ARBA00035048 spliceosomal complex (GO:0005681)

View original ARBA rule on UniProt

Type: ARBA
Status: COMPLETE
Action: ACCEPT
Confidence: 0.75

Description

Assigns GO:0005681 (spliceosomal complex) through 19 alternative condition sets, each one or two InterPro entries or CATH FunFams with a taxon. The sets cover spliceosomal cyclophilins, DEAH-box helicases, Sm proteins, snRNP proteins and other splicing factors.

Analysis Summary

Condition-set counts describe the sets recorded in this review, which may omit the full rule.

0
Domain Pairs Analyzed
19
Recorded condition sets
0
Subset Relationships
0
Redundant Annotations

No domain overlap table is shown: the cached overlap analysis for this version of the review is not available. Run just analyze-rule ARBA00035048 and re-render to add it.

Review Summary

All 19 live condition sets were examined. They match 86 reviewed entries in total; 85 carry GO:0005681 or a descendant, 70 by manual evidence. Every set has at least two reviewed matches with a manual annotation to the term or to a more specific spliceosomal complex. The rule is sound for the proteins that can be checked.

Action Rationale

Each set selects proteins curated as spliceosome components, many with experimental evidence. Every set carries a taxon condition. The counts are from Swiss-Prot, which is also what ARBA learns its rules from, so they show the condition sets are coherent rather than giving an independent error rate for unreviewed entries.

GO Annotations

GO:0005681 - spliceosomal complex
Aspect: CC

Annotation Assessments

CORRECT GO_TERM GO:0005681 - spliceosomal complex
Matched proteins: 86; incorrect:
Correct examples: Q9Y3C6, O42643, P14678, Q8IYB3, Q96DI7, O74555

Manual annotations on reviewed matches (QuickGO, retrieved 2026-11-09). Set 1: Q9Y3C6 (PPIL1), GO:0005681, IPI, PMID:30728453. Set 2: O42643 (prp22), GO:0005681, IDA, PMID:24014766. Set 8: Q8IYB3 (SRRM1), GO:0005681, IPI, PMID:39068178. Set 9: P14678 (SNRPB), GO:0005681, IPI, PMID:30728453. Set 14: Q96DI7 (SNRNP40), GO:0005681, IPI, PMID:30728453. Set 18: O74555 (bpb1), GO:0005681, IDA, PMID:24014766. The one reviewed match without the term is Q5NVL7 (Pongo abelii PPWD1, set 1), an orthologue of human PPWD1 (Q96BP3), which carries GO:0005681 IPI, PMID:39068178.

Rule Definition

Condition Sets

Condition Set 1

3 condition(s)
Notes:

UniProtKB release 2026_04: 8 reviewed entries match this set; 7 of them carry GO:0005681 or a descendant, 7 of those by a manual-evidence GO annotation. 346 unreviewed entries match. The reviewed match without the term is Q5NVL7 (Pongo abelii PPWD1).

Condition Set 2

3 condition(s)
Notes:

UniProtKB release 2026_04: 8 reviewed entries match this set; 8 of them carry GO:0005681 or a descendant, 5 of those by a manual-evidence GO annotation. 90 unreviewed entries match.

Condition Set 3

2 condition(s)
Notes:

UniProtKB release 2026_04: 7 reviewed entries match this set; 7 of them carry GO:0005681 or a descendant, 7 of those by a manual-evidence GO annotation. 4368 unreviewed entries match.

Condition Set 4

2 condition(s)
Notes:

UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0005681 or a descendant, 3 of those by a manual-evidence GO annotation. 2210 unreviewed entries match.

Condition Set 5

2 condition(s)
Notes:

UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or a descendant, 4 of those by a manual-evidence GO annotation. 2919 unreviewed entries match.

Condition Set 6

3 condition(s)
Notes:

UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or a descendant, 2 of those by a manual-evidence GO annotation. 150 unreviewed entries match.

Condition Set 7

3 condition(s)
Notes:

UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or a descendant, 4 of those by a manual-evidence GO annotation. 201 unreviewed entries match.

