ARBA00047239 positive regulation of telomere maintenance (GO:0032206)

id: ARBA00047239
description: 'Assigns GO:0032206 positive regulation of telomere maintenance through eight alternative
  condition sets of CATH FunFams, most with a taxon condition: TRF2 (Mammalia), ATM (Eukaryota), tankyrase
  (Primates), MAPK1/MAPK3 (Haplorrhini), T-complex protein 1 subunit eta (Catarrhini), RTEL1, RuvB-like
  helicase (Mus) and SLX4 (Metazoa).'
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00047239
  condition_sets:
  - number: 1
    conditions:
    - condition_type: FUNFAM
      value: 1.10.10.60:FF:000129
      curie: CATH.FUNFAM:1.10.10.60:FF:000129
      label: Telomeric repeat-binding factor 2
      negated: false
    - condition_type: FUNFAM
      value: 1.25.40.210:FF:000002
      curie: CATH.FUNFAM:1.25.40.210:FF:000002
      label: Telomeric repeat-binding factor 2
      negated: false
    - condition_type: TAXON
      value: '40674'
      curie: NCBITaxon:40674
      label: Mammalia
      negated: false
    notes: 'UniProtKB query, November 2026: 2 Swiss-Prot and 206 TrEMBL entries match. QuickGO, GO:0032206
      or a descendant on the Swiss-Prot entries: 2 with experimental evidence, 0 with other manual evidence
      only, 0 with IEA only, 0 with none. Examples: Q15554 (TERF2_HUMAN) GO:0032206 positive regulation
      of telomere maintenance, IDA, PMID:24012755; O35144 (TERF2_MOUSE) GO:0032206 positive regulation
      of telomere maintenance, IDA, PMID:15968270.'
  - number: 2
    conditions:
    - condition_type: FUNFAM
      value: 1.10.1070.11:FF:000011
      curie: CATH.FUNFAM:1.10.1070.11:FF:000011
      label: Serine-protein kinase ATM
      negated: false
    - condition_type: FUNFAM
      value: 3.30.1010.10:FF:000015
      curie: CATH.FUNFAM:3.30.1010.10:FF:000015
      label: Serine-protein kinase ATM
      negated: false
    - condition_type: TAXON
      value: '2759'
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: 'UniProtKB query, November 2026: 3 Swiss-Prot and 858 TrEMBL entries match. QuickGO, GO:0032206
      or a descendant on the Swiss-Prot entries: 2 with experimental evidence, 1 with other manual evidence
      only, 0 with IEA only, 0 with none. Examples: Q13315 (ATM_HUMAN) GO:1904358 positive regulation
      of telomere maintenance via telomere lengthening, IMP, PMID:17694070; Q62388 (ATM_MOUSE) GO:0032212
      positive regulation of telomere maintenance via telomerase, IMP, PMID:26586427.'
  - number: 3
    conditions:
    - condition_type: FUNFAM
      value: 1.10.150.50:FF:000012
      curie: CATH.FUNFAM:1.10.150.50:FF:000012
      label: Poly [ADP-ribose] polymerase
      negated: false
    - condition_type: FUNFAM
      value: 1.25.40.20:FF:000009
      curie: CATH.FUNFAM:1.25.40.20:FF:000009
      label: Poly [ADP-ribose] polymerase
      negated: false
    - condition_type: TAXON
      value: '9443'
      curie: NCBITaxon:9443
      label: Primates
      negated: false
    notes: 'UniProtKB query, November 2026: 2 Swiss-Prot and 134 TrEMBL entries match. QuickGO, GO:0032206
      or a descendant on the Swiss-Prot entries: 2 with experimental evidence, 0 with other manual evidence
      only, 0 with IEA only, 0 with none. Examples: O95271 (TNKS1_HUMAN) GO:0032212 positive regulation
      of telomere maintenance via telomerase, IDA, PMID:12782650; Q9H2K2 (TNKS2_HUMAN) GO:1904355 positive
      regulation of telomere capping, IMP, PMID:25939383.'
