cilium

GO:0005929 · Appendage · Appendage · Proposed

A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts; it is largely bounded by an extrusion of the plasma membrane, contains a longitudinal microtubule array, and is anchored to a basal body. [GO:0005929]

Synonyms: eukaryotic flagellum; microtubule-based flagellum

Has part: axoneme (GO:0005930); ciliary membrane (GO:0060170); ciliary basal body (GO:0036064); ciliary transition zone (GO:0035869)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Essential	Role
axoneme	Protein complex	part of	`GO:0005930`	ESSENTIAL	Microtubule-based core of the cilium; 9+2 axonemes in Chlamydomonas motile cilia carry outer doublets, a central pair, dynein arms, radial spokes and regulatory linkers. `GO:0005930` GO:0005930 identifies the axoneme as the microtubule and protein core of eukaryotic cilia and flagella. `DOI:10.1126/science.1128618` Nicastro et al. 2006 resolved the 9+2 Chlamydomonas axoneme architecture by cryoelectron tomography.
ciliary membrane	Other	part of	`GO:0060170`	ESSENTIAL	Specialized plasma-membrane extension that surrounds the axoneme and houses ciliary membrane proteins. `GO:0060170` GO:0060170 defines the ciliary membrane as the portion of plasma membrane surrounding a cilium. `DOI:10.1083/jcb.200504008` Pazour et al. 2005 identified proteins in purified Chlamydomonas flagella, including signal-transduction and membrane-associated candidates.
ciliary basal body	Other	part of	`GO:0036064`	ESSENTIAL	Centriole-derived microtubule cylinder at the ciliary base that anchors the organelle and nucleates axoneme growth. `GO:0036064` GO:0036064 defines the ciliary basal body as the membrane-tethered microtubule array at the base of a eukaryotic cilium. `DOI:10.1104/pp.010807` Silflow and Lefebvre 2001 reviewed basal bodies as the centriolar organizers of Chlamydomonas flagella.
ciliary transition zone	Other	part of	`GO:0035869`	UNKNOWN	Gated region between the basal body and ciliary shaft that links axonemal doublets to the ciliary membrane and helps separate ciliary contents from the cytosol. `GO:0035869` GO:0035869 defines the ciliary transition zone by Y-shaped links between axonemal microtubules and the ciliary membrane. `GO:0097546` GO:0097546 places transition fibers and the transition zone at the ciliary base where proteins are sorted before cilium entry.
intraciliary transport particle	Protein complex	acts on	`GO:0030990`	UNKNOWN	IFT protein-particle complex that moves ciliary cargo bidirectionally along axonemal microtubules to assemble and maintain the cilium. `GO:0030990` GO:0030990 identifies the intraciliary transport particle protein complex. `DOI:10.1038/nrm952` Rosenbaum and Witman 2002 review IFT particles as transport machinery for cilium and flagellum assembly and maintenance.

Taxonomic distribution

NCBITaxon:3055 Chlamydomonas reinhardtii — COMMON: Chlamydomonas cells bear paired motile eukaryotic flagella that are used as a reference system for ciliary assembly, motility and intraflagellar transport. [DOI:10.1104/pp.010807]

Canonical examples

NCBITaxon:3055 Chlamydomonas reinhardtii — Green-algal model whose purified flagella were profiled by proteomics. [DOI:10.1083/jcb.200504008]

Functions

cilium assembly GO:0060271 — The basal body, transition-zone gate and bidirectional intraflagellar transport machinery assemble the membrane-sheathed axoneme.
- DOI:10.1038/nrm952 Rosenbaum and Witman 2002 review intraflagellar transport as machinery required to build and maintain eukaryotic cilia and flagella.
cilium-dependent cell motility GO:0060285 — Motile 9+2 cilia beat through axonemal dynein activity, bending the ciliary shaft to move cells such as Chlamydomonas through liquid.
- DOI:10.1104/pp.010807 Silflow and Lefebvre 2001 review Chlamydomonas flagella as motility organelles built on a conserved eukaryotic ciliary axoneme.
- DOI:10.1126/science.1128618 Nicastro et al. 2006 used Chlamydomonas axonemes to model dynein-generated microtubule sliding forces.