Condition Set 8

2 condition(s)
Notes:

UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or a descendant, 3 of those by a manual-evidence GO annotation. 1762 unreviewed entries match.

Condition Set 9

2 condition(s)
Notes:

UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or a descendant, 2 of those by a manual-evidence GO annotation. 135 unreviewed entries match.

Condition Set 10

2 condition(s)
Notes:

UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or a descendant, 2 of those by a manual-evidence GO annotation. 70 unreviewed entries match.

Condition Set 11

2 condition(s)
Notes:

UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or a descendant, 4 of those by a manual-evidence GO annotation. 524 unreviewed entries match.

Condition Set 12

2 condition(s)
Notes:

UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or a descendant, 2 of those by a manual-evidence GO annotation. 284 unreviewed entries match.

Condition Set 13

2 condition(s)
Notes:

UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or a descendant, 2 of those by a manual-evidence GO annotation. 5 unreviewed entries match.

Condition Set 14

2 condition(s)
Notes:

UniProtKB release 2026_04: 6 reviewed entries match this set; 6 of them carry GO:0005681 or a descendant, 5 of those by a manual-evidence GO annotation. 1819 unreviewed entries match.

Condition Set 15

2 condition(s)
Notes:

UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or a descendant, 2 of those by a manual-evidence GO annotation. 1177 unreviewed entries match.

Condition Set 16

2 condition(s)
Notes:

UniProtKB release 2026_04: 5 reviewed entries match this set; 5 of them carry GO:0005681 or a descendant, 5 of those by a manual-evidence GO annotation. 1634 unreviewed entries match.

Condition Set 17

2 condition(s)
Notes:

UniProtKB release 2026_04: 5 reviewed entries match this set; 5 of them carry GO:0005681 or a descendant, 5 of those by a manual-evidence GO annotation. 514 unreviewed entries match.

Condition Set 18

2 condition(s)
Notes:

UniProtKB release 2026_04: 10 reviewed entries match this set; 10 of them carry GO:0005681 or a descendant, 2 of those by a manual-evidence GO annotation. 1122 unreviewed entries match.

Condition Set 19

2 condition(s)
Notes:

UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or a descendant, 4 of those by a manual-evidence GO annotation. 3901 unreviewed entries match.

Assessments

APPROPRIATE

GO:0005681 is the general spliceosomal complex term. Reviewed matches carry it directly or through more specific descendants such as GO:0071013 (catalytic step 2 spliceosome) and GO:0000243 (commitment complex).