  - number: 4
    conditions:
    - condition_type: FUNFAM
      value: 1.10.510.10:FF:000624
      curie: CATH.FUNFAM:1.10.510.10:FF:000624
      label: Mitogen-activated protein kinase
      negated: false
    - condition_type: FUNFAM
      value: 3.30.200.20:FF:000181
      curie: CATH.FUNFAM:3.30.200.20:FF:000181
      label: Mitogen-activated protein kinase
      negated: false
    - condition_type: TAXON
      value: '376913'
      curie: NCBITaxon:376913
      label: Haplorrhini
      negated: false
    notes: 'UniProtKB query, November 2026: 2 Swiss-Prot and 129 TrEMBL entries match. QuickGO, GO:0032206
      or a descendant on the Swiss-Prot entries: 2 with experimental evidence, 0 with other manual evidence
      only, 0 with IEA only, 0 with none. Examples: P27361 (MK03_HUMAN) GO:0032206 positive regulation
      of telomere maintenance, IMP, PMID:21531765; P28482 (MK01_HUMAN) GO:0032206 positive regulation
      of telomere maintenance, IMP, PMID:21531765.'
  - number: 5
    conditions:
    - condition_type: FUNFAM
      value: 1.10.560.10:FF:000017
      curie: CATH.FUNFAM:1.10.560.10:FF:000017
      label: T-complex protein 1 subunit eta
      negated: false
    - condition_type: FUNFAM
      value: 1.10.560.10:FF:000045
      curie: CATH.FUNFAM:1.10.560.10:FF:000045
      label: T-complex protein 1 subunit eta
      negated: false
    - condition_type: TAXON
      value: '9526'
      curie: NCBITaxon:9526
      label: Catarrhini
      negated: false
    notes: 'UniProtKB query, November 2026: 4 Swiss-Prot and 92 TrEMBL entries match. QuickGO, GO:0032206
      or a descendant on the Swiss-Prot entries: 2 with experimental evidence, 0 with other manual evidence
      only, 2 with IEA only, 0 with none. Examples: P78371 (TCPB_HUMAN) GO:0032212 positive regulation
      of telomere maintenance via telomerase, IMP, PMID:25467444; Q99832 (TCPH_HUMAN) GO:0032212 positive
      regulation of telomere maintenance via telomerase, IMP, PMID:25467444.'
  - number: 6
    conditions:
    - condition_type: FUNFAM
      value: 1.20.1160.20:FF:000006
      curie: CATH.FUNFAM:1.20.1160.20:FF:000006
      label: Regulator of telomere elongation helicase 1
      negated: false
    - condition_type: FUNFAM
      value: 1.20.1160.20:FF:000009
      curie: CATH.FUNFAM:1.20.1160.20:FF:000009
      label: Regulator of telomere elongation helicase 1
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000431
      curie: CATH.FUNFAM:3.40.50.300:FF:000431
      label: Regulator of telomere elongation helicase 1
      negated: false
    notes: 'UniProtKB query, November 2026: 6 Swiss-Prot and 313 TrEMBL entries match. QuickGO, GO:0032206
      or a descendant on the Swiss-Prot entries: 2 with experimental evidence, 1 with other manual evidence
      only, 3 with IEA only, 0 with none. Examples: Q9NZ71 (RTEL1_HUMAN) GO:1904355 positive regulation
      of telomere capping, IMP, PMID:23959892; Q0VGM9 (RTEL1_MOUSE) GO:0032206 positive regulation of
      telomere maintenance, IMP, PMID:22579284.'
  - number: 7
    conditions:
    - condition_type: FUNFAM
      value: 1.10.8.60:FF:000010
      curie: CATH.FUNFAM:1.10.8.60:FF:000010
      label: RuvB-like helicase
      negated: false
    - condition_type: TAXON
      value: '10088'
      curie: NCBITaxon:10088
      label: Mus
      negated: false
    notes: 'UniProtKB query, November 2026: 2 Swiss-Prot and 9 TrEMBL entries match. QuickGO, GO:0032206
      or a descendant on the Swiss-Prot entries: 2 with experimental evidence, 0 with other manual evidence
      only, 0 with IEA only, 0 with none. Examples: P60122 (RUVB1_MOUSE) GO:1904507 positive regulation
      of telomere maintenance in response to DNA damage, IMP, PMID:23979016; Q9WTM5 (RUVB2_MOUSE) GO:1904507
      positive regulation of telomere maintenance in response to DNA damage, IMP, PMID:23979016.'
