Details for: COL21A1

Gene ID: 81578

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: COL21A1

Ensembl ID: ENSG00000124749

Description: collagen type XXI alpha 1 chain

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • sncg GABAergic cortical interneuron CL4023015
    CSI 27.6
    rCSI 44.39%
    PRS 77.74
  • VIP GABAergic cortical interneuron CL4023016
    CSI 25.63
    rCSI 30.62%
    PRS 76.75
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 13.1
    rCSI 21.99%
    PRS 76.71
  • ependymal cell CL0000065
    CSI 12.91
    rCSI 26.19%
    PRS 72.1
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 12.71
    rCSI 39.74%
    PRS 79.75
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 10.78
    rCSI 38.81%
    PRS 74.63
  • multi-ciliated epithelial cell CL0005012
    CSI 8.26
    rCSI 8.24%
    PRS 84.25
  • stromal cell CL0000499
    CSI 6.86
    rCSI 19.31%
    PRS 86
  • sst GABAergic cortical interneuron CL4023017
    CSI 6.78
    rCSI 8.74%
    PRS 77.81
  • myofibroblast cell CL0000186
    CSI 5.83
    rCSI 8.07%
    PRS 86.67
  • fibroblast of lung CL0002553
    CSI 5.8
    rCSI 5.4%
    PRS 91.12
  • GABAergic neuron CL0000617
    CSI 5.15
    rCSI 17.26%
    PRS 76.44
  • ionocyte CL0005006
    CSI 5.09
    rCSI 5.45%
    PRS 91.3
  • Schwann cell CL0002573
    CSI 4.48
    rCSI 12.72%
    PRS 86.54
  • choroid plexus epithelial cell CL0000706
    CSI 4.23
    rCSI 6.93%
    PRS 82.65
  • alveolar type 1 fibroblast cell CL4028004
    CSI 3.9
    rCSI 4.27%
    PRS 91.39
  • extravillous trophoblast CL0008036
    CSI 3.75
    rCSI 4.63%
    PRS 88.5
  • mesenchymal stem cell CL0000134
    CSI 3.67
    rCSI 40.24%
    PRS 91.9
  • hepatic stellate cell CL0000632
    CSI 3.67
    rCSI 13.74%
    PRS 85.09
  • ciliated epithelial cell CL0000067
    CSI 3.55
    rCSI 3.12%
    PRS 81.18
  • cardiac neuron CL0010022
    CSI 3.5
    rCSI 11.21%
    PRS 88.54
  • inhibitory interneuron CL0000498
    CSI 3.35
    rCSI 7.73%
    PRS 80.7
  • cardiac muscle cell CL0000746
    CSI 3.28
    rCSI 4.71%
    PRS 82.08
  • cerebellar granule cell CL0001031
    CSI 3.25
    rCSI 4.78%
    PRS 84.61
  • blood vessel endothelial cell CL0000071
    CSI 3.23
    rCSI 6.7%
    PRS 88.16
  • ciliated cell CL0000064
    CSI 3.12
    rCSI 5.06%
    PRS 84.1
  • vascular leptomeningeal cell CL4023051
    CSI 3.11
    rCSI 5.45%
    PRS 86.22
  • lung ciliated cell CL1000271
    CSI 3.11
    rCSI 3.6%
    PRS 84.27
  • adipocyte CL0000136
    CSI 3.04
    rCSI 3.9%
    PRS 81.79
  • vascular associated smooth muscle cell CL0000359
    CSI 2.96
    rCSI 9.6%
