id: Q17595
gene_symbol: dyf-11
product_type: PROTEIN
status: COMPLETE
aliases:
- MIP-T3
- TRAF3IP1
- IFT54
- C02H7.1
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: >-
  dyf-11 encodes the Caenorhabditis elegans ortholog of MIP-T3/TRAF3IP1 (IFT54), a
  535-residue structural subunit of intraflagellar transport (IFT) complex B. IFT-B,
  together with IFT-A and the kinesin-2 and dynein-2 motors, drives the bidirectional
  transport of ciliary cargo that builds and maintains the sensory cilia of ciliated
  neurons. The protein has no catalytic domain; it comprises conserved N- and C-terminal
  TRAF3IP1 domains flanking a long charged/disordered central region and a C-terminal
  coiled coil. DYF-11 is expressed under X-box/RFX (daf-19) control specifically in
  ciliated sensory neurons and localizes to the ciliary base (transition zone/basal body)
  and along the ciliary axoneme, where it undergoes processive IFT movement. It is
  required to assemble and maintain an intact motor-IFT particle: in its absence
  kinesin-II, IFT-A, IFT-dynein and BBSome components fail to enter cilia and the axoneme
  is severely truncated, so full-length medial and distal ciliary segments do not form.
  Loss of dyf-11 therefore disrupts cilium-dependent sensory behaviors (chemosensation,
  osmotic avoidance, dauer formation, dye filling) and perturbs lipid homeostasis. The
  ciliary role is conserved: human MIP-T3 localizes to basal bodies and cilia, and
  zebrafish mipt3 is required for gastrulation movements and interacts genetically with
  the Bardet-Biedl protein Bbs4.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      InterPro2GO mapping of the TRAF3IP1 family (IPR018799) to microtubule binding
      (GO:0008017). The family is named for its microtubule-interacting property
      (MIP-T3 = Microtubule-Interacting Protein associated with TRAF3) and human MIP-T3
      was shown to bind microtubules, so the molecular-function transfer is reasonable at
      the family level.
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Standard GO_Central IBA pipeline. The phylogenetic inferences (IFT complex B
      membership, intraciliary transport, cilium assembly, axoneme and basal body
      localization) are all independently corroborated by C. elegans experimental data,
      so the IBA transfers are sound. The "regulation of microtubule cytoskeleton
      organization" transfer over-generalizes the axoneme-assembly role.
- 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: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      Electronic mapping of the UniProt cilium-axoneme subcellular-location keyword to
      GO:0005930; redundant with the experimental IDA axoneme annotation but not incorrect.
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
  reference_review:
    relevance: LOW
    correctness: LOW_QUALITY
    review_notes: >-
      ARBA machine-learning annotations. The "animal organ development" and "system
      development" terms are over-general electronic inferences that are not informative
      for a nematode sensory-cilium protein; "regulation of microtubule cytoskeleton
      organization" over-generalizes the structural axoneme-assembly role.
- id: PMID:18245347
  title: The conserved proteins CHE-12 and DYF-11 are required for sensory cilium
    function in Caenorhabditis elegans.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Bacaj, Lu & Shaham 2008 (Genetics), independent characterization of dyf-11. Cached
      record is abstract-only (full_text_available: false), but the abstract directly
      establishes that dyf-11 mutant cilia lack medial and distal segments, that DYF-11
      undergoes IFT-like movement and may act at an early stage of IFT-B particle
      assembly, and that DYF-11 is expressed in all ciliated neurons. The four WormBase
      IMP annotations to this PMID (chemotaxis, hyperosmotic response, dauer entry,
      non-motile cilium assembly) rest on full-text assays not in the cached abstract.
- id: PMID:18369462
  title: An essential role for DYF-11/MIP-T3 in assembling functional intraflagellar
    transport complexes.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Li et al. 2008 (PLoS Genet, PMC2268012), the primary cloning and functional
      characterization paper. Full text available. Establishes dyf-11 = the C. elegans
      MIP-T3/TRAF3IP1 ortholog, its localization to transition zone/basal body and
      axoneme, its bidirectional IFT movement, its identity as a novel IFT-B component,
      and its requirement for assembly/integrity of the motor-IFT machinery. Supports the
      core cellular-component, transport, and cilium-assembly annotations.
