id: Q93833
gene_symbol: che-13
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: >-
  CHE-13 is the Caenorhabditis elegans ortholog of human IFT57 (also called HIPPI;
  Chlamydomonas IFT57) and is a structural subunit of the intraflagellar transport
  complex B (IFT-B). Intraflagellar transport is the bidirectional, microtubule-motor-driven
  movement of large multiprotein particles that build and maintain cilia: kinesin-2 motors
  carry IFT-B particles and their ciliary-precursor cargo anterogradely from the ciliary
  base to the tip, and cytoplasmic dynein-2 returns them retrogradely. CHE-13/IFT57 is
  itself a component (and moving cargo) of the IFT-B particle rather than an enzyme; it
  has no known catalytic activity and contributes to assembly and integrity of the IFT-B
  complex, in part through a C-terminal coiled-coil. In C. elegans, che-13 is expressed in
  ciliated sensory neurons under control of the RFX transcription factor DAF-19, and the
  protein concentrates at the ciliary base (basal body, transition zone) and moves along
  the sensory (non-motile) ciliary axoneme, as expected for an IFT protein. CHE-13 is
  required to build the ciliary axoneme: loss-of-function mutants retain normal transition
  zones but have severely truncated axonemes with ectopically assembled doublet
  microtubules, and they mislocalize other IFT-B proteins such as OSM-5 and OSM-6. Because
  the 60 ciliated sensory neurons mediate chemosensation, osmotic avoidance and
  dauer-pathway signaling, che-13 mutants are broadly defective in these sensory behaviors
  as a downstream consequence of lacking functional cilia, and are dye-filling defective.
  IFT57 is conserved from algae to humans, and the IFT pathway it serves is central to the
  biology of ciliopathies.
alternative_products:
- name: a
  id: Q93833-1
- name: b
  id: Q93833-2
  sequence_note: VSP_043944, VSP_043945
references:
- id: GO_REF:0000015
  title: Use of the ND evidence code for Gene Ontology (GO) terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: PMID:12651157
  title: Identification of CHE-13, a novel intraflagellar transport protein required
    for cilia formation.
  findings:
  - statement: CHE-13 (F59C6.7) is required for cilia assembly and its function is
      disrupted in che-13 ciliogenic mutants; fluorescent-tagged CHE-13 concentrates at
      the ciliary base and moves along the axoneme like an IFT protein, and loss of che-13
      mislocalizes the IFT-B proteins OSM-5 and OSM-6, placing CHE-13 in IFT complex B.
    supporting_text: loss of che-13 differentially affects the localization of two known
      IFT complex B proteins, OSM-5 and OSM-6, implying that CHE-13 functions as part of
      this complex.
  - statement: che-13 expression is controlled by the RFX transcription factor DAF-19,
      like other IFT-B genes.
    supporting_text: expression of che-13 (F59C6.7/9) is regulated by the RFX-type
      transcription factor DAF-19
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Haycraft et al. 2003 (Exp Cell Res); abstract-only in cache. The
      defining che-13 cloning/characterization paper. Source of IFT-B membership, ciliary
      base/axoneme localization, DAF-19-dependent expression, the anterograde/retrograde
      IEP annotations and the OSM-5/OSM-6 mislocalization (protein-localization) evidence.
- id: PMID:16957054
  title: Caenorhabditis elegans DYF-2, an orthologue of human WDR19, is a component
    of the intraflagellar transport machinery in sensory cilia.
  findings:
  - statement: Study of the IFT machinery in which che-13 mutant analysis contributed to
      the WormBase IMP that che-13 is required for proper localization of IFT proteins.
    supporting_text: The intraflagellar transport (IFT) machinery required to build
      functional cilia consists of a multisubunit complex
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Efimenko et al. 2006; abstract-only. Primarily a DYF-2/WDR19 paper that
      does not foreground che-13; it is the GOA reference for the che-13(WBVar00144317) IMP
      to intracellular protein localization. Not overruled (curator full-text evidence).
