Occurs in

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Purpose of annotation extensions: See Annotation_Extension

Usage guidelines

What to capture with the occurs_in relation

  • occurs_in is used to specify the cellular component, cell or anatomical structure in which a Molecular Function or a Biological Process take place.
  • Using occurs_in for a Biological Process is restricted to instances where all molecular functions that are part of the process occurs in the same cellular component/cell/anatomical structure. If different steps occur in different compartments/cells/anatomical structures, then one cannot assert that the Biological Process occurs in that compartments/cells/anatomical structure.

What not to capture

To be completed

Scope of use

Domain

Domain refers to the GO terms that can be further specified with the relation.

Range Range describes the types of entities that can be used with the relation.


Usage examples for the occurs_in extension

1. Specifying the cellular location in which a molecular function takes place

Human LIG3 Isoform 1 is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair, PMID:24674627, PMID:10207110.

Annotation for LIG3
Gene product UniProtKB:P23743 LIG3
GP2term relation enables
GO term GO:0003909 DNA ligase activity, occurs in(GO:0005739 mitochondrion)
Evidence IDA
Reference PMID:24674627

2. Specifying the cell type in which a molecular function takes place

Type 4 phosphodiesterase PDE4A is a critical regulator in TCR signaling by attenuating the negative constraint of cAMP, PMID:17404263.

MF Annotation for PDE4A
Gene product UniProtKB:P27815 PDE4A
GP2term relation enables
GO term GO:0004115 3',5'-cyclic-AMP phosphodiesterase activity, occurs in(CL:0000084 T-cell)
Evidence IDA
Reference PMID:17404263
BP Annotation for PDE4A
Gene product UniProtKB:P27815 PDE4A
GP2term relation involved in
GO term GO:0043951 negative regulation of cAMP-mediated signaling, occurs in(CL:0000084 T-cell)
Evidence IDA
Reference PMID:17404263




 TO REVIEW

Enhancing Molecular Function and Biological Process Annotations

Specifying the cell or tissue type in which a process happens

More examples of this usage of occurs_in can be found on the documentation page for Column_16:_Cell_Type

Specifying the subcellular location in which a process happens

1. Protein interaction in a particular location in the cell:

Statement from paper:

Canine cardiac junctional SR vesicles were solubilized with 2% Triton X-100 and loaded on the affinity column equilibrated in EGTA-containing buffer (Fig.1). Calsequestrin-binding proteins were then eluted in buffer containing 20 mm CaCl2, a calcium concentration sufficient to disrupt all calsequestrin protein-binding interactions. Immunoblotting of the eluted fractions with triadin antibody revealed that triadin bound completely to the column and was eluted as a discrete peak in Ca2+-containing buffer (Fig. 1 A, upper)


Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) With (col 8) Annotation Extension (col 16)
P12637 CASQ2 GO:0005515 protein binding PMID:9287354 IPI P82179 TRDN occurs_in(GO:0016529 sarcoplasmic reticulum)

2. Sequestering of calcium ion at a particular location in the cell:

Statement from paper:

To characterize the effects of the new CASQ2 mutations on SR Ca2+ handling in vivo, we performed experiments in adult rat ventricular myocytes infected with adenoviral constructs. Caffeine (10 mmol/L) was applied to myocytes expressing either WT or mutant CASQ2 to evaluate the SR Ca2+-storing capacity by measurement of fluo-3 fluorescence and of Na+/Ca2+ exchange current (INCX; Figure 4A; Table 1).21 Expression of WT increased the SR Ca2+ content by 50%, whereas CASQ2 G112+5X reduced the SR content, not only as compared with WT expression but also as compared with native cells (Ad-control).


Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16)
O14958 CASQ2 GO:0051208 sequestering of calcium ion PMID:16908766 IMP occurs_in(GO:0016529 sarcoplasmic reticulum), occurs_in(CL:0000746 cardiac muscle cell)

Note the use of the comma to create a compound annotation extension. The interpretation of this annotation is CASQ2 is involved in sequestering calcium ions in the sarcoplasmic reticulum of cardiac muscle cell.

Cross-reference to Relations Ontology (RO) term

BFO:0000066 occurs in

Review Status

Last reviewed: 2021-09-29

Back to Annotation_Extension