YAR1

UniProt ID: P46683
Organism: Saccharomyces cerevisiae
Review Status: DRAFT
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Gene Description

TODO: Add description for YAR1

Existing Annotations Review

GO Term Evidence Action Reason
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific
IBA
GO_REF:0000033 		REMOVE
Summary: Manual review: DNA-binding transcription activator activity, RNA polymerase II-specific is not sufficiently supported as a direct function of YAR1.
Reason: Removed due weak mechanistic support or likely misannotation for this gene.
GO:0045944 positive regulation of transcription by RNA polymerase II
IBA
GO_REF:0000033 		REMOVE
Summary: Manual review: positive regulation of transcription by RNA polymerase II is not sufficiently supported as a direct function of YAR1.
Reason: Removed due weak mechanistic support or likely misannotation for this gene.
GO:0030907 MBF transcription complex
IBA
GO_REF:0000033 		REMOVE
Summary: Manual review: MBF transcription complex is not sufficiently supported as a direct function of YAR1.
Reason: Removed due weak mechanistic support or likely misannotation for this gene.
GO:0033309 SBF transcription complex
IBA
GO_REF:0000033 		REMOVE
Summary: Manual review: SBF transcription complex is not sufficiently supported as a direct function of YAR1.
Reason: Removed due weak mechanistic support or likely misannotation for this gene.
GO:0005515 protein binding
IPI
PMID:15611164
Genetic and biochemical interactions among Yar1, Ltv1 and Rp... 		MARK AS OVER ANNOTATED
Summary: Manual review: protein binding is too generic or over-extended for YAR1.
Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding
IPI
PMID:37968396
The social and structural architecture of the yeast protein ... 		MARK AS OVER ANNOTATED
Summary: Manual review: protein binding is too generic or over-extended for YAR1.
Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0051082 unfolded protein binding
IDA
PMID:26112308
Co-translational capturing of nascent ribosomal proteins by ... 		MODIFY
Summary: Manual review: unfolded protein binding is better represented by a more specific replacement term for YAR1.
Reason: Modified to align with current curation guidance and improve term specificity.
Proposed replacements: protein carrier chaperone
GO:0005737 cytoplasm
HDA
PMID:14562095
Global analysis of protein localization in budding yeast. 		ACCEPT
Summary: Manual review: cytoplasm is consistent with known biology of YAR1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0000056 ribosomal small subunit export from nucleus
IMP
PMID:22570489
Yar1 protects the ribosomal protein Rps3 from aggregation. 		ACCEPT
Summary: Manual review: ribosomal small subunit export from nucleus is consistent with known biology of YAR1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0000056 ribosomal small subunit export from nucleus
IGI
PMID:22570489
Yar1 protects the ribosomal protein Rps3 from aggregation. 		ACCEPT
Summary: Manual review: ribosomal small subunit export from nucleus is consistent with known biology of YAR1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0005634 nucleus
IDA
PMID:22570489
Yar1 protects the ribosomal protein Rps3 from aggregation. 		ACCEPT
Summary: Manual review: nucleus is consistent with known biology of YAR1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0005634 nucleus
IGI
PMID:22570489
Yar1 protects the ribosomal protein Rps3 from aggregation. 		ACCEPT
Summary: Manual review: nucleus is consistent with known biology of YAR1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0006970 response to osmotic stress
IMP
PMID:15611164
Genetic and biochemical interactions among Yar1, Ltv1 and Rp... 		KEEP AS NON CORE
Summary: Manual review: response to osmotic stress may be context-dependent or peripheral for YAR1.
Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0032880 regulation of protein localization
IMP
PMID:22570489
Yar1 protects the ribosomal protein Rps3 from aggregation. 		ACCEPT
Summary: Manual review: regulation of protein localization is consistent with known biology of YAR1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0032880 regulation of protein localization
IPI
PMID:22570489
Yar1 protects the ribosomal protein Rps3 from aggregation. 		ACCEPT
Summary: Manual review: regulation of protein localization is consistent with known biology of YAR1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0034599 cellular response to oxidative stress
IMP
PMID:15611164
Genetic and biochemical interactions among Yar1, Ltv1 and Rp... 		KEEP AS NON CORE
Summary: Manual review: cellular response to oxidative stress may be context-dependent or peripheral for YAR1.
Reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
GO:0042274 ribosomal small subunit biogenesis
IMP
PMID:15611164
Genetic and biochemical interactions among Yar1, Ltv1 and Rp... 		ACCEPT
Summary: Manual review: ribosomal small subunit biogenesis is consistent with known biology of YAR1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0042274 ribosomal small subunit biogenesis
IGI
PMID:15611164
Genetic and biochemical interactions among Yar1, Ltv1 and Rp... 		ACCEPT
Summary: Manual review: ribosomal small subunit biogenesis is consistent with known biology of YAR1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0051082 unfolded protein binding
IMP
PMID:22570489
Yar1 protects the ribosomal protein Rps3 from aggregation. 		MODIFY
Summary: Manual review: unfolded protein binding is better represented by a more specific replacement term for YAR1.
Reason: Modified to align with current curation guidance and improve term specificity.
Proposed replacements: protein carrier chaperone

References

GO_REF:0000033
Annotation inferences using phylogenetic trees
PMID:14562095
Global analysis of protein localization in budding yeast.
PMID:15611164
Genetic and biochemical interactions among Yar1, Ltv1 and Rps3 define novel links between environmental stress and ribosome biogenesis in Saccharomyces cerevisiae.
PMID:22570489
Yar1 protects the ribosomal protein Rps3 from aggregation.
PMID:26112308
Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones.
PMID:37968396
The social and structural architecture of the yeast protein interactome.