  - number: 8
    conditions:
    - condition_type: FUNFAM
      value: 3.30.710.10:FF:000116
      curie: CATH.FUNFAM:3.30.710.10:FF:000116
      label: SLX4 structure-specific endonuclease subunit
      negated: false
    - condition_type: TAXON
      value: '33208'
      curie: NCBITaxon:33208
      label: Metazoa
      negated: false
    notes: 'UniProtKB query, November 2026: 2 Swiss-Prot and 571 TrEMBL entries match. QuickGO, GO:0032206
      or a descendant on the Swiss-Prot entries: 2 with experimental evidence, 0 with other manual evidence
      only, 0 with IEA only, 0 with none. Examples: Q8IY92 (SLX4_HUMAN) GO:0032206 positive regulation
      of telomere maintenance, IDA, PMID:24012755; Q6P1D7 (SLX4_MOUSE) GO:1904431 positive regulation
      of t-circle formation, IMP, PMID:22579284.'
  go_annotations:
  - go_id: GO:0032206
    go_label: positive regulation of telomere maintenance
    aspect: BP
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2024-08-14'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 8
review_summary: 'All eight live condition sets were examined. In each set the Swiss-Prot matches carry
  GO:0032206 or a descendant with experimental evidence: TERF2 (IDA), ATM (IMP, telomere lengthening),
  TNKS (IDA, via telomerase), MAPK1 and MAPK3 (IMP), CCT subunits (IMP, via telomerase), RTEL1 (IMP),
  mouse RUVBL1 and RUVBL2 (IMP, in response to DNA damage) and SLX4 (IDA). The FunFam conjunctions are
  narrow: each selects two to six Swiss-Prot proteins of a single orthologous group or pair of paralogs.'
action: ACCEPT
action_rationale: Every condition set reproduces a curated experimental annotation on the proteins it
  selects, and no Swiss-Prot match lacks the term. The taxon conditions are narrower than the experimental
  evidence requires in some sets (for example Mus for RuvB-like helicases), which limits coverage but
  does not make the annotation wrong.
literature_support:
  assessment: STRONG
  notes: 'Curated GO annotations (QuickGO, November 2026): Q15554 (TERF2) GO:0032206 IDA PMID:24012755;
    Q13315 (ATM) GO:1904358 IMP PMID:17694070 and PMID:26586427; O95271 (TNKS) GO:0032212 IDA PMID:12782650;
    P28482 (MAPK1) and P27361 (MAPK3) GO:0032206 IMP PMID:21531765; P17987 (TCP1) GO:0032212 IMP PMID:25467444;
    Q8IY92 (SLX4) GO:0032206 IDA PMID:24012755. GO:0032212, GO:1904358 and GO:1904507 are is_a children
    of GO:0032206.'
go_specificity:
  assessment: APPROPRIATE
  notes: The experimental annotations are to GO:0032206 itself (TERF2, MAPK1, MAPK3, SLX4, RTEL1) or to
    its children GO:0032212, GO:1904358 and GO:1904507, so GO:0032206 is the common term across the sets.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0032206
  label: positive regulation of telomere maintenance
  assessment: CORRECT
  correct_examples:
  - Q15554
  - O35144
  - Q13315
  - Q62388
  - O95271
  - Q9H2K2
  - P27361
  - P28482
  - P78371
  - Q99832
  - Q9NZ71
  - Q0VGM9
  - P60122
  - Q9WTM5
  - Q8IY92
  - Q6P1D7
  notes: Per-set receipts are in rule.condition_sets[].notes. Accessions listed are Swiss-Prot matches
    with experimental evidence for GO:0032206 or a descendant in QuickGO.