    PRS 88.08
  • smooth muscle cell CL0000192
    CSI 2.93
    rCSI 7%
    PRS 84.19
  • astrocyte of the cerebral cortex CL0002605
    CSI 2.75
    rCSI 6.16%
    PRS 77.12
  • renal interstitial pericyte CL1001318
    CSI 2.65
    rCSI 7.31%
    PRS 87.07
  • placental villous trophoblast CL2000060
    CSI 2.62
    rCSI 4.04%
    PRS 88.23
  • mesodermal cell CL0000222
    CSI 2.5
    rCSI 3%
    PRS 88.8
  • alveolar adventitial fibroblast CL4028006
    CSI 2.46
    rCSI 3.89%
    PRS 90.82
  • contractile cell CL0000183
    CSI 2.41
    rCSI 7.11%
    PRS 89.06
  • myeloid leukocyte CL0000766
    CSI 2.3
    rCSI 2.12%
    PRS 91.03
  • bronchus fibroblast of lung CL2000093
    CSI 2.21
    rCSI 1.79%
    PRS 89.2
  • L6b glutamatergic cortical neuron CL4023038
    CSI 2.11
    rCSI 6.58%
    PRS 78.12
  • duct epithelial cell CL0000068
    CSI 1.99
    rCSI 2.91%
    PRS 93.2
  • skeletal muscle satellite cell CL0000594
    CSI 1.96
    rCSI 5.72%
    PRS 95.67
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 1.92
    rCSI 2.39%
    PRS 74.53
  • chondrocyte CL0000138
    CSI 1.85
    rCSI 2.94%
    PRS 85.15
  • L4 intratelencephalic projecting glutamatergic neuron CL4030063
    CSI 1.83
    rCSI 4.39%
    PRS 79.33
  • ciliated columnar cell of tracheobronchial tree CL0002145
    CSI 1.83
    rCSI 4.17%
    PRS 83.09
  • mesothelial cell CL0000077
    CSI 1.69
    rCSI 6.62%
    PRS 72.84
  • enteroglial cell CL4040002
    CSI 1.66
    rCSI 8.73%
    PRS 90.23
  • tracheobronchial smooth muscle cell CL0019019
    CSI 1.64
    rCSI 2.9%
    PRS 92.62
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 1.59
    rCSI 3.87%
    PRS 74.49
  • regular atrial cardiac myocyte CL0002129
    CSI 1.3
    rCSI 4.2%
    PRS 86.45
  • mesenchymal cell CL0008019
    CSI 1.3
    rCSI 3.31%
    PRS 84.79
  • mesangial cell CL0000650
    CSI 1.2
    rCSI 4.88%
    PRS 94.89
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 1.09
    rCSI 1.93%
    PRS 76.15
  • microcirculation associated smooth muscle cell CL0008035
    CSI 1.01
    rCSI 2.93%
    PRS 88.99
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 1
    rCSI 3.77%
    PRS 76.92
  • regular ventricular cardiac myocyte CL0002131
    CSI 0.85
    rCSI 5.29%
    PRS 83.64
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 0.62
    rCSI 3.66%
    PRS 77.18
  • central nervous system neuron CL2000029
    CSI 0.45
    rCSI 3.34%
    PRS 81.26
  • blood vessel smooth muscle cell CL0019018
    CSI 0.45
    rCSI 3.69%
    PRS 86.91
  • kidney interstitial cell CL1000500
    CSI 0.41
    rCSI 6.7%
    PRS 91.06

