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COL16A1 collagen type XVI alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1307, updated on 5-Mar-2024

Summary

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Official Symbol
COL16A1provided by HGNC
Official Full Name
collagen type XVI alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2193
See related
Ensembl:ENSG00000084636 MIM:120326; AllianceGenome:HGNC:2193
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
447AA; FP1572
Summary
This gene encodes the alpha chain of type XVI collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Members of this collagen family are found in association with fibril-forming collagens such as type I and II, and serve to maintain the integrity of the extracellular matrix. High levels of type XVI collagen have been found in fibroblasts and keratinocytes, and in smooth muscle and amnion. [provided by RefSeq, Jul 2008]
Expression
Broad expression in ovary (RPKM 53.1), prostate (RPKM 25.7) and 20 other tissues See more
Orthologs
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Genomic context

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Location:
1p35.2
Exon count:
74
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31652263..31704017, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31509912..31561650, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32117864..32169618, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32041927-32042647 Neighboring gene tubulointerstitial nephritis antigen like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 571 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:32070860-32072059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32080194-32080980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32083206-32083895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32090464-32090964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32090965-32091465 Neighboring gene hypocretin receptor 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32110207-32110977 Neighboring gene penta-EF-hand domain containing 1 Neighboring gene PEF1 and COL16A1 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32123622-32123860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32124291-32124792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32131402-32131941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32131942-32132480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32133021-32133558 Neighboring gene uncharacterized LOC101929444 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:32145564-32146763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32147039-32147911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32162063-32162572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32164717-32165470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32166977-32167729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 649 Neighboring gene Sharpr-MPRA regulatory region 11964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32181521-32182116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32189409-32189910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 573 Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32218779-32219393 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32219394-32220007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32220374-32220980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32221586-32222191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32222192-32222796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32227559-32228412 Neighboring gene uncharacterized LOC124903930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 576 Neighboring gene microRNA 4254

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The NC11 domain of collagen XVI is a potential biomarker for oral squamous cell carcinoma and triggers vasculogenic mimicry via upregulation of endothelial receptors VEGFR1, VEGFR2 and uPAR.
    Title: The NC11 domain of human collagen XVI induces vasculogenic mimicry in oral squamous cell carcinoma cells.
  2. High Collagen XVI expression is associated with invasion of oral squamous cell carcinoma.
    Title: Collagen XVI induces expression of MMP9 via modulation of AP-1 transcription factors and facilitates invasion of oral squamous cell carcinoma.
  3. collagen XVI plays a decisive role in the interaction of connective tissue cells with their ECM, which is impaired in pathological situations
    Title: Collagen XVI in health and disease.
  4. Gene expression profiles showed that COL16A1 was up-regulated in epidermolysis bullosa subtypes.
    Title: Epidermolysis bullosa - a group of skin diseases with different causes but commonalities in gene expression.
  5. Overexpression of type XVI collagen in aberrant oral keratinocytes leads to Kindlin-1 induction, increased Kindlin-1/beta1-integrin interaction, integrin activation and subsequently to a proliferative cellular phenotype.
    Title: Induction of type XVI collagen expression facilitates proliferation of oral cancer cells.
  6. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  8. Collagen XVI promotes persistence of intestinal subepithelial myofibroblasts in the normal and in the inflamed bowel wall by stabilizing focal adhesion contacts.
    Title: Collagen XVI induces formation of focal contacts on intestinal myofibroblasts isolated from the normal and inflamed intestinal tract.
  9. These results demonstrate de-novo expression of collagen XVI in glioblastomas as part of the tumor specific remodeling of the ECM.
    Title: Collagen XVI expression is upregulated in glioblastomas and promotes tumor cell adhesion.
  10. Not in banded collagen fibrils in dermis, but is component of specialized fibrillin-1-containing microfibrils. In cartilage matrix not in aggregates with fibrillin-1. Resides in thin, weakly banded collagen fibrils also containing collagens II and XI.
    Title: Discrete integration of collagen XVI into tissue-specific collagen fibrils or beaded microfibrils.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2021-02-01)

ClinGen Genome Curation Page
Haploinsufficency

Dosage sensitivity unlikely (Last evaluated 2021-02-01)

ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength HDA PubMed 
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables integrin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell adhesion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cell adhesion mediated by integrin IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in female pregnancy TAS
Traceable Author Statement
more info
 PubMed 
involved_in integrin activation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in integrin-mediated signaling pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of focal adhesion assembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of collagen type IX trimer IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of collagen type XVI trimer TAS
Traceable Author Statement
more info
 PubMed 
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
collagen alpha-1(XVI) chain
Names
alpha 1 type XVI collagen
collagen XVI, alpha-1 polypeptide
collagen, type XVI, alpha 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001856.4 → NP_001847.3  collagen alpha-1(XVI) chain precursor