- id: PMID:20837997
  title: Reversal of salt preference is directed by the insulin/PI3K and Gq/PKC signaling
    in Caenorhabditis elegans.
  findings: []
  reference_review:
    relevance: LOW
    correctness: UNVERIFIED
    review_notes: >-
      Adachi et al. 2010 (Genetics). The PMID resolves to the correct paper on ASE
      salt-chemotaxis plasticity, but the cached record is abstract-only and the abstract
      does not mention dyf-11; the associative-learning IMP therefore cannot be verified
      from the cache. Any dyf-11 salt-learning phenotype is an indirect consequence of
      loss of functional sensory cilia rather than a core function.
- id: PMID:28479320
  title: Dynein-Driven Retrograde Intraflagellar Transport Is Triphasic in C. elegans
    Sensory Cilia.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Yi et al. 2017 (Curr Biol). Source of the ComplexPortal (CPX-1290) NAS annotations
      placing DYF-11 in IFT complex B. Abstract-only cache, but the abstract confirms that
      an intact IFT-B complex is required for dynein-2 ciliary entry, consistent with
      DYF-11's IFT-B membership.
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: >-
      DYF-11/IFT54 is a subunit of intraflagellar transport complex B (IFT-B). This IBA
      transfer is strongly corroborated by C. elegans experimental data and by biochemical
      assignment to ComplexPortal CPX-1290.
    action: ACCEPT
    reason: >-
      Core cellular-component identity. Phylogenetically inferred and independently
      confirmed experimentally (PMID:18369462).
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: DYF-11 functions as a novel component of IFT subcomplex B
      reference_section_type: ABSTRACT
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      DYF-11 acts within the ciliary axoneme, where IFT trains move. The is_active_in
      qualifier is appropriate for an IFT-B component that translocates along the axoneme.
    action: ACCEPT
    reason: >-
      Consistent with the experimental IDA axoneme localization (PMID:18369462).
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: the DYF-11::GFP protein was found to be highly enriched at
        transition zones and within ciliary axonemes
      reference_section_type: RESULTS
- term:
    id: GO:0036064
    label: ciliary basal body
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      DYF-11 localizes to and functions at the ciliary base (transition zone/basal body),
      where IFT trains assemble and load.
    action: ACCEPT
    reason: >-
      Corroborated by the experimental IDA basal-body/transition-zone localization
      (PMID:18369462).
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: the DYF-11::GFP protein was found to be highly enriched at
        transition zones and within ciliary axonemes
      reference_section_type: RESULTS
- term:
    id: GO:0070507
    label: regulation of microtubule cytoskeleton organization
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      DYF-11's effect on microtubules is to build the axonemal microtubule structure via
      IFT, which is more precisely captured by cilium assembly (GO:0060271). The general
      "regulation of microtubule cytoskeleton organization" term over-generalizes this
      structural role and is not directly supported by evidence of a regulatory activity.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Over-general phylogenetic transfer; DYF-11 does not regulate microtubule dynamics
      per se — it is a structural IFT-B subunit whose microtubule-related role is axoneme
      assembly, already annotated as cilium assembly and intraciliary transport.
    propagation_review:
      root_cause: TERM_SCOPING_PROBLEM
      failure_modes:
      - GRANULARITY_MISMATCH
      source_entities:
      - source_id: PANTHER:PTN000773545
        source_label: TRAF3IP1 family node
        source_status: SUPPORTS_SOURCE_BUT_NOT_TARGET
        comment: >-
          The IFT54/TRAF3IP1 family node's microtubule-related activity is axonemal
          assembly via IFT, not regulation of microtubule dynamics; the transferred term
          is scoped too broadly for the structural role.
