Download S. pombe

S. pombe
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Unicellular archiascomycete
Diverged from S. cerevisiae 330- 1144 Ma
Size ~14 Mb, 3 chromosomes
No synteny
Data stored in GeneDB
Areas of interest
Nomenclature
Evolutionary relationships (orthology, paralogy,
protein family and domain)
Functional annotation (Using GO, from literature
curation, functional transfer from orthologs,
inferred electronically from protein
family/domain)
Genetic mapping data (minimal, small amount,
mostly linked to physical sequence data)
Areas of expertise/collaborations
• Literature curation
• Ontology development (GO consortium)
• Ortholog/paralog resolution (and functional
inference)
• Protein family identification (Pfam/Interpro)
• Functional mappings (e.g. Interpro2GO)
• Physical and genetic interactions (GO &
BioGRID consortiums)
• Functional prediction (Daniel Barker)
Dataflow
Links
3
Orthologs
1
Sequence analysis
4
GO curation
User submission
Literature curation
Data mining
GO associations
5
Domain /family
Family identification
2
Sequence and annotation updates
Interpro2Go
6
SPKW2GO
GOA
Biological process
101
494
537
2681
318
124
106
Cellular component
Gene count
Dubious
No GO S. pombe
Molecular function
4990
67
567 11.5%
(c.f. S. cerevisiae 612 10.5%)
GO terms
Gene count 4990
Unassigned 456
Dubious
67
Conserved
57
No GO/Pf/Ort 341
272
484
No orthologs
Of which 74
532
No S. cerevisiae ortholog
3161
41
S. cerevisiae
orthologs
Pfam coverage
S. pombe 75%
c.f.S. cerevisiae 65%
38
27
Pfam families
** Distant ortholog detection
** Submitted to Pfam
** DUF mainly eukaryotic/fungal