Raw YAML

View Source YAML 
id: ARBA00035048
description: >-
  Assigns GO:0005681 (spliceosomal complex) through 19 alternative condition sets, each one or two
  InterPro entries or CATH FunFams with a taxon. The sets cover spliceosomal cyclophilins, DEAH-box
  helicases, Sm proteins, snRNP proteins and other splicing factors.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00035048
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR002130
      curie: InterPro:IPR002130
      label: Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain
      negated: false
    - condition_type: INTERPRO
      value: IPR044666
      curie: InterPro:IPR044666
      label: Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like
      negated: false
    - condition_type: TAXON
      value: Primates
      curie: NCBITaxon:9443
      label: Primates
      negated: false
    notes: >-
      UniProtKB release 2026_04: 8 reviewed entries match this set; 7 of them carry GO:0005681 or
      a descendant, 7 of those by a manual-evidence GO annotation. 346 unreviewed entries match. The
      reviewed match without the term is Q5NVL7 (Pongo abelii PPWD1).
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR002464
      curie: InterPro:IPR002464
      label: DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site
      negated: false
    - condition_type: INTERPRO
      value: IPR007502
      curie: InterPro:IPR007502
      label: Helicase-associated domain
      negated: false
    - condition_type: TAXON
      value: Taphrinomycotina
      curie: NCBITaxon:451866
      label: Taphrinomycotina
      negated: false
    notes: >-
      UniProtKB release 2026_04: 8 reviewed entries match this set; 8 of them carry GO:0005681 or
      a descendant, 5 of those by a manual-evidence GO annotation. 90 unreviewed entries match.
  - number: 3
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000007
      curie: CATH.FunFam:3.40.50.300:FF:000007
      label: Pre-mRNA-splicing factor ATP-dependent RNA helicase
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: >-
      UniProtKB release 2026_04: 7 reviewed entries match this set; 7 of them carry GO:0005681 or
      a descendant, 7 of those by a manual-evidence GO annotation. 4368 unreviewed entries match.
  - number: 4
    conditions:
    - condition_type: FUNFAM
      value: 1.20.120.1080:FF:000001
      curie: CATH.FunFam:1.20.120.1080:FF:000001
      label: Pre-mRNA-splicing factor ATP-dependent RNA helicase
      negated: false
    - condition_type: TAXON
      value: Dikarya
      curie: NCBITaxon:451864
      label: Dikarya
      negated: false
    notes: >-
      UniProtKB release 2026_04: 3 reviewed entries match this set; 3 of them carry GO:0005681 or
      a descendant, 3 of those by a manual-evidence GO annotation. 2210 unreviewed entries match.
  - number: 5
    conditions:
    - condition_type: FUNFAM
      value: 2.130.10.10:FF:000034
      curie: CATH.FunFam:2.130.10.10:FF:000034
      label: Pre-mRNA-processing factor 17, putative
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or
      a descendant, 4 of those by a manual-evidence GO annotation. 2919 unreviewed entries match.
  - number: 6
    conditions:
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000023
      curie: CATH.FunFam:3.30.70.330:FF:000023
      label: Heterogeneous nuclear ribonucleoprotein q isoform
      negated: false
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000024
      curie: CATH.FunFam:3.30.70.330:FF:000024
      label: Heterogeneous nuclear ribonucleoprotein q isoform
      negated: false
    - condition_type: TAXON
      value: Primates
      curie: NCBITaxon:9443
      label: Primates
      negated: false
    notes: >-
      UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or
      a descendant, 2 of those by a manual-evidence GO annotation. 150 unreviewed entries match.
  - number: 7
    conditions:
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000029
      curie: CATH.FunFam:3.30.70.330:FF:000029
      label: U2 small nuclear ribonucleoprotein B''
      negated: false
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000039
      curie: CATH.FunFam:3.30.70.330:FF:000039
      label: U1 small nuclear ribonucleoprotein A
      negated: false
    - condition_type: TAXON
      value: Euarchontoglires
      curie: NCBITaxon:314146
      label: Euarchontoglires
      negated: false
    notes: >-
      UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or
      a descendant, 4 of those by a manual-evidence GO annotation. 201 unreviewed entries match.
  - number: 8
    conditions:
    - condition_type: FUNFAM
      value: 1.20.1390.10:FF:000002
      curie: CATH.FunFam:1.20.1390.10:FF:000002