- term:
    id: GO:0060271
    label: cilium assembly
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      DYF-11 is required to build full-length sensory cilia; dyf-11 nulls have severely
      truncated cilia lacking medial and distal segments.
    action: ACCEPT
    reason: >-
      Core biological process, strongly supported experimentally (PMID:18369462;
      PMID:18245347).
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: the cilia of dyf-11 mutants were truncated substantially
      reference_section_type: RESULTS
- term:
    id: GO:0042073
    label: intraciliary transport
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      DYF-11 functions in intraflagellar (intraciliary) transport as an IFT-B subunit that
      undergoes bidirectional IFT movement along the axoneme.
    action: ACCEPT
    reason: >-
      Core biological process, confirmed experimentally in worm (PMID:18369462).
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: the GFP-tagged protein moves bi-directionally along the length of
        amphid and phasmid ciliary axonemes
      reference_section_type: RESULTS
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Electronic mapping of the UniProt cilium-axoneme subcellular-location keyword.
      Redundant with the experimental IDA axoneme annotation and correct.
    action: ACCEPT
    reason: >-
      Correct location, corroborated by experimental IDA (PMID:18369462).
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: the DYF-11::GFP protein was found to be highly enriched at
        transition zones and within ciliary axonemes
      reference_section_type: RESULTS
- term:
    id: GO:0008017
    label: microtubule binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro2GO transfer for the TRAF3IP1/MIP-T3 family, which is named for its
      microtubule-interacting property; human MIP-T3 was shown to bind microtubules, and
      Li et al. suggest a proportion of C. elegans DYF-11 may associate directly with
      microtubules. This is the most informative molecular-function term available for
      DYF-11, though direct microtubule binding by the worm protein has not been
      experimentally demonstrated.
    action: ACCEPT
    reason: >-
      Best-supported molecular function; consistent with family identity and IFT-B
      axonemal role.
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: MIP-T3 proteins range in size from 484 to 625 amino acids and have
        no recognizable domains except for a predicted coiled-coil region near the
        C-terminus
      reference_section_type: RESULTS
- term:
    id: GO:0048513
    label: animal organ development
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      Over-general ARBA machine-learning inference. C. elegans lacks the vertebrate organs
      implied, and DYF-11's characterized role is restricted to sensory ciliogenesis. Not
      informative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Vague electronic annotation with no experimental support in this organism; DYF-11's
      role is specific to sensory cilium assembly/function.
- term:
    id: GO:0048731
    label: system development
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      Over-general ARBA machine-learning inference; uninformative for a sensory-cilium IFT
      protein.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Vague electronic annotation; DYF-11's characterized function is ciliogenesis, better
      captured by cilium assembly.
- term:
    id: GO:0070507
    label: regulation of microtubule cytoskeleton organization
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      Duplicate of the IBA transfer of the same term via an ARBA model. Over-generalizes
      DYF-11's structural axoneme-assembly role.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      DYF-11 is a structural IFT-B subunit, not a regulator of microtubule dynamics; the
      microtubule-related role is axoneme assembly (cilium assembly / intraciliary
      transport).
- term:
    id: GO:0005929
    label: cilium
  evidence_type: NAS
  original_reference_id: PMID:28479320
  qualifier: located_in
  review:
    summary: >-
      ComplexPortal (CPX-1290) assertion that DYF-11 localizes to the cilium. Correct but
      general; the more specific axoneme and basal-body IDA locations are also annotated.
    action: ACCEPT
    reason: >-
      Correct ciliary location; consistent with experimental IDA localization.
