Occurs in
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.
- BFO:0000007 process, which corresponds to GO Biological Process and Molecular Function
Range
Range describes the types of entities that can be used with the relation.
- GO:0110165 cellular anatomical entity
- Cell Ontology
- Uberon
- EMAPA
- Drosophila Anatomy Ontology (DAO)
- C. elegans gross anatomy ontology
- Plant Trait Ontology
- Xenopus anatomical entity
- Zebrafish anatomy and development ontology
- and many others
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.
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.
--- ===3. 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 |
Cross-reference to Relations Ontology (RO) term
Review Status
Last reviewed: 2021-10-06
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