      label: Serine/arginine repetitive matrix 1 isoform 2
      negated: false
    - condition_type: TAXON
      value: Metazoa
      curie: NCBITaxon:33208
      label: Metazoa
      negated: false
    notes: >-
      UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or
      a descendant, 3 of those by a manual-evidence GO annotation. 1762 unreviewed entries match.
  - number: 9
    conditions:
    - condition_type: FUNFAM
      value: 2.30.30.100:FF:000004
      curie: CATH.FunFam:2.30.30.100:FF:000004
      label: Small nuclear ribonucleoprotein-associated proteins
      negated: false
    - condition_type: TAXON
      value: Haplorrhini
      curie: NCBITaxon:376913
      label: Haplorrhini
      negated: false
    notes: >-
      UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or
      a descendant, 2 of those by a manual-evidence GO annotation. 135 unreviewed entries match.
  - number: 10
    conditions:
    - condition_type: FUNFAM
      value: 3.30.1560.10:FF:000001
      curie: CATH.FunFam:3.30.1560.10:FF:000001
      label: Protein mago nashi homolog
      negated: false
    - condition_type: TAXON
      value: Catarrhini
      curie: NCBITaxon:9526
      label: Catarrhini
      negated: false
    notes: >-
      UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or
      a descendant, 2 of those by a manual-evidence GO annotation. 70 unreviewed entries match.
  - number: 11
    conditions:
    - condition_type: FUNFAM
      value: 3.30.160.60:FF:000767
      curie: CATH.FunFam:3.30.160.60:FF:000767
      label: WW domain-binding protein 4
      negated: false
    - condition_type: TAXON
      value: Chordata
      curie: NCBITaxon:7711
      label: Chordata
      negated: false
    notes: >-
      UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or
      a descendant, 4 of those by a manual-evidence GO annotation. 524 unreviewed entries match.
  - number: 12
    conditions:
    - condition_type: FUNFAM
      value: 3.30.428.10:FF:000008
      curie: CATH.FunFam:3.30.428.10:FF:000008
      label: CWF19-like 2, cell cycle control
      negated: false
    - condition_type: TAXON
      value: Craniata
      curie: NCBITaxon:89593
      label: Craniata
      negated: false
    notes: >-
      UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or
      a descendant, 2 of those by a manual-evidence GO annotation. 284 unreviewed entries match.
  - number: 13
    conditions:
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000183
      curie: CATH.FunFam:3.30.70.330:FF:000183
      label: R3H domain containing protein
      negated: false
    - condition_type: TAXON
      value: Taphrinomycotina
      curie: NCBITaxon:451866
      label: Taphrinomycotina
      negated: false
    notes: >-
      UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or
      a descendant, 2 of those by a manual-evidence GO annotation. 5 unreviewed entries match.
  - number: 14
    conditions:
    - condition_type: FUNFAM
      value: 2.130.10.10:FF:000229
      curie: CATH.FunFam:2.130.10.10:FF:000229
      label: Small nuclear ribonucleoprotein U5 subunit 40
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 6 reviewed entries match this set; 6 of them carry GO:0005681 or
      a descendant, 5 of those by a manual-evidence GO annotation. 1819 unreviewed entries match.
  - number: 15
    conditions:
    - condition_type: FUNFAM
      value: 2.30.30.100:FF:000018
      curie: CATH.FunFam:2.30.30.100:FF:000018
      label: Small nuclear ribonucleoprotein Sm D2
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 2 reviewed entries match this set; 2 of them carry GO:0005681 or
      a descendant, 2 of those by a manual-evidence GO annotation. 1177 unreviewed entries match.
  - number: 16
    conditions:
    - condition_type: FUNFAM
      value: 2.30.30.100:FF:000069
      curie: CATH.FunFam:2.30.30.100:FF:000069
      label: Small nuclear ribonucleoprotein Sm D2
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 5 reviewed entries match this set; 5 of them carry GO:0005681 or
      a descendant, 5 of those by a manual-evidence GO annotation. 1634 unreviewed entries match.
  - number: 17
    conditions:
    - condition_type: FUNFAM
      value: 2.30.30.100:FF:000133
      curie: CATH.FunFam:2.30.30.100:FF:000133
      label: Small nuclear ribonucleoprotein F
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 5 reviewed entries match this set; 5 of them carry GO:0005681 or
      a descendant, 5 of those by a manual-evidence GO annotation. 514 unreviewed entries match.
  - number: 18
    conditions:
    - condition_type: FUNFAM
      value: 3.30.1370.10:FF:000024
      curie: CATH.FunFam:3.30.1370.10:FF:000024