- term:
    id: GO:0030992
    label: intraciliary transport particle B
  evidence_type: NAS
  original_reference_id: PMID:28479320
  qualifier: part_of
  review:
    summary: >-
      ComplexPortal (CPX-1290) assertion of IFT-B membership, consistent with the
      experimental IDA and phylogenetic annotations.
    action: ACCEPT
    reason: >-
      Core cellular-component identity; independently confirmed (PMID:18369462).
    supported_by:
    - reference_id: PMID:28479320
      supporting_text: intraflagellar transport (IFT)-B complex abolishes dynein-2's
        ciliary localization
      reference_section_type: ABSTRACT
- term:
    id: GO:0042073
    label: intraciliary transport
  evidence_type: NAS
  original_reference_id: PMID:28479320
  qualifier: involved_in
  review:
    summary: >-
      ComplexPortal assertion that DYF-11 functions in intraciliary transport, consistent
      with experimental data.
    action: ACCEPT
    reason: >-
      Core biological process; confirmed experimentally (PMID:18369462).
- term:
    id: GO:0060271
    label: cilium assembly
  evidence_type: NAS
  original_reference_id: PMID:28479320
  qualifier: involved_in
  review:
    summary: >-
      ComplexPortal assertion that DYF-11 functions in cilium assembly, consistent with
      the truncated-cilia phenotype of dyf-11 mutants.
    action: ACCEPT
    reason: >-
      Core biological process; strongly supported (PMID:18369462; PMID:18245347).
- term:
    id: GO:0008306
    label: associative learning
  evidence_type: IMP
  original_reference_id: PMID:20837997
  qualifier: involved_in
  review:
    summary: >-
      A dyf-11 defect in salt-chemotaxis plasticity would be an indirect consequence of
      loss of functional sensory (ASE) cilia rather than a direct role in learning/memory.
      The cited paper is cached abstract-only and its abstract does not mention dyf-11, so
      the specific evidence cannot be verified here. Retained as a pleiotropic, non-core
      sensory phenotype rather than removed (experimental IMP; defer to curator).
    action: KEEP_AS_NON_CORE
    reason: >-
      Downstream/pleiotropic behavioral consequence of ciliary dysfunction, not a core
      molecular function of an IFT-B structural subunit; supporting full text unavailable
      in the cache.
- term:
    id: GO:0036064
    label: ciliary basal body
  evidence_type: IDA
  original_reference_id: PMID:18369462
  qualifier: located_in
  review:
    summary: >-
      DYF-11::GFP is highly enriched at the transition zone/basal body in ciliated sensory
      neurons; human MIP-T3 likewise localizes to the basal body.
    action: ACCEPT
    reason: >-
      Core, directly observed cellular-component location.
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: V5 epitope-tagged human MIP-T3 also localizes to the basal body
      reference_section_type: RESULTS
- term:
    id: GO:0005930
    label: axoneme
  evidence_type: IDA
  original_reference_id: PMID:18369462
  qualifier: located_in
  review:
    summary: >-
      DYF-11::GFP is directly observed enriched within ciliary axonemes and moves along
      their length.
    action: ACCEPT
    reason: >-
      Core, directly observed cellular-component location.
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: the DYF-11::GFP protein was found to be highly enriched at
        transition zones and within ciliary axonemes
      reference_section_type: RESULTS
- term:
    id: GO:0030992
    label: intraciliary transport particle B
  evidence_type: IDA
  original_reference_id: PMID:18369462
  qualifier: part_of
  review:
    summary: >-
      DYF-11 was directly characterized as a novel component of IFT subcomplex B based on
      its IFT movement and genetic behavior relative to kinesin/BBS/IFT mutants.
    action: ACCEPT
    reason: >-
      Core cellular-component identity, directly established.
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: DYF-11 functions as a novel component of IFT subcomplex B
      reference_section_type: ABSTRACT
- term:
    id: GO:0042073
    label: intraciliary transport
  evidence_type: IMP
  original_reference_id: PMID:18369462
  qualifier: involved_in
  review:
    summary: >-
      Loss of dyf-11 disrupts IFT, mislocalizing kinesin-II, IFT-A, dynein and BBSome
      components and truncating cilia, demonstrating a functional requirement in IFT.
    action: ACCEPT
    reason: >-
      Core biological process; strong loss-of-function evidence.