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.

Comma-separated if multiple.
Comma-separated if multiple.

Legend:
  • Query Gene
  • 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 [COL21A1](/details-gene/81578) encodes the alpha-1 chain of type XXI collagen, a member of the Fibril-Associated Collagens with Interrupted Triple helices (FACIT) family ([Link](https://doi.org/10.1016/s0014-5793(01)02754-5)). Functionally, it is a structural constituent of the extracellular matrix (ECM), contributing to its tensile strength and organization. While classically associated with connective tissues, expression data from the **Overall** context reveals its most significant expression occurs in highly specific neuronal subtypes, particularly various classes of GABAergic cortical interneurons, such as [sncg GABAergic cortical interneuron](/details-cell/CL4023015) and [VIP GABAergic cortical interneuron](/details-cell/CL4023016). This unexpected expression pattern suggests that in addition to its structural role, [COL21A1](/details-gene/81578) may have specialized functions in the central nervous system. ## Cellular Roles and Expression Landscape The expression profile of [COL21A1](/details-gene/81578) indicates a prominent and specialized role within the central nervous system. In the **Overall** context, the gene shows remarkably high significance in several distinct classes of inhibitory interneurons of the cerebral cortex, including [sncg GABAergic cortical interneuron](/details-cell/CL4023015) (CSI: 27.60), [VIP GABAergic cortical interneuron](/details-cell/CL4023016) (CSI: 25.63), and [lamp5 GABAergic cortical interneuron](/details-cell/CL4023011) (CSI: 13.10). Its high significance extends to excitatory neurons as well, such as the [L5 extratelencephalic projecting glutamatergic cortical neuron](/details-cell/CL4023041) (CSI: 10.78). This strong and specific expression pattern in neuronal populations suggests a potential role in neuronal function, synaptic organization, or the specialized ECM of the brain known as the perineuronal net. Beyond the nervous system, [COL21A1](/details-gene/81578) is also a significant marker in several non-neuronal cell types. It is highly expressed in [ependymal cell](/details-cell/CL0000065) and [choroid plexus epithelial cell](/details-cell/CL0000706), which line the brain's ventricles and produce cerebrospinal fluid, indicating a possible role in the structural integrity of these critical barriers. The gene also shows relevance in mesenchymal-derived cells, such as [stromal cell](/details-cell/CL0000499), [myofibroblast cell](/details-cell/CL0000186), and [fibroblast of lung](/details-cell/CL0002553), which is more consistent with the traditional roles of collagens in providing structural support to tissues. ## Pathways and Molecular Function The annotated functions of [COL21A1](/details-gene/81578) are centered on the biology of the extracellular matrix. As a collagen, its primary molecular function is to act as an [extracellular matrix structural constituent conferring tensile strength](/details-go/GO:0030020). It participates in the formation of the [collagen trimer](/details-go/GO:0005581), a foundational step for building the [collagen-containing extracellular matrix](/details-go/GO:0062023). Consistent with these roles, [COL21A1](/details-gene/81578) is involved in several key Reactome pathways governing the collagen life cycle. These include [Collagen biosynthesis and modifying enzymes](/details-pathway/R-HSA-1650814), [Collagen chain trimerization](/details-pathway/R-HSA-8948216), and the broader process of [Collagen formation](/details-pathway/R-HSA-1474290). Ultimately, its expression and function contribute to the overall organization and maintenance of the ECM, as detailed in the [Extracellular matrix organization](/details-pathway/R-HSA-1474244) pathway. The specific expression in diverse neuronal subtypes suggests that these canonical ECM-related pathways are likely co-opted for specialized functions within the unique microenvironment of the brain. ## Research Directions The strikingly high expression of [COL21A1](/details-gene/81578) in specific cortical interneurons, rather than in classic connective tissue cells, suggests a non-canonical role for this collagen in the central nervous system. This observation forms the basis for several testable hypotheses. 1. **Hypothesis 1:** [COL21A1](/details-gene/81578) is a key component of the perineuronal net (PNN) surrounding specific GABAergic interneurons, where it is critical for synaptic stabilization and the regulation of neuronal plasticity. Its specific expression pattern suggests it may define the composition of the PNN for certain neuronal subtypes. 2. **Hypothesis 2:** In [ependymal cell](/details-cell/CL0000065)s and [choroid plexus epithelial cell](/details-cell/CL0000706)s, [COL21A1](/details-gene/81578) contributes to the structural integrity and selective permeability of the blood-cerebrospinal fluid barrier. Its dysregulation could lead to compromised barrier function, potentially contributing to neuroinflammatory or neurodegenerative conditions. To test the role of [COL21A1](/details-gene/81578) in cortical interneuron function (Hypothesis 1), a conditional knockout mouse model could be generated to specifically delete the gene in neuronal subtypes where it is highly expressed (e.g., using a VIP-Cre or Sst-Cre driver line). Subsequent analysis using super-resolution microscopy combined with lectin staining (for PNNs) and immunohistochemistry for synaptic markers (e.g., PSD-95, Synaptophysin) would allow for detailed examination of its impact on PNN structure and synaptic integrity. Electrophysiological recordings from these neurons would further reveal any functional consequences on their firing properties and synaptic transmission. Given its extracellular location and high specificity for certain cell types, [COL21A1](/details-gene/81578) could present a novel therapeutic target. If its role in maintaining synaptic stability is confirmed, delivering recombinant [COL21A1](/details-gene/81578) protein or developing small molecules to enhance its expression could be a strategy to promote neuronal circuit stability in conditions like epilepsy or after brain injury. Conversely, if its accumulation in the ECM becomes pathological in certain neurological diseases, targeting it for degradation via engineered enzymes or blocking its interactions with cell surface receptors could be a viable therapeutic approach.

