Details for: CNTD1

Gene ID: 124817

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: CNTD1

Ensembl ID: ENSG00000176563

Description: cyclin N-terminal domain containing 1

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • multi-ciliated epithelial cell CL0005012
    CSI 2.59
    rCSI 2.58%
    PRS 95.18
  • ependymal cell CL0000065
    CSI 2.07
    rCSI 4.2%
    PRS 89.02
  • CD8-positive, alpha-beta memory T cell, CD45RO-positive CL0001203
    CSI 1.27
    rCSI 1.54%
    PRS 84.92
  • ciliated columnar cell of tracheobronchial tree CL0002145
    CSI 1.03
    rCSI 2.35%
    PRS 93.8
  • parietal cell CL0000162
    CSI 0.61
    rCSI 5.23%
    PRS 97.51

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

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  • Node Color (Target Cell CSI, relative to current network):
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    • High
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    • 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 [CNTD1](/details-gene/124817) (Cyclin N-terminal Domain Containing 1) is a protein-coding gene located on chromosome 17q21.2-q21.31. Functional annotations strongly implicate [CNTD1](/details-gene/124817) in core meiotic processes, including the regulation of the meiotic cell cycle and reciprocal recombination, with a specific role noted in spermatogenesis. Consistent with a function in DNA recombination, the protein localizes to the nucleus, chromosomes, and sites of DNA double-strand breaks. Despite its well-defined role in meiosis, expression data reveals its highest significance in several somatic cell types, most notably in various ciliated epithelial cells. This suggests that [CNTD1](/details-gene/124817) may possess additional, context-dependent functions outside of the germline. The existence and sequence of this gene have been validated through multiple large-scale sequencing and cDNA cloning projects [Link](https://doi.org/10.1038/ng1285), [Link](https://doi.org/10.1101/gr.2596504). ## Cellular Roles and Expression Landscape The expression profile of [CNTD1](/details-gene/124817) presents a notable dichotomy between its annotated function and its observed cellular landscape. **Overall**, the gene shows its highest significance in terminally differentiated, ciliated cell populations. * **Ciliated Epithelial Cells:** [CNTD1](/details-gene/124817) is a significant marker in [multi-ciliated epithelial cell](/details-cell/CL0005012) (CSI: 2.59), [ependymal cell](/details-cell/CL0000065) (CSI: 2.07), and [ciliated columnar cell of tracheobronchial tree](/details-cell/CL0002145) (CSI: 1.03). This strong and consistent signal across multiple types of ciliated cells suggests a potential role in cilia formation, maintenance, or function, an area of biology not captured by its current functional annotations. * **Immune and Secretory Cells:** The gene also displays moderate significance in [CD8-positive, alpha-beta memory T cell, CD45RO-positive](/details-cell/CL0001203) (CSI: 1.27) and [parietal cell](/details-cell/CL0000162) (CSI: 0.61). Its role in these specialized immune and gastric acid-secreting cells is currently undefined. The prominent expression in somatic cells, particularly ciliated epithelia, is unexpected given its established functional links to meiosis and germline development. This suggests either a moonlighting function for [CNTD1](/details-gene/124817) in these specialized cell types or that its function in DNA repair is particularly relevant in these cellular contexts. ## Pathways and Molecular Function Functional annotation data provides a clear picture of [CNTD1](/details-gene/124817)'s involvement in sexual reproduction and genome maintenance. * **Meiotic Recombination:** [CNTD1](/details-gene/124817) is annotated to the biological processes of [reciprocal meiotic recombination](/details/GO:0007131) and [regulation of meiotic cell cycle](/details/GO:0051445). This indicates a critical role in the exchange of genetic material between homologous chromosomes during meiosis I, a process essential for generating genetic diversity. Its annotated role in [spermatogenesis](/details/GO:0007283) further specifies its function within the male germline. * **Cellular Localization:** The protein's localization to the [nucleus](/details/GO:0005634), the [chromosome](/details/GO:0005694), and specifically to the [site of double-strand break](/details/GO:00035861) is highly consistent with a direct role in DNA repair and recombination. This suggests it may be a component of the machinery that processes and repairs programmed DNA breaks that initiate meiotic crossing over. While these pathways are well-defined for germ cells, their direct applicability to terminally differentiated, non-dividing cells like ciliated epithelia remains an open question. It is possible the DNA repair aspect of its function is utilized in these long-lived somatic cells to maintain genomic integrity. ## Research Directions The discrepancy between the meiotic function of [CNTD1](/details-gene/124817) and its expression profile in somatic ciliated cells is a key area for future research. **Proposed Hypotheses:** 1. [CNTD1](/details-gene/124817) possesses a moonlighting function in ciliated cells, where it is repurposed for a role in the biogenesis, structural integrity, or function of cilia, possibly through interactions with the microtubule organizing center or basal body. 2. The expression of [CNTD1](/details-gene/124817) in ciliated cells and memory T cells reflects a heightened requirement for genomic maintenance or a specialized DNA damage response in these long-lived cell types, leveraging its known role in processing DNA breaks. 3. The functional significance of [CNTD1](/details-gene/124817) is primarily restricted to germ cells, and its expression in some somatic tissues may be a form of transcriptional noise or a vestigial remnant without significant functional consequence. **Suggested Experimental Approach:** To test the hypothesis of a moonlighting function in ciliated cells (Hypothesis 1), an *in vitro* air-liquid interface (ALI) culture system for primary human bronchial epithelial cells could be utilized. Differentiating these cells at an ALI robustly induces multiciliogenesis. A loss-of-function study could be performed by transducing the basal progenitor cells with shRNA or a CRISPR-Cas9 system targeting [CNTD1](/details-gene/124817). Following differentiation, the effects on cilia could be quantified by assessing the number of ciliated cells, cilia length, and beat frequency using immunofluorescence microscopy and high-speed video analysis. Proteomic analysis of the [CNTD1](/details-gene/124817) interactome in these cells could further reveal novel binding partners related to cilia or basal body structures. **Therapeutic Potential:** Given its critical role in spermatogenesis, [CNTD1](/details-gene/124817) could be explored as a potential target for non-hormonal male contraception. Inhibition of its function would be expected to disrupt meiosis and sperm production. However, its significant expression in somatic tissues, including the respiratory epithelium and T cells, raises substantial concerns about potential off-target effects of systemic inhibition. Any therapeutic strategy would require a highly targeted delivery system to the testes to be considered viable. Currently, its link to pathology is not established, limiting its immediate appeal as a target for disease intervention outside of fertility.