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: 'DYF-11 is an intraflagellar transport protein critical for the
        formation of full-length, functional sensory cilia'
      reference_section_type: DISCUSSION
- term:
    id: GO:0045184
    label: establishment of protein localization
  evidence_type: IMP
  original_reference_id: PMID:18369462
  qualifier: involved_in
  review:
    summary: >-
      In dyf-11 mutants, IFT-associated proteins (CHE-11/IFT-A, OSM-5/IFT-B, XBX-1/dynein,
      BBS-7, KAP-1/kinesin-II) fail to enter cilia. This is specifically the failure to
      localize proteins to the cilium, better captured by GO:0061512 "protein localization
      to cilium" than by the very general "establishment of protein localization".
    action: MODIFY
    reason: >-
      Term too general; the experiment shows DYF-11 is required for delivering IFT proteins
      into the cilium.
    proposed_replacement_terms:
    - id: GO:0061512
      label: protein localization to cilium
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: none of the proteins were observed to enter the (truncated) amphid
        and phasmid cilia
      reference_section_type: RESULTS
- term:
    id: GO:0055088
    label: lipid homeostasis
  evidence_type: IMP
  original_reference_id: PMID:18369462
  qualifier: involved_in
  review:
    summary: >-
      dyf-11 mutants show increased intestinal Nile Red (lipid) staining, rescued by
      DYF-11::GFP, reflecting the conserved cilia-lipid connection. This is a downstream
      systemic consequence of ciliary dysfunction, not a core molecular function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Real, rescued loss-of-function phenotype but pleiotropic/indirect (secondary to
      defective sensory-cilia signaling), not a core function of an IFT-B subunit.
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: indicative of an increased lipid accumulation phenotype
      reference_section_type: RESULTS
- term:
    id: GO:0065003
    label: protein-containing complex assembly
  evidence_type: IMP
  original_reference_id: PMID:18369462
  qualifier: involved_in
  review:
    summary: >-
      DYF-11 is required to assemble a functional motor-IFT particle, including loading of
      the kinesin-II motor; in its absence multiple IFT components fail to assemble/enter
      cilia. The term is general but captures this assembly role.
    action: ACCEPT
    reason: >-
      Supported by loss-of-function mislocalization of IFT-machinery components; DYF-11 is
      needed for assembly/integrity of the IFT particle.
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: may help with the assembly of Kinesin-II onto the IFT complex
      reference_section_type: DISCUSSION
- term:
    id: GO:0006935
    label: chemotaxis
  evidence_type: IMP
  original_reference_id: PMID:18245347
  qualifier: involved_in
  review:
    summary: >-
      dyf-11 mutants are chemotaxis-defective because their sensory cilia are truncated and
      nonfunctional. This is a sensory readout downstream of the ciliary defect rather than
      a direct chemotaxis function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic sensory-behavior phenotype secondary to loss of functional cilia; not a
      core molecular function.
    supported_by:
    - reference_id: PMID:18245347
      supporting_text: chemotaxis defective
      reference_section_type: ABSTRACT
- term:
    id: GO:0006972
    label: hyperosmotic response
  evidence_type: IMP
  original_reference_id: PMID:18245347
  qualifier: involved_in
  review:
    summary: >-
      Annotation reflects the osmotic-avoidance (Osm) phenotype of dyf-11 mutants, a
      cilium-dependent sensory behavior. It is a downstream consequence of nonfunctional
      sensory cilia rather than a direct role in the cellular hyperosmotic stress response.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic sensory-behavior phenotype secondary to ciliary dysfunction; retained as
      non-core (experimental IMP; defer to curator on full text).