- id: PMID:17314406
  title: 'Sensory ciliogenesis in Caenorhabditis elegans: assignment of IFT components
    into distinct modules based on transport and phenotypic profiles.'
  findings:
  - statement: The C. elegans IFT machinery is organized into modules, including an IFT
      subcomplex B module to which che-13 belongs, based on in vivo transport and
      phenotypic profiles.
    supporting_text: the C. elegans IFT machinery has a modular design, consisting of
      modules IFT-subcomplex A, IFT-subcomplex B, and a BBS protein complex
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Ou et al. 2007 (Mol Biol Cell); abstract-only. Source of the IDA IFT
      particle B membership annotation for che-13.
- id: PMID:1732156
  title: Genetic analysis of chemosensory control of dauer formation in Caenorhabditis
    elegans.
  findings:
  - statement: che-13 is among the cilium-structure genes whose mutation causes
      structurally defective chemosensory cilia, placing it at a single step in the
      dauer-formation epistasis pathway.
    supporting_text: Dauer-defective mutations in nine genes cause structurally defective
      chemosensory cilia, thereby blocking chemosensation.
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Vowels & Thomas 1992; abstract-only. Basis for the che-13 cilium-assembly
      IGI as a genetic requirement for functional chemosensory cilia in the dauer pathway.
- id: PMID:18337471
  title: Functional redundancy of the B9 proteins and nephrocystins in Caenorhabditis
    elegans ciliogenesis.
  findings:
  - statement: Study of B9/nephrocystin ciliogenesis in which che-13 was used as an
      IFT/ciliary reference; source of a WormBase axoneme IDA for che-13.
    supporting_text: the C. elegans B9 proteins form a complex that localizes to the base
      of cilia
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Williams et al. 2008; abstract-only. Primarily a B9/nephrocystin paper
      that does not foreground che-13; it is the GOA reference for one of the che-13
      axoneme IDA annotations. Not overruled (curator full-text evidence).
- id: PMID:22922713
  title: The BBSome controls IFT assembly and turnaround in cilia.
  findings:
  - statement: Establishes that the IFT particle (including IFT-B) is assembled at the
      ciliary base before entering the cilium; used here as the MGI reference for che-13
      ciliary basal body localization.
    supporting_text: the BBSome (refs 3, 4), a group of conserved proteins affected in
      human Bardet-Biedl syndrome
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Wei et al. 2012 (Nat Cell Biol); full text available. The paper is about
      DYF-2 and the BBSome and does not name che-13; it is the MGI reference for the che-13
      ciliary basal body IDA. Basal-body localization is independently established for
      che-13 (concentrates at the ciliary base, PMID:12651157), so the annotation is not
      overruled.
- id: PMID:2428682
  title: Mutant sensory cilia in the nematode Caenorhabditis elegans.
  findings:
  - statement: che-13(e1805) mutants have normal ciliary transition zones but severely
      shortened axonemes with ectopic doublet microtubules, establishing CHE-13 as
      required for axoneme (cilium) assembly rather than transition-zone formation, and
      they are dye-filling / chemosensory defective.
    supporting_text: The cilia in che-13 (e1805), osm-1 (p808), osm-5 (p813), and osm-6
      (p811) mutants have normal transition zones and severely shortened axonemes.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Perkins et al. 1986 (Dev Biol); abstract-only. Foundational
      ultrastructural characterization of the che-13 ciliary phenotype and its
      dye-filling/chemosensory defects.
- id: PMID:28479320
  title: Dynein-Driven Retrograde Intraflagellar Transport Is Triphasic in C. elegans
    Sensory Cilia.
  findings:
  - statement: Ciliary entry of dynein-2 requires an intact IFT-B complex (of which
      CHE-13 is a component); this study is the ComplexPortal source (CPX-1290) for
      che-13 IFT-B/IFT particle B membership, intraciliary transport, cilium assembly
      and ciliary localization.
    supporting_text: Disruption of the dynein-2 tail domain, light intermediate chain,
      or intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary
      localization
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Yi et al. 2017 (Curr Biol); abstract-only. Identifies che-13 in IFT
      complex B by mass spectrometry (UniProt SUBUNIT) and underlies the ComplexPortal NAS
      annotations for IFT particle B membership, intraciliary transport, cilium assembly
      and cilium.
existing_annotations:
- term:
    id: GO:0030992
    label: intraciliary transport particle B
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: part_of
  review:
    summary: CHE-13/IFT57 is a structural subunit of the IFT-B particle; this is the single
      most important annotation for the gene, supported by orthology to IFT57 and by
      ComplexPortal (CPX-1290).
    action: ACCEPT
    reason: Core molecular role. CHE-13 is the C. elegans IFT57 ortholog and a member of
      Intraflagellar transport complex B; phylogenetic inference agrees with the direct
      C. elegans data.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: loss of che-13 differentially affects the localization of two known
        IFT complex B proteins, OSM-5 and OSM-6, implying that CHE-13 functions as part of
        this complex.