    See identical proteins and their annotated locations for NP_001847.3

    Status: REVIEWED

    Source sequence(s)
    AC114488, BC064839, M92642, S57132
    Consensus CDS
    CCDS41297.1
    UniProtKB/Swiss-Prot
    Q07092, Q16593, Q59F89, Q71RG9
    Related
    ENSP00000362776.3, ENST00000373672.8
    Conserved Domains (2) summary
    pfam01391
    Location:756 → 803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    31652263..31704017 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047446435.1 → XP_047302391.1  collagen alpha-1(XVI) chain isoform X9

  2. XM_047446431.1 → XP_047302387.1  collagen alpha-1(XVI) chain isoform X7

  3. XM_017000339.2 → XP_016855828.1  collagen alpha-1(XVI) chain isoform X2

  4. XM_047446432.1 → XP_047302388.1  collagen alpha-1(XVI) chain isoform X8

  5. XM_011540724.2 → XP_011539026.1  collagen alpha-1(XVI) chain isoform X6

    Conserved Domains (2) summary
    pfam01391
    Location:685 → 744
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains

  6. XM_011540723.2 → XP_011539025.1  collagen alpha-1(XVI) chain isoform X5

    Conserved Domains (2) summary
    pfam01391
    Location:756 → 803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains

  7. XM_005270481.2 → XP_005270538.1  collagen alpha-1(XVI) chain isoform X4

    Conserved Domains (2) summary
    pfam01391
    Location:756 → 803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains

  8. XM_017000338.2 → XP_016855827.1  collagen alpha-1(XVI) chain isoform X1

  9. XM_011540722.2 → XP_011539024.1  collagen alpha-1(XVI) chain isoform X3

    Conserved Domains (2) summary
    pfam01391
    Location:756 → 803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains

  10. XM_047446439.1 → XP_047302395.1  collagen alpha-1(XVI) chain isoform X10

  11. XM_011540727.3 → XP_011539029.1  collagen alpha-1(XVI) chain isoform X11

    Conserved Domains (1) summary
    pfam01391
    Location:454 → 501
    Collagen; Collagen triple helix repeat (20 copies)

  12. XM_011540728.3 → XP_011539030.1  collagen alpha-1(XVI) chain isoform X13

    Conserved Domains (1) summary
    pfam01391
    Location:241 → 288
    Collagen; Collagen triple helix repeat (20 copies)

  13. XM_017000340.3 → XP_016855829.1  collagen alpha-1(XVI) chain isoform X14

  14. XM_017000341.2 → XP_016855830.1  collagen alpha-1(XVI) chain isoform X17

  15. XM_047446440.1 → XP_047302396.1  collagen alpha-1(XVI) chain isoform X12

  16. XM_011540730.2 → XP_011539032.1  collagen alpha-1(XVI) chain isoform X16

    Related
    ENSP00000362772.3, ENST00000373668.7
    Conserved Domains (2) summary
    pfam01391
    Location:756 → 803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains

  17. XM_011540729.2 → XP_011539031.1  collagen alpha-1(XVI) chain isoform X15

    Conserved Domains (2) summary
    pfam01391
    Location:756 → 803
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains

RNA

  1. XR_001736983.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    31509912..31561650 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334483.1 → XP_054190458.1  collagen alpha-1(XVI) chain isoform X9

  2. XM_054334481.1 → XP_054190456.1  collagen alpha-1(XVI) chain isoform X7

  3. XM_054334476.1 → XP_054190451.1  collagen alpha-1(XVI) chain isoform X2

  4. XM_054334482.1 → XP_054190457.1  collagen alpha-1(XVI) chain isoform X8

  5. XM_054334480.1 → XP_054190455.1  collagen alpha-1(XVI) chain isoform X6

  6. XM_054334479.1 → XP_054190454.1  collagen alpha-1(XVI) chain isoform X5

  7. XM_054334478.1 → XP_054190453.1  collagen alpha-1(XVI) chain isoform X4

  8. XM_054334475.1 → XP_054190450.1  collagen alpha-1(XVI) chain isoform X1

  9. XM_054334477.1 → XP_054190452.1  collagen alpha-1(XVI) chain isoform X3

  10. XM_054334484.1 → XP_054190459.1  collagen alpha-1(XVI) chain isoform X10

  11. XM_054334485.1 → XP_054190460.1  collagen alpha-1(XVI) chain isoform X11

  12. XM_054334487.1 → XP_054190462.1  collagen alpha-1(XVI) chain isoform X13

  13. XM_054334488.1 → XP_054190463.1  collagen alpha-1(XVI) chain isoform X14

  14. XM_054334491.1 → XP_054190466.1  collagen alpha-1(XVI) chain isoform X17

  15. XM_054334486.1 → XP_054190461.1  collagen alpha-1(XVI) chain isoform X12

  16. XM_054334490.1 → XP_054190465.1  collagen alpha-1(XVI) chain isoform X16

  17. XM_054334489.1 → XP_054190464.1  collagen alpha-1(XVI) chain isoform X15

RNA

  1. XR_008485931.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q07092.2 GenPept UniProtKB/Swiss-Prot:Q07092

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