confidence: 0.8
corrections:
- date: '2026-11-10'
  withdrawn_claim: Condition set 1 mixes the archaeal thermosome (IPR054827, "Thermosome subunit alpha"),
    which does not exist in Primates, with eukaryotic CCT; remove it.
  correction: IPR054827 is the family "TCP-1 chaperonin-like", found on eukaryotic CCT subunits as well
    as archaeal thermosomes. The set is no longer in the live rule.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'InterPro API: IPR054827 name "TCP-1 chaperonin-like", type family'
  - 'UniProtKB query (xref:interpro-IPR054827) AND (reviewed:true) AND (taxonomy_id:2759): 96 entries;
    with taxonomy_id:2157: 37 entries'
  - 'UniProtKB query (xref:interpro-IPR054827) AND (xref:interpro-IPR002194) AND (reviewed:true) AND (organism_id:9606):
    8 entries (CCT subunits)'
- date: '2026-11-10'
  withdrawn_claim: ATM triggers senescence at dysfunctional telomeres, which is negative regulation; the
    ATM set is a broad multifunctional family where membership does not predict telomere function.
  correction: The two-FunFam conjunction matches three Swiss-Prot proteins, all ATM orthologs, and ATM
    has experimental annotation to a child of the rule's term.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - 'UniProtKB query for set 2 with reviewed:true: Q13315 (ATM_HUMAN), ATM_MOUSE, ATM_PIG'
  - Q13315 GO:1904358 positive regulation of telomere maintenance via telomere lengthening, IMP, PMID:17694070
    and PMID:26586427 (BHF-UCL)
  - GO:1904358 is_a GO:0032206 (QuickGO)
- date: '2026-11-10'
  withdrawn_claim: The MAPK set covers the MAPK family (ERK, p38, JNK) with only indirect effects and
    should be removed.
  correction: The mammalian Swiss-Prot matches of the live set are MAPK1 and MAPK3, which are annotated
    to the rule's own term from a mutant phenotype.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - P28482 (MAPK1) GO:0032206 IMP PMID:21531765 (BHF-UCL)
  - P27361 (MAPK3) GO:0032206 IMP PMID:21531765 (BHF-UCL)
  - 'Live set 4: 1.10.510.10:FF:000624 AND 3.30.200.20:FF:000181 AND Haplorrhini; Swiss-Prot matches MK01_HUMAN,
    MK03_HUMAN'
- date: '2026-11-10'
  withdrawn_claim: PARP signatures are broad; add domain architecture constraints to distinguish tankyrases.
  correction: The conjunction already selects only tankyrases.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - 'UniProtKB query (xref:"funfam-1.10.150.50:FF:000012") AND (xref:"funfam-1.25.40.20:FF:000009") AND
    (reviewed:true): TNKS1_HUMAN, TNKS2_HUMAN, TNKS1_MOUSE, TNKS2_MOUSE'
  - O95271 (TNKS) GO:0032212 IDA PMID:12782650 and PMID:18221737
- date: '2026-11-10'
  withdrawn_claim: TRF2 is a protective factor, so the term is mismatched and the set should move to GO:0000723.
  correction: TERF2 carries the rule's term from a direct assay.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - Q15554 (TERF2) GO:0032206 IDA PMID:24012755 (ComplexPortal)
- date: '2026-11-10'
  withdrawn_claim: RuvB-like helicases are general chromatin remodelers and the set should be removed.
  correction: The mouse proteins the set selects are annotated to a child of the rule's term from a mutant
    phenotype.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - RUVB1_MOUSE and RUVB2_MOUSE GO:1904507 positive regulation of telomere maintenance in response to
    DNA damage, IMP, PMID:23979016
  - GO:1904507 is_a GO:0032206 (QuickGO)
- date: '2026-11-10'
  withdrawn_claim: The very low average Jaccard similarity (0.043) between condition sets shows poor biological
    coherence.
  correction: Condition sets are alternatives; that they match different proteins says nothing about whether
    each is correct.
  error_type: OTHER
  evidence:
  - Per-set evidence in rule.condition_sets[].notes