Genular Protein ID: 3341240979

Symbol: CNTD1_HUMAN

Name: N/A

UniProtKB Accession Codes:

Q8N815 Q658Q6 Q8NEP1

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 4 Ensembl 1 ExpressionAtlas 1 GO 7 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HPA 1 InParanoid 1 InterPro 2 KEGG 1 MANE-Select 1 MIM 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 2 STRING 1 SUPFAM 1 SignaLink 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 neXtProt 1

Citations:

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

Sequence Information:

  • Length: 330
  • Mass: 36921
  • Checksum: 6A08ED50392706ED
  • Sequence:
    • MDGPMRPRSA SLVDFQFGVV ATETIEDALL HLAQQNEQAV REASGRLGRF REPQIVEFVF 
LLSEQWCLEK SVSYQAVEIL ERFMVKQAEN ICRQATIQPR DNKRESQNWR ALKQQLVNKF 
TLRLVSCVQL ASKLSFRNKI ISNITVLNFL QALGYLHTKE ELLESELDVL KSLNFRINLP 
TPLAYVETLL EVLGYNGCLV PAMRLHATCL TLLDLVYLLH EPIYESLLRA SIENSTPSQL 
QGEKFTSVKE DFMLLAVGII AASAFIQNHE CWSQVVGHLQ SITGIALASI AEFSYAILTH 
GVGANTPGRQ QSIPPHLAAR ALKTVASSNT

Genular Protein ID: 3499312567

Symbol: B4DXR6_HUMAN

Name: N/A

UniProtKB Accession Codes:

B4DXR6

Database IDs:

Antibodypedia 1 Bgee 1 BioGRID-ORCS 1 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 5 Ensembl 2 Gene3D 1 GeneTree 1 HGNC 1 HOGENOM 1 InterPro 1 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 Proteomes 2 RefSeq 4 SUPFAM 1 UCSC 1 VEuPathDB 1

Citations:

PubMed ID: 11237011

Title: Initial sequencing and analysis of the human genome.

PubMed ID: 11237011

DOI: 10.1038/35057062

PubMed ID: 11181995

Title: The sequence of the human genome.

PubMed ID: 11181995

DOI: 10.1126/science.1058040

PubMed ID: 15496913

Title: Finishing the euchromatic sequence of the human genome.

PubMed ID: 15496913

DOI: 10.1038/nature03001

PubMed ID: 16625196

Title: DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

PubMed ID: 16625196

DOI: 10.1038/nature04689

Sequence Information:

  • Length: 247
  • Mass: 27424
  • Checksum: 097A00AC5925CA47
  • Sequence:
    • MVKQAENICR QATIQPRDNK RESQNWRALK QQLVNKFTLR LVSCVQLASK LSFRNKIISN 
ITVLNFLQAL GYLHTKEELL ESELDVLKSL NFRINLPTPL AYVETLLEVL GYNGCLVPAM 
RLHATCLTLL DLVYLLHEPI YESLLRASIE NSTPSQLQGE KFTSVKEDFM LLAVGIIAAS 
AFIQNHECWS QVVGHLQSIT GIALASIAEF SYAILTHGVG ANTPGRQQSI PPHLAARALK 
TVASSNT