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PomBase curation
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"residue extensions" to review and note "type" #3729

Open ValWood opened 1 month ago

ValWood commented 1 month ago 
          > What do we have annotated as "residue extensions"

I cheated and looked in the GAF file rather than querying Chado. There are 15 annotations with a residue() or modified_residue() extension.

8 of those are protein binding annotations:

PomBase SPAC12B10.10    nod1            GO:0005515      PMID:23966468   IPI     PomBase:SPAC31A2.16     F       medial cortical node Gef2-related protein Nod1            protein taxon:4896      20141023        PomBase residue(957-1101)
PomBase SPAC31A2.16     gef2            GO:0005515      PMID:23966468   IPI     PomBase:SPAC12B10.10    F       RhoGEF Gef2             protein taxon:4896        20131105        PomBase residue(329-419)
PomBase SPAC6F6.16c     tpz1            GO:0005515      PMID:24013504   IPI     PomBase:SPAC19G12.13c   F       shelterin complex subunit Tpz1  SPAC6F6.18c|mug169        protein taxon:4896      20131112        PomBase residue(426-450)
PomBase SPAC6F6.16c     tpz1            GO:0005515      PMID:24013504   IPI     PomBase:SPAC26H5.06     F       shelterin complex subunit Tpz1  SPAC6F6.18c|mug169        protein taxon:4896      20131112        PomBase residue(488-499)
PomBase SPBC27B12.02    mis19           GO:0005515      PMID:24774534   IPI     PomBase:SPCC970.12      F       kinetochore protein Mis19/Eic1  SPBC30B4.10|eic1|kis1     protein taxon:4896      20140605        PomBase residue(4-63)
PomBase SPBC27B12.02    mis19           GO:0005515      PMID:24774534   IPI     PomBase:SPCC1672.10     F       kinetochore protein Mis19/Eic1  SPBC30B4.10|eic1|kis1     protein taxon:4896      20140605        PomBase residue(53-112)
PomBase SPCC74.02c      ppn1            GO:0005515      PMID:33711009   IPI     PomBase:SPBC776.02c     F       mRNA cleavage and polyadenylation specificity factor complex associated protein (PNUTS)           protein taxon:4896      20221007        PomBase residue(506639)
PomBase SPCC74.02c      ppn1            GO:0005515      PMID:33711009   IPI     PomBase:SPAC824.04      F       mRNA cleavage and polyadenylation specificity factor complex associated protein (PNUTS)           protein taxon:4896      20221007        PomBase residue(506639)

Here are the other 7:

PomBase SPAC22E12.09c   krp1            GO:0004252      PMID:9418887    IMP             F       kexin   krp     protein taxon:4896      20111021 PomBase  has_input(PomBase:SPAC22E12.09c),part_of(GO:0016485),residue(S371)
PomBase SPBC428.08c     clr4            GO:0043130      PMID:34524082   EXP             F       histone lysine H3-K9 methyltransferase (Suv39) Clr4               protein taxon:4896      20211108        PomBase residue(243-261)
PomBase SPCC1672.06c    asp1            GO:0016887      PMID:35536002   IDA             F       diphosphoinositol pentakisphosphate kinase/IP8 pyrophosphatase    vip1    protein taxon:4896      20221012        PomBase residue(1-385)
PomBase SPCC1672.06c    asp1            GO:0052723      PMID:35536002   IDA             F       diphosphoinositol pentakisphosphate kinase/IP8 pyrophosphatase    vip1    protein taxon:4896      20221012        PomBase residue(1-385)
PomBase SPCC4B3.15      mid1            GO:0008289      PMID:15572668   EXP             F       anillin-related medial ring protein Mid1        dmf1      protein taxon:4896      20240412        PomBase residue(681-688)
PomBase SPNCRNA.530     sno530          GO:0030563      PMID:37403782   EXP             F       small nucleolar RNA sno530              sncRNA  taxon:4896        20230710        PomBase has_input(PomBase:SPSNRNA.06),modified_residue(A64),part_of(GO:0016180)
PomBase SPSNORNA.25     snoZ30          GO:0030563      PMID:37403782   EXP             F       C/D containing snoRNA Z30       mgU6-47 snoRNA  taxon:4896        20230710        PomBase has_input(PomBase:SPSNRNA.06),modified_residue(A41),part_of(GO:0016180)

Originally posted by @kimrutherford in https://github.com/pombase/pombase-chado/issues/1194#issuecomment-2272198883

ValWood commented 1 month ago

Decide which "types" we want to annotate , and how we will know what they are (should be clear from context) i.e. active site autocleavage site (note that these should all refer to the annotated protein)