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COL16A1 Gene

protein-coding   GIFtS: 56
GCID: GC01M032117

Collagen, Type XVI, Alpha 1

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Collagen, Type XVI, Alpha 11 2
447AA2
Alpha 1 Type XVI Collagen2
Collagen Alpha-1(XVI) Chain2
Collagen XVI, Alpha-1 Polypeptide2

External Ids:    HGNC: 21931   Entrez Gene: 13072   Ensembl: ENSG000000846367   OMIM: 1203265   UniProtKB: Q070923   

Export aliases for COL16A1 gene to outside databases

Previous GC identifers: GC01M031925 GC01M031102 GC01M031544 GC01M031620 GC01M031786 GC01M031890 GC01M030235


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. GO annotations related to this gene include integrin binding. An important paralog of this gene is COL25A1.

UniProtKB/Swiss-Prot: COGA1_HUMAN, Q07092
Function: 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 (Collagen, type XVI, alpha 1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL16A1 gene promoter:
         ISGF-3   GATA-3   MIF-1   IRF-1   Nkx2-5   PPAR-alpha   PPAR-gamma1   POU2F1   HOXA5   POU2F1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL16A1 promoter sequence
   Search Chromatin IP Primers for COL16A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL16A1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p35-p34   Ensembl cytogenetic band:  1p35.2   HGNC cytogenetic band: 1p35-p34

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

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M032117:  view genomic region     (about GC identifiers)

Start:
32,117,848 bp from pter      End:
32,169,920 bp from pter
Size:
52,073 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: COGA1_HUMAN, Q07092 (See protein sequence)
Recommended Name: Collagen alpha-1(XVI) chain precursor  
Size: 1604 amino acids; 157751 Da
Subunit: 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
Developmental stage: Transiently elevated expression during gestation, and decrease at term
Secondary accessions: Q16593 Q59F89 Q71RG9
Alternative splicing: 2 isoforms:  Q07092-1   Q07092-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for COL16A1: NX_Q07092

Explore proteomics data for COL16A1 at MOPED

Post-translational modifications: 

  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the
    chains1
  • Glycosylated1
  • Glycosylation2 at Asn47, Asn327
  • Modification sites at PhosphoSitePlus

  • See COL16A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001847.3  
    ENSEMBL proteins: 
     ENSP00000362776   ENSP00000390281   ENSP00000411457   ENSP00000362772   ENSP00000362771  
     ENSP00000271069  
    Reactome Protein details: Q07092

    COL16A1 Human Recombinant Protein Products:

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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for COL16A1 

     
    antibodies-online proteins for COL16A1 (2 products) 

     
    Search antibodies-online for peptides for COL16A1

    COL16A1 Antibody Products:

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    antibodies-online antibodies for COL16A1 (6 products) 

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    Search eBioscience for ELISAs for COL16A1 
    antibodies-online kits for COL16A1 (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    COLLAGEN: Collagens

    3 InterPro protein domains:
     IPR001791 Laminin_G
     IPR008160 Collagen
     IPR008985 ConA-like_lec_gl_sf

    Graphical View of Domain Structure for InterPro Entry Q07092

    ProtoNet protein and cluster: Q07092

    3 Blocks protein domains:
    IPB003129 Thrombospondin
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    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
    Similarity: Belongs to the fibril-associated collagens with interrupted helices (FACIT) family
    Similarity: Contains 8 collagen-like domains
    Similarity: Contains 1 laminin G-like domain


    Find genes that share domains with COL16A1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: COGA1_HUMAN, Q07092
    Function: Involved in mediating cell attachment and inducing integrin-mediated cellular reactions, such as cell
    spreading and alterations in cell morphology

         Genatlas biochemistry entry for COL16A1:
    collagen,type XVI,alpha 1,with features of fibril associated collagen with interrupted helices (?FACIT variant)

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005178integrin binding IDA16754661
    GO:0005515protein binding IPI15165854
         
    Find genes that share ontologies with COL16A1           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for COL16A1