- term:
    id: GO:0043053
    label: dauer entry
  evidence_type: IMP
  original_reference_id: PMID:18245347
  qualifier: involved_in
  review:
    summary: >-
      dyf-11 mutants are dauer-formation defective, consistent with loss of the ciliary
      sensory input that governs the dauer decision. Downstream consequence of ciliary
      dysfunction.
    action: KEEP_AS_NON_CORE
    reason: >-
      Pleiotropic developmental phenotype secondary to defective sensory-cilia signaling;
      not a core molecular function.
    supported_by:
    - reference_id: PMID:18369462
      supporting_text: found that dyf-11 mutants are Daf-d at both temperatures
      reference_section_type: RESULTS
- term:
    id: GO:1905515
    label: non-motile cilium assembly
  evidence_type: IMP
  original_reference_id: PMID:18245347
  qualifier: involved_in
  review:
    summary: >-
      C. elegans sensory cilia are non-motile, and DYF-11 is required to build them: in
      dyf-11 mutants the medial and distal ciliary segments are absent. This is the most
      specific and accurate biological-process term for DYF-11.
    action: ACCEPT
    reason: >-
      Core biological process; the specific non-motile-cilium wording matches the worm
      sensory cilium and is directly supported.
    supported_by:
    - reference_id: PMID:18245347
      supporting_text: medial and distal segments are absent
      reference_section_type: ABSTRACT
core_functions:
- description: >-
    DYF-11/IFT54 (MIP-T3/TRAF3IP1 ortholog) is a structural subunit of intraflagellar
    transport (IFT) complex B in ciliated sensory neurons. It localizes to the ciliary
    base (transition zone/basal body) and axoneme, undergoes bidirectional IFT, and is
    required for assembling and maintaining a functional motor-IFT particle. In its
    absence kinesin-II, IFT-A, IFT-dynein and BBSome components fail to enter cilia, the
    axoneme is truncated, and full-length sensory cilia do not form. Its only informative
    molecular-function term is microtubule binding (the MIP-T3 family property); it has no
    catalytic domain and acts as a structural/adaptor component of IFT-B.
  molecular_function:
    id: GO:0008017
    label: microtubule binding
  in_complex:
    id: GO:0030992
    label: intraciliary transport particle B
  directly_involved_in:
  - id: GO:0042073
    label: intraciliary transport
  - id: GO:1905515
    label: non-motile cilium assembly
  - id: GO:0061512
    label: protein localization to cilium
  locations:
  - id: GO:0036064
    label: ciliary basal body
  - id: GO:0005930
    label: axoneme
  supported_by:
  - reference_id: PMID:18369462
    supporting_text: DYF-11 functions as a novel component of IFT subcomplex B
    reference_section_type: ABSTRACT
  - reference_id: PMID:18369462
    supporting_text: the GFP-tagged protein moves bi-directionally along the length of
      amphid and phasmid ciliary axonemes
    reference_section_type: RESULTS
  - reference_id: PMID:18245347
    supporting_text: function at an early stage of IFT-B particle assembly
    reference_section_type: ABSTRACT
knowledge_gaps:
- gap_statement: >-
    The specific molecular function of DYF-11/IFT54 within IFT complex B is undefined. It
    has no catalytic domain and only a C-terminal coiled coil; whether it binds microtubules
    directly in C. elegans, and which specific IFT-B subunit(s) it bridges (vertebrate IFT54
    partners with IFT20), is not established. It reads as MF-dark despite a well-defined
    cellular role.
  boundary: >-
    DYF-11 is firmly established as an IFT-B subunit that localizes to the transition
    zone/basal body and axoneme, undergoes bidirectional IFT, and is required for assembling
    a functional motor-IFT particle and building full-length sensory cilia. Its only
    informative GO molecular-function term is the family-level microtubule binding
    (GO:0008017), which has not been experimentally demonstrated for the worm protein.
  gap_kind:
  - BIOLOGY
  - ONTOLOGY
  dark_aspect: MF_DARK
  status: OPEN
  significance: >-
    IFT54/TRAF3IP1 is a conserved core IFT-B protein whose human ortholog is linked to
    ciliopathy phenotypes; defining its molecular activity (microtubule binding vs a
    specific IFT-B scaffolding interaction) is central to understanding IFT-B architecture.
