Details for: CCDC61

Gene ID: 729440

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: CCDC61

Ensembl ID: ENSG00000104983

Description: coiled-coil domain containing 61

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • VIP GABAergic cortical interneuron CL4023016
    CSI 2.8
    rCSI 3.35%
    PRS 95.57
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 2.79
    rCSI 4.93%
    PRS 95.65
  • lung ciliated cell CL1000271
    CSI 2.75
    rCSI 3.18%
    PRS 96.93
  • ependymal cell CL0000065
    CSI 2.68
    rCSI 5.43%
    PRS 92.38
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 2.67
    rCSI 3.32%
    PRS 94.98
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 1.98
    rCSI 3.33%
    PRS 95.9
  • intestinal crypt stem cell of small intestine CL0009017
    CSI 1.73
    rCSI 4.67%
    PRS 99.01
  • deuterosomal cell CL4033044
    CSI 1.69
    rCSI 5.73%
    PRS 95.6
  • L6b glutamatergic cortical neuron CL4023038
    CSI 0.86
    rCSI 2.69%
    PRS 95.68
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 0.74
    rCSI 2.66%
    PRS 94.8

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

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  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [CCDC61](/details-gene/729440) (Coiled-Coil Domain Containing 61) is a protein-coding gene located on chromosome 19q13.32. The protein product is a key component of microtubule-organizing centers, particularly the centrosome and the basal bodies of cilia. Functional annotations and expression data strongly indicate its involvement in processes requiring highly organized microtubule structures, such as cell division, cell projection organization, and ciliogenesis. Recent studies have established its role in controlling centrosome cohesion, mitotic spindle assembly, and the formation of centriolar subdistal appendages, identifying it as a paralog of the well-known centriole duplication factor SAS6 ([Link](https://doi.org/10.1111/boc.201900038); [Link](https://doi.org/10.1016/j.str.2020.04.010)). **Overall**, [CCDC61](/details-gene/729440) shows significant expression in a diverse set of cells, including various neuronal subtypes, ciliated epithelial cells, and stem cells, underscoring its fundamental role in cellular architecture and proliferation. ## Cellular Roles and Expression Landscape The expression profile of [CCDC61](/details-gene/729440) highlights its importance in cells with specialized microtubule-based structures. Within the **Overall** context, it is a significant marker in several types of inhibitory neurons, including [VIP GABAergic cortical interneurons](/details-cell/CL4023016) (CSI: 2.80), [caudal ganglionic eminence derived cortical interneurons](/details-cell/CL4023064) (CSI: 2.79), and [pvalb GABAergic cortical interneurons](/details-cell/CL4023018) (CSI: 2.67). This suggests a potential role in establishing or maintaining the complex dendritic and axonal arbors characteristic of these cells. Beyond the nervous system, [CCDC61](/details-gene/729440) is highly significant in motile ciliated cells, such as [lung ciliated cells](/details-cell/CL1000271) (CSI: 2.75) and [ependymal cells](/details-cell/CL0000065) (CSI: 2.68). This expression pattern is consistent with its established function in ciliogenesis and the organization of basal bodies ([Link](https://doi.org/10.1016/j.str.2020.04.010)). Its high significance in [deuterosomal cells](/details-cell/CL4033044) (CSI: 1.69), which are specialized precursors for multiciliated cells, further solidifies this role. Additionally, [CCDC61](/details-gene/729440) shows notable expression in actively dividing cell populations like [intestinal crypt stem cells of the small intestine](/details-cell/CL0009017) (CSI: 1.73). This is consistent with its critical function in mitotic spindle assembly, a process essential for cell proliferation ([Link](https://doi.org/10.1091/mbc.e18-02-0115)). The collective expression data paints a picture of [CCDC61](/details-gene/729440) as a crucial structural protein for both dynamic mitotic machinery and stable ciliary structures. ## Pathways and Molecular Function The functions of [CCDC61](/details-gene/729440) are primarily centered on the organization and regulation of the microtubule cytoskeleton. Its molecular functions include [microtubule binding](/details-cell/GO:0008017) and [identical protein binding](/details-cell/GO:0042802), suggesting it acts as a structural or scaffolding protein that may self-assemble. **Biological Process annotations further clarify its roles:** * **Centrosome and Spindle Assembly:** It is implicated in [centriole assembly](/details-cell/GO:0098534) and [mitotic spindle assembly](/details-cell/GO:0090307). This is supported by its localization to the [centrosome](/details-cell/GO:0005813) and the broader [microtubule organizing center](/details-cell/GO:0005815), consistent with its expression in proliferating cells. * **Ciliogenesis:** [CCDC61](/details-gene/729440) is involved in [cell projection organization](/details-cell/GO:0030030) and is a component of the [ciliary basal body](/details-cell/GO:0036064), [centriolar satellite](/details-cell/GO:0034451), and [centriolar subdistal appendage](/details-cell/GO:0120103). These roles directly explain its high significance in ciliated cell types. Research has demonstrated that hVFL3/[CCDC61](/details-gene/729440) is a necessary component of mother centriole subdistal appendages required for proper centrosome positioning and cohesion ([Link](https://doi.org/10.1111/boc.201900038)). These annotated functions provide a clear molecular basis for the observed expression pattern of [CCDC61](/details-gene/729440) across diverse cell types that rely heavily on microtubule-based structures for their function and integrity. ## Research Directions Given the fundamental role of [CCDC61](/details-gene/729440) in microtubule organization, future research should focus on its cell-type-specific functions and its potential involvement in human disease, particularly ciliopathies and neurodevelopmental disorders. **Proposed Hypotheses:** 1. Given its high expression in multiple cortical interneuron subtypes and its role in microtubule organization, [CCDC61](/details-gene/729440) may be essential for the migration, maturation, and synaptic integration of these neurons during cortical development by regulating the non-centrosomal microtubule arrays that define their complex morphology. 2. Dysfunction of [CCDC61](/details-gene/729440) in [intestinal crypt stem cells](/details-cell/CL0009017) may impair primary cilia formation, leading to aberrant Wnt or Hedgehog signaling, thereby disrupting the balance between self-renewal and differentiation and potentially contributing to intestinal pathologies. **Experimental Approach:** To test the second hypothesis, one could utilize human intestinal organoid cultures. A CRISPR-Cas9 knockout of [CCDC61](/details-gene/729440) would be generated in these organoids. The subsequent effects on organoid development, proliferation (via EdU staining), and differentiation (via IHC for markers like MUC2 and CHGA) would be quantified. Critically, the structure and prevalence of primary cilia on LGR5-positive stem cells would be assessed using immunofluorescence for ciliary markers (e.g., ARL13B, acetylated tubulin). Downstream signaling alterations could be confirmed via RNA-sequencing to analyze the transcriptomes of control versus knockout organoids, with a specific focus on Wnt and Hedgehog pathway target genes. **Therapeutic Potential:** As a core structural protein involved in cell division and ciliogenesis, [CCDC61](/details-gene/729440) is unlikely to be a suitable direct therapeutic target for inhibition, as this would likely cause significant toxicity to healthy proliferating and ciliated tissues. However, its mutations could be diagnostic markers for certain ciliopathies or neurological disorders. Therapeutic strategies might instead focus on modulating downstream pathways affected by [CCDC61](/details-gene/729440) dysfunction, rather than targeting the protein itself. Gene therapy to restore its function in specific tissues could be a long-term possibility for monogenic diseases caused by its deficiency.

