Annotation Extension Relation:occurs in

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Definition

Identifies the cell, tissue, cellular component or anatomical entity in which the molecular function or biological process occurs.

Child terms

  • None.

Scope of use

Domain

BFO:0000007 ! process (Biological Process or Molecular Function)

Range

ENTITY_UNION:0000006 ! entity

Annotation Extension Usage Examples

Enhancing Molecular Function and Biological Process Annotations

Specifying the cell or tissue type in which a process happens

1. Differentiation of a particular cell type:

Statement from paper:

REN promoted neuronal differentiation of neural committed progenitor cells of CNS (ST14A cells, Fig. 7 A) or PNS (N2a cells, Fig. 7 B) origin.


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.

Using examples (from above) to demonstrate Folding_and_Unfolding using the relationship occurs_in

2. A protein's involvement in changing a particular cell's shape:

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)


Folded/unfolded Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) With (col 8) Annotation Extension (col 16) Parent terms of new folded GO term
Unfolded P12637 CASQ2 GO:0005515 protein binding PMID:9287354 IPI P82179 TRDN occurs_in(GO:0016529 sarcoplasmic reticulum)
Folded P12637 CASQ2 GO:0005515 protein binding PMID:9287354 IPI P82179 TRDN No new GO term created

OWL class expression: GO:0005515 protein binding occurs_in SOME 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).


Folded/unfolded Gene Name (col 2) GO ID (col 5) Reference (col 6) Evidence (col 7) Annotation Extension (col 16) Parent terms of new folded GO term
Unfolded O14958 CASQ2 GO:0051208 sequestering of calcium ion PMID:16908766 IMP occurs_in(GO:0016529 sarcoplasmic reticulum), occurs_in(CL:0000746 cardiac muscle cell)
Folded O14958 CASQ2 New GO term sequestering of calcium ion in sarcoplasmic reticulum PMID:16908766 IMP is_a GO:0016529 sequestering of calcium ion
Folded O14958 CASQ2 New GO term sequestering of calcium ion in cardiac muscle cell PMID:16908766 IMP is_a GO:0016529 sequestering of calcium ion
Folded O14958 CASQ2 New GO term sequestering of calcium ion in sarcoplasmic reticulum of cardiac muscle cell PMID:16908766 IMP is_a GO:0016529 sequestering of calcium ion, is_a New GO term sequestering of calcium ion in sarcoplasmic reticulum, is_a New GO term sequestering of calcium ion in cardiac muscle cell

OWL class expression: GO:0016529 sequestering of calcium ion occurs_in SOME GO:0016529 sarcoplasmic reticulum

OWL class expression: GO:0016529 sequestering of calcium ion occurs_in SOME CL:0000746 cardiac muscle cell

OWL class expression: GO:0016529 sequestering of calcium ion occurs_in SOME ( CL:0000746 GO:0016529 sarcoplasmic reticulum AND part_of SOME cardiac muscle cell



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