Genular Protein ID: 1557718669

Symbol: COLA1_HUMAN

Name: Collagen alpha-1(XXI) chain

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 11566190

Title: A new FACIT of the collagen family: COL21A1.

PubMed ID: 11566190

DOI: 10.1016/s0014-5793(01)02754-5

PubMed ID: 11863369

Title: Genomic organization and characterization of the human type XXI collagen (COL21A1) gene.

PubMed ID: 11863369

DOI: 10.1006/geno.2002.6712

PubMed ID: 11230166

Title: Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs.

PubMed ID: 11230166

DOI: 10.1101/gr.gr1547r

PubMed ID: 15498874

Title: Large-scale cDNA transfection screening for genes related to cancer development and progression.

PubMed ID: 15498874

DOI: 10.1073/pnas.0404089101

PubMed ID: 14702039

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

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 14574404

Title: The DNA sequence and analysis of human chromosome 6.

PubMed ID: 14574404

DOI: 10.1038/nature02055

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: 957
  • Mass: 99369
  • Checksum: 4C5CDF5E6656A675
  • Sequence:
  • MAHYITFLCM VLVLLLQNSV LAEDGEVRSS CRTAPTDLVF ILDGSYSVGP ENFEIVKKWL 
    VNITKNFDIG PKFIQVGVVQ YSDYPVLEIP LGSYDSGEHL TAAVESILYL GGNTKTGKAI 
    QFALDYLFAK SSRFLTKIAV VLTDGKSQDD VKDAAQAARD SKITLFAIGV GSETEDAELR 
    AIANKPSSTY VFYVEDYIAI SKIREVMKQK LCEESVCPTR IPVAARDERG FDILLGLDVN 
    KKVKKRIQLS PKKIKGYEVT SKVDLSELTS NVFPEGLPPS YVFVSTQRFK VKKIWDLWRI 
    LTIDGRPQIA VTLNGVDKIL LFTTTSVING SQVVTFANPQ VKTLFDEGWH QIRLLVTEQD 
    VTLYIDDQQI ENKPLHPVLG ILINGQTQIG KYSGKEETVQ FDVQKLRIYC DPEQNNRETA 
    CEIPGFNGEC LNGPSDVGST PAPCICPPGK PGLQGPKGDP GLPGNPGYPG QPGQDGKPGY 
    QGIAGTPGVP GSPGIQGARG LPGYKGEPGR DGDKGDRGLP GFPGLHGMPG SKGEMGAKGD 
    KGSPGFYGKK GAKGEKGNAG FPGLPGPAGE PGRHGKDGLM GSPGFKGEAG SPGAPGQDGT 
    RGEPGIPGFP GNRGLMGQKG EIGPPGQQGK KGAPGMPGLM GSNGSPGQPG TPGSKGSKGE 
    PGIQGMPGAS GLKGEPGATG SPGEPGYMGL PGIQGKKGDK GNQGEKGIQG QKGENGRQGI 
    PGQQGIQGHH GAKGERGEKG EPGVRGAIGS KGESGVDGLM GPAGPKGQPG DPGPQGPPGL 
    DGKPGREFSE QFIRQVCTDV IRAQLPVLLQ SGRIRNCDHC LSQHGSPGIP GPPGPIGPEG 
    PRGLPGLPGR DGVPGLVGVP GRPGVRGLKG LPGRNGEKGS QGFGYPGEQG PPGPPGPEGP 
    PGISKEGPPG DPGLPGKDGD HGKPGIQGQP GPPGICDPSL CFSVIARRDP FRKGPNY