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate COL16A1 (see all 12):
    hsa-miR-181c hsa-miR-3065-3p hsa-miR-29a hsa-miR-29c hsa-miR-181a hsa-miR-181d hsa-miR-1184 hsa-miR-513b
    SwitchGear 3'UTR luciferase reporter plasmidCOL16A1 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    COGA1_HUMAN, Q07092: Secreted, extracellular space, extracellular matrix
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    endoplasmic reticulum4
    cytosol2
    golgi apparatus2
    plasma membrane2
    mitochondrion1
    nucleus1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005597collagen type XVI TAS1284248
    GO:0005788endoplasmic reticulum lumen TAS--

    Find genes that share ontologies with COL16A1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for COL16A1 About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.75
    Intrinsic Prothrombin Activation Pathway0.39
    Collagen formation0.75
    Blood Coagulation Cascade0.38
    2Integrin Pathway
    FAK1 Signaling0.67
    UPA-UPAR Pathway0.56
    Integrin Pathway0.67
    Inhibition of Angiogenesis by TSP10.50
    GnRH Signaling0.56
    Transendothelial Migration of Leukocytes0.38
    3ERK Signaling
    Rho Family GTPases0.61
    Molecular Mechanisms of Cancer0.51
    ERK Signaling0.61
    ILK Signaling0.49
    MAPK Signaling0.58
    4Degradation of the extracellular matrix
    Degradation of the extracellular matrix0.43
    Extracellular matrix organization0.34
    Collagen degradation0.43
    5Phospholipase-C Pathway
    Phospholipase-C Pathway0.56
    PTEN Pathway0.56


    Find genes that share SuperPaths with COL16A1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL16A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    3 Reactome Pathways for COL16A1
        Integrin cell surface interactions
    Collagen biosynthesis and modifying enzymes
    Collagen degradation


        Pathway & Disease-focused RT2 Profiler PCR Array including COL16A1: 
              Extracellular Matrix & Adhesion Molecules in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for COL16A1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for COL16A1 (Q070922, 3 ENSP000003627764) via UniProtKB, MINT, STRING, and/or I2D (see all 42)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GFAPP141362, 3, ENSP000002534084MINT-6743170 I2D: score=1 STRING: ENSP00000253408
    COL4A1P024622, ENSP000003649794MINT-6743179 STRING: ENSP00000364979
    SUMO1P631653, ENSP000003760764I2D: score=1 STRING: ENSP00000376076
    COL10A1ENSP000002432224STRING: ENSP00000243222
    COL11A1ENSP000003511634STRING: ENSP00000351163
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion IDA16754661
    GO:0007229integrin-mediated signaling pathway TAS16754661
    GO:0007565female pregnancy TAS1284248
    GO:0022617extracellular matrix disassembly TAS--
    GO:0030198extracellular matrix organization TAS--

    Find genes that share ontologies with COL16A1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for COL16A1 (COGA1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for COL16A1 gene: 
    NM_001856.3  

    Unigene Cluster for COL16A1:

    Collagen, type XVI, alpha 1
    Hs.368921  [show with all ESTs]
    Unigene Representative Sequence: NM_001856
    18 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000373672(uc001btj.1 uc001btk.1) ENST00000488128 ENST00000488897
    ENST00000461217 ENST00000440437 ENST00000466829 ENST00000470799 ENST00000482910
    ENST00000468459 ENST00000479100 ENST00000458715 ENST00000373668(uc001btl.4)
    ENST00000474000 ENST00000482478 ENST00000529928 ENST00000373667 ENST00000532877
    ENST00000271069
    miRNA
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    hsa-miR-181c hsa-miR-3065-3p hsa-miR-29a hsa-miR-29c hsa-miR-181a hsa-miR-181d hsa-miR-1184 hsa-miR-513b
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      QuantiFast Probe-based Assays in human, mouse, rat COL16A1

    Additional mRNA sequence: 

    AB209571.1 AF370368.1 BC064839.1 BC118655.1 M92642.1 S57132.1 X14963.1 X15038.1 

    16 DOTS entries:

    DT.444233  DT.99990364  DT.95298015  DT.40231039  DT.75130869  DT.433295  DT.95154274  DT.100645420 
    DT.121442523  DT.75192513  DT.91829406  DT.92425382  DT.100750193  DT.313921  DT.91754176  DT.92425383 

