COL16A1 (collagen type XVI alpha 1 chain)

Gene

• Entrez ID: 1307
• Gene name: Collagen type XVI alpha 1 chain
• Gene symbol: COL16A1
• Synonyms (NCBI Gene): 447AA, FP1572
• Chromosome: 1
• Chromosome location: 1p35.2
• 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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT053039	hsa-miR-181a-5p	Luciferase reporter assay, qRT-PCR, Western blot	23238588
MIRT902509	hsa-miR-129-5p	CLIP-seq
MIRT902510	hsa-miR-1343	CLIP-seq
MIRT902511	hsa-miR-181a	CLIP-seq
MIRT902512	hsa-miR-181b	CLIP-seq
MIRT902513	hsa-miR-181c	CLIP-seq
MIRT902514	hsa-miR-181d	CLIP-seq
MIRT902515	hsa-miR-24	CLIP-seq
MIRT902516	hsa-miR-3065-5p	CLIP-seq
MIRT902517	hsa-miR-3613-3p	CLIP-seq
MIRT902518	hsa-miR-365	CLIP-seq
MIRT902519	hsa-miR-3663-5p	CLIP-seq
MIRT902520	hsa-miR-371-5p	CLIP-seq
MIRT902521	hsa-miR-371b-5p	CLIP-seq
MIRT902522	hsa-miR-375	CLIP-seq
MIRT902523	hsa-miR-378g	CLIP-seq
MIRT902524	hsa-miR-3937	CLIP-seq
MIRT902525	hsa-miR-4262	CLIP-seq
MIRT902526	hsa-miR-4437	CLIP-seq
MIRT902527	hsa-miR-4463	CLIP-seq
MIRT902528	hsa-miR-4674	CLIP-seq
MIRT902529	hsa-miR-4698	CLIP-seq
MIRT902530	hsa-miR-513b	CLIP-seq
MIRT902531	hsa-miR-543	CLIP-seq
MIRT902532	hsa-miR-649	CLIP-seq
MIRT902533	hsa-miR-938	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005178	Function	Integrin binding	IDA	16754661
GO:0005515	Function	Protein binding	IPI	15165854, 16754661
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IEA
GO:0005597	Component	Collagen type XVI trimer	TAS	1284248
GO:0005604	Component	Basement membrane	IBA
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0007155	Process	Cell adhesion	IDA	16754661
GO:0007155	Process	Cell adhesion	IEA
GO:0007229	Process	Integrin-mediated signaling pathway	TAS	16754661
GO:0007565	Process	Female pregnancy	TAS	1284248
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	HDA	28344315
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	IBA
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	RCA	25037231, 27068509, 28327460, 28675934
GO:0031012	Component	Extracellular matrix	HDA	25037231, 27068509, 28327460, 28344315, 28675934
GO:0033622	Process	Integrin activation	IDA	16754661
GO:0033627	Process	Cell adhesion mediated by integrin	IDA	16754661
GO:0051894	Process	Positive regulation of focal adhesion assembly	IDA	24466237
GO:0071230	Process	Cellular response to amino acid stimulus	IEA

Other IDs

• MIM: 120326
• HGNC: 2193
• e!Ensembl: ENSG00000084636

Protein

• UniProt ID: Q07092
• Protein name: Collagen alpha-1(XVI) chain
• Protein function: Involved in mediating cell attachment and inducing integrin-mediated cellular reactions, such as cell spreading and alterations in cell morphology.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01391	Collagen	371 → 426	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	571 → 635	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	666 → 726	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	786 → 843	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	1008 → 1075	Collagen triple helix repeat (20 copies)	Repeat
  PF01391	Collagen	1470 → 1526	Collagen triple helix repeat (20 copies)	Repeat

• Tissue specificity: TISSUE SPECIFICITY: In papillary dermis, is a component of specialized fibrillin-1-containing microfibrils, whereas in territorial cartilage matrix, it is localized to a discrete population of thin, weakly banded collagen fibrils in association with other
• Sequence:

  MWVSWAPGLWLLGLWATFGHGANTGAQCPPSQQEGLKLEHSSSLPANVTGFNLIHRLSLM
  KTSAIKKIRNPKGPLILRLGAAPVTQPTRRVFPRGLPEEFALVLTLLLKKHTHQKTWYLF
  QVTDANGYPQISLEVNSQERSLELRAQGQDGDFVSCIFPVPQLFDLRWHKLMLSVAGRVA
  SVHVDCSSASSQPLGPRRPMRPVGHVFLGLDAEQGKPVSFDLQQVHIYCDPELVLEEGCC
  EILPAGCPPETSKARRDTQSNELIEINPQSEGKVYTRCFCLEEPQNSEVDAQLTGRISQK
  AERGAKVHQETAADECPPCVHGARDSNVTLAPSGPKGGKGERGLPGPPGSKGEKGARGND
  CVRISPDAPLQCAEGPKGEKGESGALGPSGLPGSTGEKGQKGEKGDGGIKGVPGKPGRDG
  RPGEICVIGPKGQKGDPGFVGPEGLAGEPGPPGLPGPPGIGLPGTPGDPGGPPGPKGDKG
  SSGIPGKEGPGGKPGKPGVKGEKGDPCEVCPTLPEGFQNFVGLPGKPGPKGEPGDPVPAR
  GDPGIQGIKGEKGEPCLSCSSVVGAQHLVSSTGASGDVGSPGFGLPGLPGRAGVPGLKGE
  KGNFGEAGPAGSPGPPGPVGPAGIKGAKGEPCEPCPALSNLQDGDVRVVALPGPSGEKGE
  PGPPGFGLPGKQGKAGERGLKGQKGDAGNPGDPGTPGTTGRPGLSGEPGVQGPAGPKGEK
  GDGCTACPSLQGTVTDMAGRPGQPGPKGEQGPEGVGRPGKPGQPGLPGVQGPPGLKGVQG
  EPGPPGRGVQGPQGEPGAPGLPGIQGLPGPRGPPGPTGEKGAQGSPGVKGATGPVGPPGA
  SVSGPPGRDGQQGQTGLRGTPGEKGPRGEKGEPGECSCPSQGDLIFSGMPGAPGLWMGSS
  WQPGPQGPPGIPGPPGPPGVPGLQGVPGNNGLPGQPGLTAELGSLPIEQHLLKSICGDCV
  QGQRAHPGYLVEKGEKGDQGIPGVPGLDNCAQCFLSLERPRAEEARGDNSEGDPGCVGSP
  GLPGPPGLPGQRGEEGPPGMRGSPGPPGPIGPPGFPGAVGSPGLPGLQGERGLTGLTGDK
  GEPGPPGQPGYPGATGPPGLPGIKGERGYTGSAGEKGEPGPPGSEGLPGPPGPAGPRGER
  GPQGNSGEKGDQGFQGQPGFPGPPGPPGFPGKVGSPGPPGPQAEKGSEGIRGPSGLPGSP
  GPPGPPGIQGPAGLDGLDGKDGKPGLRGDPGPAGPPGLMGPPGFKGKTGHPGLPGPKGDC
  GKPGPPGSTGRPGAEGEPGAMGPQGRPGPPGHVGPPGPPGQPGPAGISAVGLKGDRGATG
  ERGLAGLPGQPGPPGHPGPPGEPGTDGAAGKEGPPGKQGFYGPPGPKGDPGAAGQKGQAG
  EKGRAGMPGGPGKSGSMGPVGPPGPAGERGHPGAPGPSGSPGLPGVPGSMGDMVNYDEIK
  RFIRQEIIKMFDERMAYYTSRMQFPMEMAAAPGRPGPPGKDGAPGRPGAPGSPGLPGQIG
  REGRQGLPGVRGLPGTKGEKGDIGIGIAGENGLPGPPGPQGPPGYGKMGATGPMGQQGIP
  GIPGPPGPMGQPGKAGHCNPSDCFGAMPMEQQYPPMKTMKGPFG

• Sequence length: 1604

Pathways

KEGG:

Protein digestion and absorption

Reactome:

Collagen biosynthesis and modifying enzymes
Integrin cell surface interactions
Collagen chain trimerization

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPEN-ANGLE GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
THORACIC AORTIC ANEURYSM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Relationship Type	References	Evidence Score
Cardiomyopathy Dilated	Associate	27936202	★☆☆☆☆ Found in Text Mining only
Fibrosis	Associate	33860034	★☆☆☆☆ Found in Text Mining only
Obesity	Associate	27919438	★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Associate	35741755	★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Associate	28402931	★☆☆☆☆ Found in Text Mining only
Tissue Adhesions	Associate	33860034	★☆☆☆☆ Found in Text Mining only