Special Cases

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This page lists special curation issues

Contents

RTE, TE

Decision in August, 2014, to annotate (literature topics, maybe GO) genes of each RTE or TE class that are most representative. E.g., in PMID:24369430 it's reported that DIRS1 RTEs are upregulated in the rrpC mutant. Annotated (literature and in GO extension) are DDB_G0267260 (ORF1), DDB_G0267258 (ORF2 fragment), DDB_G0267338 (ORF3) as representatives of the 3 DIRS1 ORFs. These are among the longest and all in Crick direction. List here all classes with representative genes:

  • DIRS1 / RTE: DDB_G0267260, DDB_G0267258, DDB_G0267338

Actin

Decision on 2/15/2010 to annotate actin when a paper has important information about actin. Annotations are made as literature topics and GO. We'll annotate the 17 identical actins as well as the three actins that are very similar to those. Paste the following line into the Literature tool:

DDB_G0289553
DDB_G0274133
DDB_G0289005
DDB_G0289663
DDB_G0274135
DDB_G0280545
DDB_G0269234
DDB_G0274601
DDB_G0288879
DDB_G0274129
DDB_G0274599
DDB_G0274137
DDB_G0272520
DDB_G0272248
DDB_G0274727
DDB_G0274285
DDB_G0274561
DDB_G0289811
DDB_G0275023
DDB_G0289487

For Protein2GO, there is one UniProt ID for the 17 identical, and 3 IDs for the 3 similar; add annotation to one of the 4 ids, then copy annotation to 3 others, all separated by a comma:
P07830, Q54GX7, Q553U6, P07829

Update 10-MAR-2011

Petra and Bob discussed actin annotations and associating papers to actin genes. Only associate papers to actin if actin itself has been the target of experiments, i.e. not if actin is used as a reference or an analytical tool. However, if authors demonstrate binding of another protein with actin, this should be associated.
Literature and GO annotation is easy in bulk, but strain and phenotype annotations are not. Accordingly, strain and phenotype annotations would need to be submitted to Yulia to add in bulk to all actin genes. But phenotype annotations should be rare.

Update 15-SEP-2011

Literature and GO annotation tools have changed. GO needs to be copied to just 4 UniProt IDs in the GOa tool, as all identical actins are in one entry; Litrature need to paste gene IDs.pf









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