Genular Protein ID: 4176990251

Symbol: B3KU30_HUMAN

Name: N/A

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 14702039

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

PubMed ID: 14702039

DOI: 10.1038/ng1285

Sequence Information:

  • Length: 314
  • Mass: 33170
  • Checksum: A0846A878C744813
  • Sequence:
  • MAHQASLEHR DLREAKVNLE FKGCLGLLGS RENQEQRVPQ ENQDTWVYPG FKEKRGTKEI 
    KVKKVFRVKR EKMEDREFQG NREFKAIMVQ KERGEKGEPG VRGAIGSKGE SGVDGLMGPA 
    GPKGQPGDPG PQGPPGLDGK PGREFSEQFI RQVCTDVIRA QLPVLLQSGR IRNCDHCLSQ 
    HGSPGIPGPP GPIGPEGPRG LPGLPGRDGV PGLVGVPGRP GVRGLKGLPG RNGEKGSQGF 
    GYPGEQGPPG PPGPEGPPGI SKEGPPGDPG LPGKDGDHGK PGIQGQPGPP GICDPSLCFS 
    VIARRDPFRK GPNY

Genular Protein ID: 3837728552

Symbol: B7ZLK3_HUMAN

Name: N/A

UniProtKB Accession Codes:

Database IDs:

Citations:

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: 957
  • Mass: 99341
  • Checksum: D8448FAD5ABDD52E
  • Sequence:
  • MAHYITFLCM VLVLLLQNSV LAEDGEVRSS CRTAPTDLVF ILDGSYSVGP ENFEIVKKWL 
    VNITKNFDIG PKFIQVGVVQ YSDYPVLEIP LGSYDSGEHL TAAVESILYL GGNTKTGKAI 
    QFALDYLFAK SSRFLTKIAV VLTDGKSQDD VKDAAQAARD SKITLFAIGV GSETEDAELK 
    AIANKPSSTY VFYVEDYIAI SKIREVMKQK LCEESVCPTR IPVAARDERG FDILLGLDVN 
    KKVKKRIQLS PKKIKGYEVT SKVDLSELTS NVFPEGLPPS YVFVSTQRFK VKKIWDLWRI 
    LTIDGRPQIA VTLNGVDKIL LFTTTSVING SQVVTFANPQ VKTLFDEGWH QIRLLVTEQD 
    VTLYIDDQQI ENKPLHPVLG ILINGQTQIG KYSGKEETVQ FDVQKLRIYC DPEQNNRETA 
    CEIPGFNGEC LNGPSDVGST PAPCICPPGK PGLQGPKGDP GLPGNPGYPG QPGQDGKPGY 
    QGIAGTPGVP GSPGIQGARG LPGYKGEPGR DGDKGDRGLP GFPGLHGMPG SKGEMGAKGD 
    KGSPGFYGKK GAKGEKGNAG FPGLPGPAGE PGRHGKDGLM GSPGFKGEAG SPGAPGQDGT 
    RGEPGIPGFP GNRGLMGQKG EIGPPGQQGK KGAPGMPGLM GSNGSPGQPG TPGSKGSKGE 
    PGIQGMPGAS GLKGEPGATG SPGEPGYMGL PGIQGKKGDK GNQGEKGIQG QKGENGRQGI 
    PGQQGIQGHH GAKGERGEKG EPGVRGAIGS KGESGVDGLM GPAGPKGQPG DPGPQGPPGL 
    DGKPGREFSE QFIRQVCTDV IRAQLPVLLQ SGRIRNCDHC LSQHGSPGIP GPPGPIGPEG 
    PRGLPGLPGR DGVPGLVGVP GRPGVRGLKG LPGRNGEKGS QGFGYPGEQG PPGPPGPEGP 
    PGISKEGPPG DPGLPGKDGD HGKPGIQGQP GPPGICDPSL CFSVIARRDP FRKGPNY