  (in these cases it 
is possible that both variants occur, but we have used the new 
experimentally supported one)
iv) A couple of genes were "un-merged"  and one merged.
A small number of changes were larger, and involved additional N or C 
terminal exons, and occasionally gross changes to coding sequence.

As there are a large number of changes it is possible that  your gene(s) 
of interest could be affected.
All of the updated genes are annotated with:
"warning, gene structure updated "PMID:xxxxxxxx" (this will change to  
PMID:21511999 when GeneDB is next updated)
in the "controlled curation" section of the gene page

New Genes
New gene structures have been created for the new genes reported
All new genes identified in this analysis are annotated with:
"warning, new gene PMID:xxxxxxxx" (this will change to  PMID:21511999 
when GeneDB is next updated)
in the "controlled curation" section of the gene page

ncRNAs
All non coding RNAs were imported.
Some are clearly coincident with existing predicted RNAs (However, some 
of the previously annotated RNA's may appear on the incorrect strand as 
they were derived from Affymetrix data),
Over time, these will be assessed and merged where appropriate.

UTRs
The UTRs derived from the Broad data have been used for the consensus 
UTR set,  the precedence for the current annotated consensus set is now :
Individual published sources> PMID:21511999 >PMID:20118936
We hope to make the entire datasets available in the new PomBase.

If you have any questions, please direct them to the new helpdesk, 
helpdesk at pombase.ac.uk, or send your query directly using the curator 
feedback on the GeneDB web page.






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