  resolution: >-
    Test direct microtubule binding of purified DYF-11; map its IFT-B interaction partners
    (e.g. an IFT20 ortholog) by biochemistry/structure; isolate separation-of-function
    alleles; consider a molecular-function term for an IFT-B structural/scaffolding subunit
    activity.
  provenance:
  - reference_id: PMID:18369462
    supporting_text: MIP-T3 proteins range in size from 484 to 625 amino acids and have no
      recognizable domains except for a predicted coiled-coil region near the C-terminus
    reference_section_type: RESULTS
  - reference_id: PMID:18369462
    supporting_text: that affects the core machinery, remains to be determined
    reference_section_type: RESULTS
- gap_statement: >-
    How DYF-11 promotes assembly/loading of the kinesin-II motor and other IFT components
    onto trains at the ciliary base is not understood at the mechanistic level, nor is it
    resolved whether it acts specifically at an early step of IFT-B particle assembly.
  boundary: >-
    Loss of dyf-11 mislocalizes kinesin-II (KAP-1), IFT-A (CHE-11), dynein (XBX-1) and
    BBSome (BBS-7) components so they fail to enter cilia, and DYF-11 undergoes IFT-like
    movement and may act early in IFT-B assembly; the molecular steps linking DYF-11 to
    motor/particle assembly are undefined.
  gap_kind:
  - BIOLOGY
  dark_aspect: RESIDUAL_SUBGAP
  status: OPEN
  significance: >-
    DYF-11 has a more severe assembly phenotype than typical IFT-B mutants and uniquely
    affects kinesin-II loading, so its mechanism bears on how the anterograde motor is
    coupled to IFT trains.
  resolution: >-
    Order the IFT-B assembly hierarchy with epistasis/live-imaging and in vitro
    reconstitution; determine whether DYF-11 directly contacts kinesin-II or acts through
    other IFT-B subunits.
  provenance:
  - reference_id: PMID:18245347
    supporting_text: function at an early stage of IFT-B particle assembly
    reference_section_type: ABSTRACT
  - reference_id: PMID:18369462
    supporting_text: may help with the assembly of Kinesin-II onto the IFT complex
    reference_section_type: DISCUSSION
- gap_statement: >-
    Whether C. elegans DYF-11 has an IFT-independent role — for example in dendrite/neurite
    protein trafficking, analogous to the vertebrate MIP-T3/DISC1 axis — is untested.
  boundary: >-
    DYF-11::GFP is occasionally seen in dendritic extensions beyond the cilium, and
    vertebrate MIP-T3 interacts with DISC1 and microtubules in neurite/centrosome contexts;
    no non-ciliary function has been assayed in the worm.
  gap_kind:
  - BIOLOGY
  dark_aspect: RESIDUAL_SUBGAP
  status: OPEN
  significance: >-
    Distinguishing a dedicated ciliary IFT role from a broader neuronal trafficking role
    would clarify whether MIP-T3/TRAF3IP1 acquired dual functions during evolution.
  resolution: >-
    Assay dyf-11 dendritic transport and non-ciliary phenotypes with cell-type-specific
    rescue and cargo-trafficking reporters.
  provenance:
  - reference_id: PMID:18369462
    supporting_text: Whether C. elegans DYF-11 has dendrite-associated functions whose
      disruption could affect ciliogenesis represents an interesting question that will need
      to be addressed
    reference_section_type: DISCUSSION
suggested_questions:
- question: >-
    Does C. elegans DYF-11 bind microtubules directly, or is its microtubule association
    mediated through other IFT-B subunits?
- question: >-
    Which IFT-B subunit(s) does DYF-11 contact directly, and does it partner with an IFT20
    ortholog as vertebrate IFT54 does?
suggested_experiments:
- description: >-
    In vitro microtubule co-sedimentation and IFT-B reconstitution assays with purified
    DYF-11 to define direct microtubule binding and subunit interactions.
- description: >-
    Live-imaging epistasis of GFP-tagged IFT components in dyf-11 and other IFT-B mutant
    backgrounds to order DYF-11 within the IFT-B assembly hierarchy.