Genular Protein ID: 2485649112

Symbol: CCD61_HUMAN

Name: Coiled-coil domain-containing protein 61

UniProtKB Accession Codes:

Q9Y6R9 C8CAP4 Q9HDB6

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CDD 1 CTD 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 3 Ensembl 3 ExpressionAtlas 1 GO 11 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 1 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PDB 1 PDBsum 1 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pharos 1 PhosphoSitePlus 1 Proteomes 1 ProteomicsDB 1 Pumba 1 RNAct 1 RefSeq 3 SMR 1 STRING 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 15057824

Title: The DNA sequence and biology of human chromosome 19.

PubMed ID: 15057824

DOI: 10.1038/nature02399

PubMed ID: 17081983

Title: Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.

PubMed ID: 17081983

DOI: 10.1016/j.cell.2006.09.026

PubMed ID: 19413330

Title: Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.

PubMed ID: 19413330

DOI: 10.1021/ac9004309

PubMed ID: 19690332

Title: Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.

PubMed ID: 19690332

DOI: 10.1126/scisignal.2000007

PubMed ID: 20068231

Title: Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

PubMed ID: 20068231

DOI: 10.1126/scisignal.2000475

PubMed ID: 21406692

Title: System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.

PubMed ID: 21406692

DOI: 10.1126/scisignal.2001570

PubMed ID: 22814378

Title: N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB.

PubMed ID: 22814378

DOI: 10.1073/pnas.1210303109

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

DOI: 10.1021/pr300630k

PubMed ID: 24275569

Title: An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.

PubMed ID: 24275569

DOI: 10.1016/j.jprot.2013.11.014

PubMed ID: 30354798

Title: Ccdc61 controls centrosomal localization of Cep170 and is required for spindle assembly and symmetry.

PubMed ID: 30354798

DOI: 10.1091/mbc.e18-02-0115

PubMed ID: 31789463

Title: hVFL3/CCDC61 is a component of mother centriole subdistal appendages required for centrosome cohesion and positioning.

PubMed ID: 31789463

DOI: 10.1111/boc.201900038

PubMed ID: 32375023

Title: CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions.

PubMed ID: 32375023

DOI: 10.1016/j.str.2020.04.010

Sequence Information:

  • Length: 512
  • Mass: 57368
  • Checksum: 2DCB8BAFAF5B532E
  • Sequence:
    • MDQPAGLQVD YVFRGVEHAV RVMVSGQVLE LEVEDRMTAD QWRGEFDAGF IEDLTHKTGN 
FKQFNIFCHM LESALTQSSE SVTLDLLTYT DLESLRNRKM GGRPGSLAPR SAQLNSKRYL 
ILIYSVEFDR IHYPLPLPYQ GKPDPVVLQG IIRSLKEELG RLQGLDGQNT RDTRENEIWH 
LREQVSRLAS EKRELEAQLG RSREEALAGR AARQEAEALR GLVRGLELEL RQERGLGHRV 
AGRRGQDCRR LAKELEEAKA SERSLRARLK TLTSELALYK RGRRTPPVQP PPTREDRASS 
SRERSASRGR GAARSSSRES GRGSRGRGRP ARPSPSPTGG RALRFDPTAF VKAKERKQRE 
IQMKQQQRNR LGSGGSGDGP SVSWSRQTQP PAALTGRGDA PNRSRNRSSS VDSFRSRCSS 
ASSCSDLEDF SESLSRGGHR RRGKPPSPTP WSGSNMKSPP VERSHHQKSL ANSGGWVPIK 
EYSSEHQAAD MAEIDARLKA LQEYMNRLDM RS