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

Summary

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: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 1p35.2

Exon count:: 74

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (31652263..31704017, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (31509912..31561650, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (32117864..32169618, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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.
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.
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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

SHGC-35321 (e-PCR)
- UniSTS:45868

RH69199 (e-PCR)
- UniSTS:73013

SHGC-155471 (e-PCR)
- UniSTS:182089

STS-W96115 (e-PCR)
- UniSTS:25967

COL16A1_1437 (e-PCR)
- UniSTS:277112

STS-M92642 (e-PCR)
- UniSTS:73133

G15937 (e-PCR)
- UniSTS:72120

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	HDA more info	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
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
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 more info	PubMed
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

Go to the top of the page Help

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)

Go to the top of the page Help

NEW Try the new Transcript table

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)

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

31652263..31704017 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047446435.1 → XP_047302391.1 collagen alpha-1(XVI) chain isoform X9
XM_047446431.1 → XP_047302387.1 collagen alpha-1(XVI) chain isoform X7
XM_017000339.2 → XP_016855828.1 collagen alpha-1(XVI) chain isoform X2
XM_047446432.1 → XP_047302388.1 collagen alpha-1(XVI) chain isoform X8
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
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
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
XM_017000338.2 → XP_016855827.1 collagen alpha-1(XVI) chain isoform X1
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
XM_047446439.1 → XP_047302395.1 collagen alpha-1(XVI) chain isoform X10
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)
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)
XM_017000340.3 → XP_016855829.1 collagen alpha-1(XVI) chain isoform X14
XM_017000341.2 → XP_016855830.1 collagen alpha-1(XVI) chain isoform X17
XM_047446440.1 → XP_047302396.1 collagen alpha-1(XVI) chain isoform X12
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
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