- term:
    id: GO:0042073
    label: intraciliary transport
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: As an IFT-B subunit and moving IFT cargo, CHE-13 is directly involved in
      intraciliary transport.
    action: ACCEPT
    reason: Core biological process. Fluorescent CHE-13 moves along the axoneme as an IFT
      protein and is part of the transported IFT-B particle.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0005929
    label: cilium
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: CHE-13 localizes to and functions within the cilium; phylogenetic inference
      agrees with direct C. elegans localization data.
    action: ACCEPT
    reason: Cilium localization is directly supported (CHE-13 concentrates at the ciliary
      base and moves along the axoneme) and is a core aspect of che-13 function.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0005815
    label: microtubule organizing center
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Phylogenetically propagated MTOC localization. In C. elegans the directly
      demonstrated site is the ciliary basal body, which is a specialized (docked, modified
      centriole) microtubule organizing center.
    action: KEEP_AS_NON_CORE
    reason: Not wrong but generic; the experimentally supported location is the more
      specific ciliary basal body (GO:0036064). Retained as a non-core, orthology-based
      location rather than removed.
- term:
    id: GO:1905515
    label: non-motile cilium assembly
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: CHE-13 is required to build the sensory (non-motile) ciliary axoneme;
      phylogenetic inference is corroborated by the loss-of-function ultrastructural
      phenotype.
    action: ACCEPT
    reason: Core process, appropriately specific (C. elegans sensory cilia are non-motile).
      che-13 mutants have severely truncated axonemes.
    supported_by:
    - reference_id: PMID:2428682
      supporting_text: The cilia in che-13 (e1805), osm-1 (p808), osm-5 (p813), and osm-6
        (p811) mutants have normal transition zones and severely shortened axonemes.
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Phylogenetically propagated Golgi localization from the IFT57/HIPPI family.
      There is no experimental support for a Golgi pool of CHE-13 in C. elegans; the
      protein's demonstrated sites are the ciliary base, basal body, transition zone and
      axoneme.
    action: MARK_AS_OVER_ANNOTATED
    reason: Over-propagated IBA. IFT57/HIPPI family members have varied non-ciliary
      associations, but CHE-13's directly observed localization is entirely ciliary. No
      C. elegans evidence places CHE-13 in the Golgi.
    propagation_review:
      root_cause: PROPAGATION_BAD
      failure_modes:
      - COMPARTMENT_OR_COMPLEX_MISMATCH
      source_entities:
      - source_id: PANTHER:PTN000410691
        source_label: IFT57/HIPPI family node
        source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: UniProt SubCell mapping to axoneme, consistent with the direct C. elegans
      IDA localization data.
    action: ACCEPT
    reason: Core ciliary localization; CHE-13 moves along the axoneme and is directly
      observed there (corroborated by IDA in PMID:12651157/18337471).
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0005929
    label: cilium
  evidence_type: NAS
  original_reference_id: PMID:28479320
  qualifier: located_in
  review:
    summary: ComplexPortal (CPX-1290) statement that CHE-13 localizes to the cilium,
      consistent with direct experimental data.
    action: ACCEPT
    reason: Core ciliary localization; corroborated by IDA/IBA evidence.
    supported_by:
    - reference_id: PMID:28479320
      supporting_text: Disruption of the dynein-2 tail domain, light intermediate chain,
        or intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary
        localization
- term:
    id: GO:0030992
    label: intraciliary transport particle B
  evidence_type: NAS
  original_reference_id: PMID:28479320
  qualifier: part_of
  review:
    summary: ComplexPortal assertion of CHE-13 membership in IFT particle B, the core
      structural annotation, based on the C. elegans IFT-B complex identified by mass
      spectrometry.