Mechanism graphs

Intraflagellar transport builds the ciliary axoneme (ASSEMBLY)

A basal body seeds axoneme extension, a transition-zone gate organizes entry into the membrane-bounded ciliary compartment, and intraflagellar-transport particles move cargo along axonemal microtubules for cilium assembly.

Subject	Predicate	Object	Evidence
ciliary basal body	nucleates	axoneme	`GO:0036064` GO:0036064 defines the ciliary basal body as the axoneme-growth nucleation site.
axoneme	forms core of	cilium	`DOI:10.1126/science.1128618` Nicastro et al. 2006 resolved the axonemal core from Chlamydomonas flagella.
ciliary membrane	bounds	cilium	`GO:0060170` GO:0060170 defines the ciliary membrane as the plasma-membrane portion around the cilium.
ciliary transition zone	gates entry into	cilium	`GO:0035869` GO:0035869 identifies the ciliary transition zone as a membrane-linked ciliary gate.
intraciliary transport particle	transports cargo along	axoneme	`DOI:10.1038/nrm952` Rosenbaum and Witman 2002 review bidirectional IFT-particle transport along the Chlamydomonas axoneme.
intraciliary transport particle	supports	cilium assembly	`DOI:10.1038/nrm952` Rosenbaum and Witman 2002 review IFT as a requirement for cilium and flagellum assembly and maintenance.

Discussions

INTERPRETATION (RESOLVED): Should bacterial-type flagella or archaeal-type flagella be merged under the cilium record? GO:0005929 explicitly scopes cilium to the membrane-sheathed, microtubule-based eukaryotic organelle. Bacterial-type flagella and archaeal-type flagella are nonhomologous prokaryotic appendages with separate GO identities and separate CellStructureMech records.

Evidence

GO:0005929 Gene Ontology cellular-component term for the cilium.
DOI:10.1104/pp.010807 Silflow and Lefebvre 2001, 'Assembly and Motility of Eukaryotic Cilia and Flagella. Lessons from Chlamydomonas reinhardtii', Plant Physiology.
DOI:10.1038/nrm952 Rosenbaum and Witman 2002, 'Intraflagellar transport', Nature Reviews Molecular Cell Biology.
DOI:10.1083/jcb.200504008 Pazour, Agrin, Leszyk and Witman 2005, 'Proteomic analysis of a eukaryotic cilium', Journal of Cell Biology.
DOI:10.1126/science.1128618 Nicastro et al. 2006, 'The Molecular Architecture of Axonemes Revealed by Cryoelectron Tomography', Science.

Curation history

2026-09-12T03:11:20Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-12T03:12:13Z codex · EXPANDED_RECORD — Added GO cilium synonymy and substructure groundings, Chlamydomonas scope, assembly and motility functions, cilium literature evidence, an IFT-based assembly graph, and a resolved bacterial/archaeal flagellum boundary discussion.
2026-09-12T03:12:26Z codex · FIX_COMPONENT_TYPE — Changed the GO-grounded ciliary membrane domain component type from LIPID to OTHER.
2026-09-12T03:19:23Z codex · SCOPE_CANONICAL_EXAMPLE — Narrowed the Chlamydomonas canonical-example note to the purified-flagella proteomics claim supported by its single DOI reference.
2026-09-12T03:24:41Z codex · ADDRESSED_PR_REVIEW — Resolved PR #570 review issues #571 and #572 by adding GO:0030990 intraciliary transport particle as cilium-associated machinery and retyping basal-body and transition-zone substructures as OTHER.
2026-09-12T03:27:49Z codex · ADDRESS_QC — Changed the associated IFT particle machinery essentiality from ESSENTIAL to UNKNOWN to match corpus component-role invariants.

Source: data/structures/appendage/cilium.yaml