      label: Branchpoint-bridging protein-like protein
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 10 reviewed entries match this set; 10 of them carry GO:0005681 or
      a descendant, 2 of those by a manual-evidence GO annotation. 1122 unreviewed entries match.
  - number: 19
    conditions:
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000105
      curie: CATH.FunFam:3.30.70.330:FF:000105
      label: HIV Tat-specific factor 1 homolog
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      UniProtKB release 2026_04: 4 reviewed entries match this set; 4 of them carry GO:0005681 or
      a descendant, 4 of those by a manual-evidence GO annotation. 3901 unreviewed entries match.
  go_annotations:
  - go_id: GO:0005681
    go_label: spliceosomal complex
    aspect: CC
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2023-03-22'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 19
review_summary: >-
  All 19 live condition sets were examined. They match 86 reviewed entries in total; 85 carry GO:0005681
  or a descendant, 70 by manual evidence. Every set has at least two reviewed matches with a manual
  annotation to the term or to a more specific spliceosomal complex. The rule is sound for the proteins
  that can be checked.
action: ACCEPT
action_rationale: >-
  Each set selects proteins curated as spliceosome components, many with experimental evidence. Every
  set carries a taxon condition. The counts are from Swiss-Prot, which is also what ARBA learns its
  rules from, so they show the condition sets are coherent rather than giving an independent error
  rate for unreviewed entries.
go_specificity:
  assessment: APPROPRIATE
  notes: >-
    GO:0005681 is the general spliceosomal complex term. Reviewed matches carry it directly or through
    more specific descendants such as GO:0071013 (catalytic step 2 spliceosome) and GO:0000243 (commitment
    complex).
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0005681
  label: spliceosomal complex
  assessment: CORRECT
  matched_protein_count: 86
  correct_examples:
  - Q9Y3C6
  - O42643
  - P14678
  - Q8IYB3
  - Q96DI7
  - O74555
  notes: >-
    Manual annotations on reviewed matches (QuickGO, retrieved 2026-11-09). Set 1: Q9Y3C6 (PPIL1),
    GO:0005681, IPI, PMID:30728453. Set 2: O42643 (prp22), GO:0005681, IDA, PMID:24014766. Set 8:
    Q8IYB3 (SRRM1), GO:0005681, IPI, PMID:39068178. Set 9: P14678 (SNRPB), GO:0005681, IPI, PMID:30728453.
    Set 14: Q96DI7 (SNRNP40), GO:0005681, IPI, PMID:30728453. Set 18: O74555 (bpb1), GO:0005681, IDA,
    PMID:24014766. The one reviewed match without the term is Q5NVL7 (Pongo abelii PPWD1, set 1),
    an orthologue of human PPWD1 (Q96BP3), which carries GO:0005681 IPI, PMID:39068178.
confidence: 0.75
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    With 17 condition sets the rule exceeds recommended limits, analysis is computationally prohibitive,
    and it should be cut to fewer than 12 sets.
  correction: >-
    The number of condition sets is not evidence about whether the annotations are right. All 19 live
    sets were checked against Swiss-Prot.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - >-
    UniProtKB release 2026_04: the 19 sets match 86 reviewed entries, 85 of which carry GO:0005681
    or a descendant.
- date: '2026-11-10'
  withdrawn_claim: >-
    Taxonomic scope is missing: several conditions have no taxonomic restriction and the restrictions
    are inconsistent.
  correction: >-
    Every live condition set has a taxon condition. Restrictions differ between sets because each
    set is a separate alternative for a different protein family.
  error_type: TAXON_MISREAD
  evidence:
  - >-
    UniProt ARBA API, ARBA00035048, modified 2026-07-18, retrieved 2026-11-09: 19 condition sets,
    each with one taxon condition (7 Eukaryota, 12 narrower taxa).
- date: '2026-11-10'
  withdrawn_claim: >-
    Several sets target similar families, which indicates redundancy and a need to consolidate.
  correction: >-
    Sets are alternatives. Two sets for related families do not produce conflicting or wrong annotations,
    since the rule has a single consequent.
  error_type: OTHER
  evidence:
  - 'UniProt ARBA API, ARBA00035048: one annotation, GO:0005681.'
- date: '2026-11-10'
  withdrawn_claim: Statements about the rule were supported by quotations from ARBA00035048.enriched.json.
  correction: >-
    That file is not in the rule folder, so the quotations cannot be checked and are no longer cited.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - >-
    rules/arba/ARBA00035048/ contains the review, its HTML rendering, an analysis summary and a research
    note only.