    action: ACCEPT
    reason: Core molecular role, redundant with and reinforcing the IBA/IDA IFT-B
      membership annotations.
    supported_by:
    - reference_id: PMID:28479320
      supporting_text: Disruption of the dynein-2 tail domain, light intermediate chain,
        or intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary
        localization
- term:
    id: GO:0042073
    label: intraciliary transport
  evidence_type: NAS
  original_reference_id: PMID:28479320
  qualifier: involved_in
  review:
    summary: ComplexPortal statement of IFT-B involvement in intraciliary transport.
    action: ACCEPT
    reason: Core process consistent with CHE-13 being a transported IFT-B subunit.
    supported_by:
    - reference_id: PMID:28479320
      supporting_text: Disruption of the dynein-2 tail domain, light intermediate chain,
        or intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary
        localization
- term:
    id: GO:0060271
    label: cilium assembly
  evidence_type: NAS
  original_reference_id: PMID:28479320
  qualifier: involved_in
  review:
    summary: ComplexPortal statement of IFT-B involvement in cilium assembly.
    action: ACCEPT
    reason: Core process; redundant with the IMP/IGI cilium-assembly annotations. The
      non-motile cilium assembly child term (GO:1905515) is the most specific form for
      C. elegans.
    supported_by:
    - reference_id: PMID:2428682
      supporting_text: The cilia in che-13 (e1805), osm-1 (p808), osm-5 (p813), and osm-6
        (p811) mutants have normal transition zones and severely shortened axonemes.
- term:
    id: GO:0060271
    label: cilium assembly
  evidence_type: IGI
  original_reference_id: PMID:1732156
  qualifier: involved_in
  review:
    summary: Genetic-interaction evidence placing che-13 among cilium-structure genes
      required for chemosensory cilium function in the dauer pathway.
    action: ACCEPT
    reason: Core process; che-13 is one of the cilium-structure genes whose mutation gives
      structurally defective chemosensory cilia.
    supported_by:
    - reference_id: PMID:1732156
      supporting_text: Dauer-defective mutations in nine genes cause structurally defective
        chemosensory cilia, thereby blocking chemosensation.
- term:
    id: GO:0003674
    label: molecular_function
  evidence_type: ND
  original_reference_id: GO_REF:0000015
  qualifier: enables
  review:
    summary: Root-level placeholder recording that no specific molecular function had been
      assigned at the time of annotation.
    action: KEEP_AS_NON_CORE
    reason: Retained as the standard ND placeholder. A subunit-specific molecular function
      (structural molecule activity within IFT-B) is now proposed as a NEW annotation and
      in core_functions; no catalytic activity is known or expected for this scaffolding
      subunit.
- term:
    id: GO:0005198
    label: structural molecule activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: CHE-13/IFT57 has no catalytic activity; as an IFT-B subunit its molecular
      function is best captured as a subunit-specific structural molecule activity.
    action: NEW
    reason: Proposed new molecular-function annotation reflecting CHE-13's role as a
      structural subunit of the IFT-B particle (the current GOA carries only the ND root
      MF for this gene). This IBA/GO_REF:0000033 evidence pairing does NOT currently exist
      in the GOA export; it is the expected phylogenetic evidence basis if the annotation
      were made (IFT57 orthologues across species are IFT-B structural subunits). Ideally a
      more specific 'structural constituent of intraflagellar transport particle' term (see
      proposed_new_terms) would be used.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: loss of che-13 differentially affects the localization of two known
        IFT complex B proteins, OSM-5 and OSM-6, implying that CHE-13 functions as part of
        this complex.