📄 View Raw YAML

 
id: P46683
gene_symbol: YAR1
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: 'TODO: Add description for YAR1'
existing_annotations:
- term:
    id: GO:0001228
    label: DNA-binding transcription activator activity, RNA polymerase II-specific
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Manual review: DNA-binding transcription activator activity, RNA polymerase II-specific is not sufficiently supported as a direct function of YAR1.'
    action: REMOVE
    reason: Removed due weak mechanistic support or likely misannotation for this gene.
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Manual review: positive regulation of transcription by RNA polymerase II is not sufficiently supported as a direct function of YAR1.'
    action: REMOVE
    reason: Removed due weak mechanistic support or likely misannotation for this gene.
- term:
    id: GO:0030907
    label: MBF transcription complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Manual review: MBF transcription complex is not sufficiently supported as a direct function of YAR1.'
    action: REMOVE
    reason: Removed due weak mechanistic support or likely misannotation for this gene.
- term:
    id: GO:0033309
    label: SBF transcription complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Manual review: SBF transcription complex is not sufficiently supported as a direct function of YAR1.'
    action: REMOVE
    reason: Removed due weak mechanistic support or likely misannotation for this gene.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15611164
  review:
    summary: 'Manual review: protein binding is too generic or over-extended for YAR1.'
    action: MARK_AS_OVER_ANNOTATED
    reason: Marked over-annotated because more specific terms capture the biology more accurately.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37968396
  review:
    summary: 'Manual review: protein binding is too generic or over-extended for YAR1.'
    action: MARK_AS_OVER_ANNOTATED
    reason: Marked over-annotated because more specific terms capture the biology more accurately.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:26112308
  review:
    summary: 'Manual review: unfolded protein binding is better represented by a more specific replacement term for YAR1.'
    action: MODIFY
    reason: Modified to align with current curation guidance and improve term specificity.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier chaperone
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: HDA
  original_reference_id: PMID:14562095
  review:
    summary: 'Manual review: cytoplasm is consistent with known biology of YAR1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0000056
    label: ribosomal small subunit export from nucleus
  evidence_type: IMP
  original_reference_id: PMID:22570489
  review:
    summary: 'Manual review: ribosomal small subunit export from nucleus is consistent with known biology of YAR1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0000056
    label: ribosomal small subunit export from nucleus
  evidence_type: IGI
  original_reference_id: PMID:22570489
  review:
    summary: 'Manual review: ribosomal small subunit export from nucleus is consistent with known biology of YAR1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:22570489
  review:
    summary: 'Manual review: nucleus is consistent with known biology of YAR1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IGI
  original_reference_id: PMID:22570489
  review:
    summary: 'Manual review: nucleus is consistent with known biology of YAR1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0006970
    label: response to osmotic stress
  evidence_type: IMP
  original_reference_id: PMID:15611164
  review:
    summary: 'Manual review: response to osmotic stress may be context-dependent or peripheral for YAR1.'
    action: KEEP_AS_NON_CORE
    reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
- term:
    id: GO:0032880
    label: regulation of protein localization
  evidence_type: IMP
  original_reference_id: PMID:22570489
  review:
    summary: 'Manual review: regulation of protein localization is consistent with known biology of YAR1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0032880
    label: regulation of protein localization
  evidence_type: IPI
  original_reference_id: PMID:22570489
  review:
    summary: 'Manual review: regulation of protein localization is consistent with known biology of YAR1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0034599
    label: cellular response to oxidative stress
  evidence_type: IMP
  original_reference_id: PMID:15611164
  review:
    summary: 'Manual review: cellular response to oxidative stress may be context-dependent or peripheral for YAR1.'
    action: KEEP_AS_NON_CORE
    reason: Kept as non-core to preserve potentially valid context-specific annotation without elevating it to core function.
- term:
    id: GO:0042274
    label: ribosomal small subunit biogenesis
  evidence_type: IMP
  original_reference_id: PMID:15611164
  review:
    summary: 'Manual review: ribosomal small subunit biogenesis is consistent with known biology of YAR1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0042274
    label: ribosomal small subunit biogenesis
  evidence_type: IGI
  original_reference_id: PMID:15611164
  review:
    summary: 'Manual review: ribosomal small subunit biogenesis is consistent with known biology of YAR1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IMP
  original_reference_id: PMID:22570489
  review:
    summary: 'Manual review: unfolded protein binding is better represented by a more specific replacement term for YAR1.'
    action: MODIFY
    reason: Modified to align with current curation guidance and improve term specificity.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier chaperone
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: PMID:14562095
  title: Global analysis of protein localization in budding yeast.
  findings: []
- id: PMID:15611164
  title: Genetic and biochemical interactions among Yar1, Ltv1 and Rps3 define novel links between environmental stress and ribosome biogenesis in Saccharomyces cerevisiae.
  findings: []
- id: PMID:22570489
  title: Yar1 protects the ribosomal protein Rps3 from aggregation.
  findings: []
- id: PMID:26112308
  title: Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones.
  findings: []
- id: PMID:37968396
  title: The social and structural architecture of the yeast protein interactome.
  findings: []