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We add the corresponding Evidence code in comment line if the forms have been observed in vitro (ECO:0000181) or in vivo (ECO:0000178).

[Term]
id: PR:000037408
name: transcription factor SPEECHLESS phosphorylated 1 (Arabidopsis thaliana)
def: "A transcription factor SPEECHLESS that has been phosphorylated in several Ser or Thr residues with then MAPK consensus motif Px[ST]P in Arabidopsis thaliana. Example: UniProtKB:Q700C7-1, Ser-193, MOD:00046|Ser-211, MOD:00046|Thr-214, MOD:00047|Ser-219, MOD:00046|Ser-255, MOD:00046." [PRO:LVM, PMID:19008449]
comment: Category=organism-modification. Evidence=(ECO:0000181).
is_a: PR:Q700C7 ! transcription factor SPEECHLESS (Arabidopsis thaliana)
relationship: only_in_taxon NCBITaxon:3702 ! Arabidopsis thaliana

 


As the starting point, the information about PTMs comes from the CC PTM and the FT lines in UniProtKB report. In addition, other useful resources are Phosphosite, Reactome, PUBMED and RLIMS-P (http://pir.georgetown.edu/pirwww/iprolink/rlimsp.shtml).

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Example for organism-specific

[Term]
id: <PR ID>
name: <term name> (organism name)
def: <definition> [<evidence source>]
comment: Category=organism-complex.
xref: <DB if applies>
is_a: <GO complex ID/PR complex ID>
relationship: has_component <PR ID1> {cardinality="<number, optional>"} ! <PR term name 1>
relationship: has_component <PR IDn> {cardinality="<number, optional>"} ! <PR term name n>
relationship: only_in_taxon NCBITaxon:<taxID> ! <organism name>

 

Real Example:

[Term]
id: PR:000026434
name: DNA replication factor C complex (human)
def: "A DNA replication factor C complex whose components are encoded in the genome of human." [PRO:DAN, Reactome:REACT_4881]
comment: Category=organism-complex.
synonym: "RFC heteropentamer (human)" EXACT [Reactome:REACT_4881]

xref: Reactome:REACT_4881

is_a: GO:0005663 ! DNA replication factor C complex
relationship: has_component PR:P35250 {cardinality="1"} ! replication factor C subunit 2 (human)
relationship: has_component PR:P40938 {cardinality="1"} ! replication factor C subunit 3 (human)
relationship: has_component PR:P35249 {cardinality="1"} ! replication factor C subunit 4 (human)
relationship: has_component PR:P35251 {cardinality="1"} ! replication factor C subunit 1 (human)
relationship: has_component PR:P40937 {cardinality="1"} ! replication factor C subunit 5 (human)
relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens

 Species non-specific terms

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