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IDA
  original_reference_id: PMID:12651157
  qualifier: located_in
  review:
    summary: CHE-13 is directly observed moving along the ciliary axoneme.
    action: ACCEPT
    reason: Core ciliary localization directly demonstrated by fluorescent-tagged CHE-13.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0030992
    label: intraciliary transport particle B
  evidence_type: IDA
  original_reference_id: PMID:17314406
  qualifier: part_of
  review:
    summary: che-13 is assigned to the IFT subcomplex B module based on in vivo transport
      and phenotypic profiling.
    action: ACCEPT
    reason: Core molecular role; direct assignment of che-13 to the IFT-B module.
    supported_by:
    - reference_id: PMID:17314406
      supporting_text: the C. elegans IFT machinery has a modular design, consisting of
        modules IFT-subcomplex A, IFT-subcomplex B, and a BBS protein complex
- term:
    id: GO:0035720
    label: intraciliary anterograde transport
  evidence_type: IEP
  original_reference_id: PMID:12651157
  qualifier: involved_in
  review:
    summary: CHE-13 moves anterogradely along the axoneme as an IFT-B particle component.
    action: ACCEPT
    reason: Core process. Directly reflects the observed IFT movement of tagged CHE-13
      from the ciliary base toward the tip.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0035721
    label: intraciliary retrograde transport
  evidence_type: IEP
  original_reference_id: PMID:12651157
  qualifier: involved_in
  review:
    summary: As an IFT-B particle component, CHE-13 is also recycled retrogradely along
      the axoneme.
    action: ACCEPT
    reason: Core process. IFT-B particles (including CHE-13) are carried bidirectionally;
      retrograde recycling is part of the IFT cycle.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:1905515
    label: non-motile cilium assembly
  evidence_type: IMP
  original_reference_id: PMID:2428682
  qualifier: involved_in
  review:
    summary: che-13 mutants fail to build full sensory (non-motile) cilia; this is the most
      precise cilium-assembly term for the worm's sensory cilia.
    action: ACCEPT
    reason: Core process, and appropriately specific. Directly supported by the
      ultrastructural phenotype (severely shortened axonemes).
    supported_by:
    - reference_id: PMID:2428682
      supporting_text: The cilia in che-13 (e1805), osm-1 (p808), osm-5 (p813), and osm-6
        (p811) mutants have normal transition zones and severely shortened axonemes.
- term:
    id: GO:0035869
    label: ciliary transition zone
  evidence_type: IDA
  original_reference_id: PMID:12651157
  qualifier: located_in
  review:
    summary: CHE-13 is directly localized at/through the ciliary transition zone as it
      moves between the ciliary base and the axoneme.
    action: ACCEPT
    reason: Core localization consistent with IFT trafficking through the transition zone.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0036064
    label: ciliary basal body
  evidence_type: IDA
  original_reference_id: PMID:22922713
  qualifier: located_in
  review:
    summary: CHE-13 localizes to the ciliary basal body, where IFT particles assemble
      before entering the cilium.
    action: ACCEPT
    reason: Core localization at the site of IFT assembly; consistent with CHE-13
      concentrating at the ciliary base. The MGI reference (PMID:22922713) is a
      DYF-2/BBSome paper that does not name che-13, but basal-body localization is
      independently established for CHE-13 and the experimental annotation is not overruled.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IDA
  original_reference_id: PMID:18337471
  qualifier: located_in
  review:
    summary: A second WormBase IDA supporting CHE-13 axoneme localization.
    action: ACCEPT
    reason: Core ciliary localization; redundant with the PMID:12651157 axoneme IDA. The
      cited B9/nephrocystin paper does not foreground che-13, but axoneme localization is
      well established and the annotation is not overruled.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0008104
    label: intracellular protein localization
  evidence_type: IMP
  original_reference_id: PMID:16957054
  qualifier: involved_in
  review:
    summary: che-13 loss-of-function mislocalizes the IFT-B proteins OSM-5 and OSM-6,
      i.e. CHE-13 is required for delivering/localizing ciliary proteins. The generic
      "intracellular protein localization" term understates this; the specific process is
      protein localization to the cilium.
    action: MODIFY
    reason: The evidence (che-13 mutant mislocalizes IFT-B proteins into cilia) supports a
      more specific and informative term. Replace the generic GO:0008104 with GO:0061512
      protein localization to cilium.
    proposed_replacement_terms:
    - id: GO:0061512
      label: protein localization to cilium
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: loss of che-13 differentially affects the localization of two known
        IFT complex B proteins, OSM-5 and OSM-6, implying that CHE-13 functions as part of
        this complex.
