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Aliases for COL16A1 Gene

Aliases for COL16A1 Gene

  • Collagen, Type XVI, Alpha 1 2 3
  • Collagen XVI, Alpha-1 Polypeptide 3
  • Collagen Alpha-1(XVI) Chain 3
  • Alpha 1 Type XVI Collagen 3
  • FP1572 3
  • 447AA 3

External Ids for COL16A1 Gene

Previous GeneCards Identifiers for COL16A1 Gene

  • GC01M031925
  • GC01M031102
  • GC01M031544
  • GC01M031620
  • GC01M031786
  • GC01M031890
  • GC01M032117
  • GC01M030235

Summaries for COL16A1 Gene

Entrez Gene Summary for COL16A1 Gene

  • 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]

GeneCards Summary for COL16A1 Gene

COL16A1 (Collagen, Type XVI, Alpha 1) is a Protein Coding gene. Among its related pathways are ERK Signaling and ERK Signaling. GO annotations related to this gene include integrin binding. An important paralog of this gene is COL21A1.

UniProtKB/Swiss-Prot for COL16A1 Gene

  • Involved in mediating cell attachment and inducing integrin-mediated cellular reactions, such as cell spreading and alterations in cell morphology.

Gene Wiki entry for COL16A1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL16A1 Gene

Genomics for COL16A1 Gene

Regulatory Elements for COL16A1 Gene

Genomic Location for COL16A1 Gene

Start:
31,652,247 bp from pter
End:
31,704,319 bp from pter
Size:
52,073 bases
Orientation:
Minus strand

Genomic View for COL16A1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL16A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL16A1 Gene

Proteins for COL16A1 Gene

  • Protein details for COL16A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q07092-COGA1_HUMAN
    Recommended name:
    Collagen alpha-1(XVI) chain
    Protein Accession:
    Q07092
    Secondary Accessions:
    • Q16593
    • Q59F89
    • Q71RG9

    Protein attributes for COL16A1 Gene

    Size:
    1604 amino acids
    Molecular mass:
    157751 Da
    Quaternary structure:
    • Homotrimer. Interacts with FBN1, fibronectin and integrins ITGA1/ITGB1 and ITGA2/ITGB1. Integrin ITGA1/ITGB1 binds to a unique site within COL16A1 located close to its C-terminal end between collagenous domains COL1-COL3.

    Alternative splice isoforms for COL16A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL16A1 Gene

Proteomics data for COL16A1 Gene at MOPED

Post-translational modifications for COL16A1 Gene

  • Glycosylated.
  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains
  • Glycosylation at Asn47 and Asn327
  • Modification sites at PhosphoSitePlus

Other Protein References for COL16A1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for COL16A1 Gene

Domains for COL16A1 Gene

Gene Families for COL16A1 Gene

HGNC:

Suggested Antigen Peptide Sequences for COL16A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q07092

UniProtKB/Swiss-Prot:

COGA1_HUMAN :
  • Q07092
Domain:
  • This sequence defines eighteen different domains, nine triple-helical domains (COL9 to COL1) and ten non-triple-helical domains (NC10 to NC1). The numerous interruptions in the triple helix may make this molecule either elastic or flexible
  • Contains 8 collagen-like domains.
  • Contains 1 laminin G-like domain.
Family:
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
genes like me logo Genes that share domains with COL16A1: view

Function for COL16A1 Gene

Molecular function for COL16A1 Gene

GENATLAS Biochemistry:
collagen,type XVI,alpha 1,with features of fibril associated collagen with interrupted helices (?FACIT variant)
UniProtKB/Swiss-Prot Function:
Involved in mediating cell attachment and inducing integrin-mediated cellular reactions, such as cell spreading and alterations in cell morphology.

Gene Ontology (GO) - Molecular Function for COL16A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005178 integrin binding IDA 16754661
GO:0005515 protein binding IPI 15165854
genes like me logo Genes that share ontologies with COL16A1: view

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for COL16A1 Gene

Localization for COL16A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL16A1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL16A1 Gene COMPARTMENTS Subcellular localization image for COL16A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
cytosol 2
golgi apparatus 2
plasma membrane 2
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for COL16A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005597 collagen type XVI trimer TAS 1284248
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL16A1: view

Pathways for COL16A1 Gene

genes like me logo Genes that share pathways with COL16A1: view

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Extracellular Matrix & Adhesion Molecules in human,mouse,rat

Gene Ontology (GO) - Biological Process for COL16A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IDA 16754661
GO:0007229 integrin-mediated signaling pathway TAS 16754661
GO:0007565 female pregnancy TAS 1284248
GO:0022617 extracellular matrix disassembly TAS --
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with COL16A1: view

Transcripts for COL16A1 Gene

Unigene Clusters for COL16A1 Gene

Collagen, type XVI, alpha 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL16A1

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL16A1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21a · 21b ^ 22 ^
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: -
SP9: -
SP10:

ExUns: 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29a · 29b ^ 30 ^ 31a · 31b ^ 32 ^ 33
SP1:
SP2: -
SP3: -
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for COL16A1 Gene

GeneLoc Exon Structure for
COL16A1
ECgene alternative splicing isoforms for
COL16A1

Expression for COL16A1 Gene

mRNA expression in normal human tissues for COL16A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues for COL16A1 Gene

This gene is overexpressed in Kidney (12.5), Cerebrospinal fluid (9.0), and Bone marrow mesenchymal stem cell (6.9).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for COL16A1 Gene

SOURCE GeneReport for Unigene cluster for COL16A1 Gene Hs.368921

mRNA Expression by UniProt/SwissProt for COL16A1 Gene

Q07092-COGA1_HUMAN
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 collagens (at protein level). In the placenta, where it is found in the amnion, a membranous tissue lining the amniotic cavity. Within the amnion, it is found in an acellular, relatively dense layer of a complex network of reticular fibers. Also located to a fibroblast layer beneath this dense layer. Exists in tissues in association with other types of collagen.
genes like me logo Genes that share expressions with COL16A1: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and Expression partners for COL16A1 Gene

Orthologs for COL16A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL16A1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia COL16A1 35
  • 87.93 (n)
  • 89.45 (a)
COL16A1 36
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL16A1 35
  • 89.01 (n)
  • 90.08 (a)
COL16A1 36
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col16a1 35
  • 85.6 (n)
  • 88.86 (a)
Col16a1 16
Col16a1 36
  • 89 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia COL16A1 35
  • 98.51 (n)
  • 98.11 (a)
COL16A1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col16a1 35
  • 85.68 (n)
  • 88.34 (a)
oppossum
(Monodelphis domestica)
Mammalia COL16A1 36
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL16A1 36
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL16A1 35
  • 64.67 (n)
  • 66.07 (a)
COL16A1 36
  • 67 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL16A1 36
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497018 35
  • 59.62 (n)
  • 56.81 (a)
zebrafish
(Danio rerio)
Actinopterygii col16a1 36
  • 53 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG42342 36
  • 31 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea col-99 36
  • 34 (a)
OneToMany
Species with no ortholog for COL16A1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COL16A1 Gene

ENSEMBL:
Gene Tree for COL16A1 (if available)
TreeFam:
Gene Tree for COL16A1 (if available)

Paralogs for COL16A1 Gene

Paralogs for COL16A1 Gene

Selected SIMAP similar genes for COL16A1 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with COL16A1: view

Variants for COL16A1 Gene

Sequence variations from dbSNP and Humsavar for COL16A1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs909000 -- 31,702,835(+) GAGAG(C/T)AGGTC intron-variant
rs909002 -- 31,674,034(+) GTTGC(C/T)ACAAC intron-variant
rs945215 -- 31,655,947(+) CTCTC(C/T)GCAGC intron-variant
rs1061389 -- 31,652,642(-) TCCCC(A/C)CCTGC utr-variant-3-prime
rs1061392 -- 31,652,559(-) TTTTT(G/T)TTGTT utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for COL16A1 Gene

Variant ID Type Subtype PubMed ID
dgv46e1 CNV Complex 17122850
dgv209n71 CNV Loss 21882294
nsv470708 CNV Loss 18288195
nsv818123 CNV Loss 17921354
nsv870517 CNV Loss 21882294
nsv528364 CNV Loss 19592680
nsv461028 CNV Loss 19166990

Relevant External Links for COL16A1 Gene

HapMap Linkage Disequilibrium report
COL16A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL16A1 Gene

Disorders for COL16A1 Gene

Relevant External Links for COL16A1

Genetic Association Database (GAD)
COL16A1
Human Genome Epidemiology (HuGE) Navigator
COL16A1

No disorders were found for COL16A1 Gene.

No data available for MalaCards , OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES , Novoseek inferred disease relationships and Genatlas for COL16A1 Gene

Publications for COL16A1 Gene

  1. Cloning and chromosomal location of human alpha 1(XVI) collagen. (PMID: 1631157) Pan T.-C. … Chu M.-L. (Proc. Natl. Acad. Sci. U.S.A. 1992) 2 3 4
  2. Recombinant analysis of human alpha 1 (XVI) collagen. Evidence for processing of the N-terminal globular domain. (PMID: 7882999) Tillet E. … Timpl R. (Eur. J. Biochem. 1995) 3 4
  3. Biosynthesis and processing of type XVI collagen in human fibroblasts and smooth muscle cells. (PMID: 9022684) Grassel S. … Chu M.-L. (Eur. J. Biochem. 1996) 3 4
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 48
  5. Discrete integration of collagen XVI into tissue-specific collagen fibrils or beaded microfibrils. (PMID: 12782140) Kassner A. … Grassel S. (Matrix Biol. 2003) 3 4

Products for COL16A1 Gene

Sources for COL16A1 Gene

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