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Aliases for COL16A1 Gene

Aliases for COL16A1 Gene

  • Collagen Type XVI Alpha 1 Chain 2 3 5
  • 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 Chain) is a Protein Coding gene. Among its related pathways are Integrin Pathway and ERK Signaling. Gene Ontology (GO) annotations related to this gene include integrin binding. An important paralog of this gene is COL22A1.

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

Additional gene information for COL16A1 Gene

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

Genomics for COL16A1 Gene

GeneHancer (GH) Regulatory Elements for COL16A1 Gene

Promoters and enhancers for COL16A1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I031699 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 560 +1.5 1539 6.7 SMAD1 FOXA2 MLX ARID4B DMAP1 E2F8 ZNF143 FOS DEK SP5 COL16A1 ENSG00000235790 ADGRB2 SNRNP40 PEF1 TINAGL1 LOC105378626 TSSK3 MTMR9LP GC01M031668
GH01I031062 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20.9 +639.9 639900 4.4 CLOCK FEZF1 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 ZNF263 MEF2D SSRP1 PUM1 COL16A1 ZCCHC17 ENSG00000229447 LAPTM5 GC01P031057
GH01I031924 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19 -231.5 -231514 22.1 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 GC01P031934 PTP4A2 TXLNA SNRNP40 KHDRBS1 RBBP4 ENSG00000229447 TSSK3 ZBTB8A TMEM39B
GH01I031787 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 17.1 -84.6 -84627 2.9 HDGF PKNOX1 CLOCK SMAD1 ARID4B SIN3A FEZF1 ZNF2 POLR2B E2F8 ENSG00000254545 SNRNP40 TSSK3 TMEM39B RBBP4 COL16A1 TXLNA ENSG00000229447 KHDRBS1 FAM229A
GH01I032262 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 18.8 -561.1 -561069 4.8 ZNF493 ZNF529 ZFP64 RARA ZNF213 SCRT2 ZNF654 ZNF680 ZBTB11 CEBPB TXLNA RBBP4 SNRNP40 KHDRBS1 TSSK3 TMEM39B ZBTB8A ZNF362 DCDC2B S100PBP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around COL16A1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COL16A1 gene promoter:

Genomic Locations for COL16A1 Gene

Genomic Locations for COL16A1 Gene
chr1:31,652,247-31,704,319
(GRCh38/hg38)
Size:
52,073 bases
Orientation:
Minus strand
chr1:32,117,848-32,169,920
(GRCh37/hg19)

Genomic View for COL16A1 Gene

Genes around COL16A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL16A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for COL16A1 Gene

No data available for DME Specific Peptides for COL16A1 Gene

Domains & Families for COL16A1 Gene

Gene Families for COL16A1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

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 :
  • 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.
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
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.
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.

Phenotypes From GWAS Catalog for COL16A1 Gene

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

Animal Model Products

miRNA for COL16A1 Gene

miRTarBase miRNAs that target COL16A1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL16A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
cytosol 3
plasma membrane 2
golgi apparatus 2
mitochondrion 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Plasma membrane (2)
See all subcellular structures

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:0005581 collagen trimer 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 & Interactions for COL16A1 Gene

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

Gene Ontology (GO) - Biological Process for COL16A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,IDA 16754661
GO:0007229 integrin-mediated signaling pathway TAS 16754661
GO:0007565 female pregnancy TAS 1284248
GO:0030198 extracellular matrix organization TAS --
GO:0033622 integrin activation IDA 16754661
genes like me logo Genes that share ontologies with COL16A1: view

No data available for SIGNOR curated interactions for COL16A1 Gene

Drugs & Compounds for COL16A1 Gene

No Compound Related Data Available

Transcripts for COL16A1 Gene

Unigene Clusters for COL16A1 Gene

Collagen, type XVI, alpha 1:
Representative Sequences:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for COL16A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED 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 in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for COL16A1 Gene



NURSA nuclear receptor signaling pathways regulating expression of COL16A1 Gene:

COL16A1

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.

Evidence on tissue expression from TISSUES for COL16A1 Gene

  • Spleen(4.2)
genes like me logo Genes that share expression patterns with COL16A1: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia COL16A1 33 34
  • 98.51 (n)
dog
(Canis familiaris)
Mammalia COL16A1 33 34
  • 89.01 (n)
cow
(Bos Taurus)
Mammalia COL16A1 33 34
  • 87.93 (n)
rat
(Rattus norvegicus)
Mammalia Col16a1 33
  • 85.68 (n)
mouse
(Mus musculus)
Mammalia Col16a1 33 16 34
  • 85.6 (n)
oppossum
(Monodelphis domestica)
Mammalia COL16A1 34
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL16A1 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL16A1 33 34
  • 64.67 (n)
lizard
(Anolis carolinensis)
Reptilia COL16A1 34
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497018 33
  • 59.62 (n)
zebrafish
(Danio rerio)
Actinopterygii col16a1 34
  • 53 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG42342 34
  • 31 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea col-99 34
  • 34 (a)
OneToMany
Species where no ortholog for COL16A1 was found in the sources mined by GeneCards:
  • 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

(6) 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 Variation AA Info Type
rs1000062415 -- 31,672,242(-) A/G downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000217320 -- 31,666,248(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000401131 -- 31,695,286(-) A/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000427270 -- 31,695,000(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000432758 -- 31,654,953(-) A/G genic_downstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
esv2758930 CNV loss 17122850
nsv1000976 CNV loss 25217958
nsv461028 CNV loss 19166990
nsv470708 CNV loss 18288195
nsv472148 CNV novel sequence insertion 20440878
nsv528364 CNV loss 19592680
nsv545951 CNV gain 21841781
nsv545952 CNV gain 21841781
nsv545953 CNV loss 21841781
nsv818123 CNV loss 17921354
nsv950385 CNV deletion 24416366

Variation tolerance for COL16A1 Gene

Residual Variation Intolerance Score: 69.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.42; 90.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COL16A1 Gene

Human Gene Mutation Database (HGMD)
COL16A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL16A1

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

Disorders for COL16A1 Gene

Additional Disease Information for COL16A1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for COL16A1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for COL16A1 Gene

Publications for COL16A1 Gene

  1. Cloning and chromosomal location of human alpha 1(XVI) collagen. (PMID: 1631157) Pan TC … Chu ML (Proceedings of the National Academy of Sciences of the United States of America 1992) 2 3 4 58
  2. 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 SD … DREAM investigators (Diabetes care 2010) 3 44 58
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  4. Collagen XVI harbors an integrin alpha1 beta1 recognition site in its C-terminal domains. (PMID: 16754661) Eble JA … Grässel S (The Journal of biological chemistry 2006) 3 4 58
  5. Molecular structure and interaction of recombinant human type XVI collagen. (PMID: 15165854) Kassner A … Grässel S (Journal of molecular biology 2004) 3 4 58

Products for COL16A1 Gene

Sources for COL16A1 Gene

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