- term:
    id: GO:0036064
    label: ciliary basal body
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: Sequence-similarity transfer of basal-body localization from the mouse IFT57
      ortholog (UniProtKB:Q8BXG3), consistent with the direct C. elegans data.
    action: ACCEPT
    reason: Core localization; redundant with the IDA basal-body annotation and consistent
      with CHE-13 concentrating at the ciliary base.
    supported_by:
    - reference_id: PMID:12651157
      supporting_text: concentrates at the base of cilia and moves along the axoneme as
        expected for an IFT protein
- term:
    id: GO:0007635
    label: chemosensory behavior
  evidence_type: IMP
  original_reference_id: PMID:2428682
  qualifier: involved_in
  review:
    summary: che-13 mutants are chemosensory-defective (dye-filling defective) because
      their chemosensory cilia are truncated; this is a downstream consequence of defective
      cilia, not a direct signalling role of CHE-13.
    action: KEEP_AS_NON_CORE
    reason: Indirect, downstream sensory phenotype of ciliary loss rather than a core
      molecular/biological function of CHE-13. Retained (curator IMP) but marked non-core.
    supported_by:
    - reference_id: PMID:2428682
      supporting_text: Mutations in 14 genes prevent dye uptake and disrupt chemosensory
        behaviors.
core_functions:
- description: CHE-13/IFT57 is a structural subunit of the intraflagellar transport complex
    B (IFT-B), the anterograde IFT particle that is itself carried as cargo by kinesin-2
    and returned by dynein-2. It scaffolds the IFT-B particle (it has no independent
    catalytic activity) and is required to build and maintain the sensory ciliary axoneme
    in C. elegans ciliated neurons.
  supported_by:
  - reference_id: PMID:12651157
    supporting_text: loss of che-13 differentially affects the localization of two known
      IFT complex B proteins, OSM-5 and OSM-6, implying that CHE-13 functions as part of
      this complex.
  - reference_id: PMID:2428682
    supporting_text: The cilia in che-13 (e1805), osm-1 (p808), osm-5 (p813), and osm-6
      (p811) mutants have normal transition zones and severely shortened axonemes.
  molecular_function:
    id: GO:0005198
    label: structural molecule activity
  directly_involved_in:
  - id: GO:0042073
    label: intraciliary transport
  - id: GO:1905515
    label: non-motile cilium assembly
  locations:
  - id: GO:0005930
    label: axoneme
  - id: GO:0036064
    label: ciliary basal body
  - id: GO:0035869
    label: ciliary transition zone
  in_complex:
    id: GO:0030992
    label: intraciliary transport particle B
proposed_new_terms:
- proposed_name: structural constituent of intraflagellar transport particle
  proposed_definition: A structural molecule activity in which a protein acts as a
    structural subunit of an intraflagellar transport (IFT) particle (IFT-A or IFT-B),
    contributing to the assembly and integrity of the particle that is trafficked along
    the ciliary axoneme by kinesin-2 and dynein-2 motors.
  justification: CHE-13/IFT57 and its IFT-B/IFT-A paralogs act as structural subunits of
    the IFT particle, a role currently expressible only as the generic GO:0005198
    structural molecule activity. A dedicated MF term would capture the shared function of
    IFT structural subunits.
  supported_by:
  - reference_id: PMID:12651157
    supporting_text: loss of che-13 differentially affects the localization of two known
      IFT complex B proteins, OSM-5 and OSM-6, implying that CHE-13 functions as part of
      this complex.
knowledge_gaps:
- gap_statement: The specific intra-complex protein contacts of CHE-13/IFT57 within the
    C. elegans IFT-B particle have not been experimentally mapped. In vertebrates IFT57
    sits in the peripheral IFT-B1 region and helps couple IFT-B to the IFT-A/dynein-2
    machinery, but which IFT-B subunits CHE-13 directly contacts in the worm, and whether
    its C-terminal coiled-coil versus its disordered N-terminal/central segments mediate
    these contacts, is undetermined.
  boundary: It is firmly established that CHE-13 is an IFT-B/IFT57 structural subunit that
    concentrates at the ciliary base, moves bidirectionally by IFT along the axoneme, is
    required for axoneme assembly, and is needed for proper localization of other IFT-B
    proteins (OSM-5, OSM-6).
  gap_kind:
  - BIOLOGY
  - ONTOLOGY
  dark_aspect: MF_DARK
  status: OPEN
  significance: Defining CHE-13's specific IFT-B contacts would explain how the IFT-B
    particle is built in vivo and how the IFT57 orthologue contributes to IFT-B integrity
    and ciliopathy-relevant IFT defects.
  resolution: In vivo proximity labeling (BioID/TurboID) or cross-linking mass spectrometry
    of tagged CHE-13 in ciliated neurons, plus structure determination of the C. elegans
    IFT-B subcomplex, paired with an ontology term for structural constituent of the IFT
    particle.
  provenance:
  - reference_id: PMID:12651157
    supporting_text: loss of che-13 differentially affects the localization of two known
      IFT complex B proteins, OSM-5 and OSM-6, implying that CHE-13 functions as part of
      this complex.
  proposed_terms:
  - proposed_name: structural constituent of intraflagellar transport particle
    proposed_definition: A structural molecule activity in which a protein acts as a
      structural subunit of an intraflagellar transport (IFT) particle (IFT-A or IFT-B),
      contributing to assembly and integrity of the particle trafficked along the ciliary
      axoneme.
    justification: GO currently expresses this role only as the generic 'structural
      molecule activity' (GO:0005198).
- gap_statement: It is not resolved whether the severely truncated axoneme of che-13
    mutants reflects failure to deliver specific axonemal cargo (e.g. tubulin or motility-
    related proteins) versus a general loss of IFT-B particle integrity that mislocalizes
    the whole complex. The che-13 mutant phenotype (short axonemes; OSM-5/OSM-6
    mislocalization) is consistent with either mechanism.
  boundary: che-13 is required for axoneme assembly and for proper localization of other
    IFT-B proteins; UniProt notes a possible role in ciliary entrance/transport of specific
    cargo, but no direct CHE-13 cargo-selection activity has been demonstrated.
  gap_kind:
  - BIOLOGY
  dark_aspect: MF_DARK
  status: OPEN
  significance: Distinguishing a cargo-delivery role from a particle-integrity role would
    clarify whether IFT57/CHE-13 has any cargo-specific function beyond scaffolding IFT-B.
  resolution: Separation-of-function alleles or domain deletions of che-13 with live
    imaging of tagged axonemal cargo (tubulin) and IFT-B markers to test whether specific
    cargo delivery can be uncoupled from IFT-B assembly.
  provenance:
  - reference_id: PMID:2428682
    supporting_text: The cilia in che-13 (e1805), osm-1 (p808), osm-5 (p813), and osm-6
      (p811) mutants have normal transition zones and severely shortened axonemes.
  - reference_id: PMID:12651157
    supporting_text: loss of che-13 differentially affects the localization of two known
      IFT complex B proteins, OSM-5 and OSM-6, implying that CHE-13 functions as part of
      this complex.
suggested_questions:
- question: Which IFT-B subunits does CHE-13/IFT57 directly contact in C. elegans, and is
    the C-terminal coiled-coil required for those contacts?
  experts:
  - Oliver E. Blacque
- question: Do the two che-13 splice isoforms (a/b) have distinct expression or function in
    ciliated sensory neurons?
  experts: []
suggested_experiments:
- hypothesis: CHE-13/IFT57 bridges specific IFT-B subunits via its C-terminal coiled-coil,
    and disrupting this region selectively destabilizes part of IFT-B.
  description: Perform in vivo proximity labeling (TurboID) with full-length and
    coiled-coil-deleted CHE-13 expressed in ciliated neurons, followed by mass spectrometry,
    to map region-specific IFT-B interaction partners.
  experiment_type: proximity labeling / interaction mapping
- hypothesis: The truncated axoneme of che-13 mutants reflects failure to deliver axonemal
    cargo by IFT-B rather than a transition-zone defect.
  description: Use live imaging of tagged tubulin and IFT-B markers (e.g. OSM-6) in che-13
    partial loss-of-function backgrounds to quantify anterograde cargo delivery versus
    transition-zone integrity.
  experiment_type: live-cell imaging
tags:
- caeel-ciliopathy