    Selected AceView cDNA sequences (see all 106):

    AA682251 CB215004 BM707745 BG697379 AI686616 X15038 AI656575 BF223892 
    BF434543 CR611324 X14963 AA770215 BU182098 BC064839 CF455572 CA394098 
    BP363100 BU733264 BF058423 BF718643 AI589349 BQ001266 BM664872 BM544904 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for COL16A1 (see all 10)    About this scheme

    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:                                                                                                                                                            

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


    ECgene alternative splicing isoforms for COL16A1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    COL16A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAGGGGCCTT
    COL16A1 Expression
    About this image


    COL16A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 11) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 6 entries
             Chondrocytes Zeugopod Epiphyseal End
             TGFbeta3+BMP7-induced chondrocytes
     
     Cartilage (Muscoskeletal System)    fully expand to see all 5 entries
             Chondrocytes Zeugopod Epiphyseal End
             TGFbeta3+BMP7-induced chondrocytes
     
     Epithelial Cells
             Outer Root Sheath Cells Outer Root Sheath
     
     Kidney (Urinary System)
             Metanephros
     
     Hair (Integumentary System)
             Outer Root Sheath Cells Outer Root Sheath
    COL16A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL16A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.368921

    UniProtKB/Swiss-Prot: COGA1_HUMAN, Q07092
    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

        Pathway & Disease-focused RT2 Profiler PCR Array including COL16A1: 
              Extracellular Matrix & Adhesion Molecules in human mouse rat

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    QuantiFast Probe-based Assays in human, mouse, rat COL16A1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL16A1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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    This gene was present in the common ancestor of animals.

    Orthologs for COL16A1 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col16a11 , 5 collagen, type XVI, alpha 11, 5 85.6(n)1
    88.86(a)1
      4 (63.43 cM)5
    1075811  NM_028266.51  NP_082542.31 
     1300478405 
    chicken
    (Gallus gallus)
    Aves COL16A11 collagen, type XVI, alpha 1 64.67(n)
    66.07(a)
      430477  XM_003642581.2  XP_003642629.2 
    lizard
    (Anolis carolinensis)
    Reptilia COL16A16
    collagen, type XVI, alpha 1
    69(a)
    1 ↔ 1
    GL343308.1(445179-593713)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004970181 collagen alpha-1(XVI) chain-like 59.62(n)
    56.81(a)
      100497018  XM_004919225.1  XP_004919282.1 
    zebrafish
    (Danio rerio)
    Actinopterygii col16a16
    collagen, type XVI, alpha 1
    53(a)
    1 ↔ 1
    19(40022486-40173904) ENSDARG00000009194
    fruit fly
    (Drosophila melanogaster)
    Insecta CG423426
    --
    31(a)
    1 → many
    3R(12328523-12397082)
    worm
    (Caenorhabditis elegans)
    Secernentea col-996
    Protein COL-99, isoform a (col-99) mRNA, complete ...
    34(a)
    1 → many
    IV(138461-147919) WBGene00000674


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section

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    Paralogs for COL16A1 gene
    COL25A12  COL19A12  COL9A12  COL22A12  COL13A12  COL9A32  COL9A22  COL21A12  
    COL23A12  
    6 SIMAP similar genes for COL16A1 using alignment to 6 protein entries:     COGA1_HUMAN (see all proteins):
    SFTPD    COL17A1    COLEC11    FCN2    COL7A1    MARCO

    Find genes that share paralogs with COL16A1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
    About This Section

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    Selected SNPs for COL16A1 (see all 1436)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1836995761,2
    --30289259(+) ACACAC/TGTAAG 1 -- us2k10--------
    rs783132331,2
    C--32117373(+) AGGTTC/TCATCT 1 -- ds50010--------
    rs771905551,2
    C--32117374(+) GGTTCC/TATCTC 1 -- ds50010--------
    rs1388079151,2
    --32117388(+) TCCCAA/GAGAAG 1 -- ds50010--------
    rs1140715661,2
    --32117429(+) GCCTGC/TCTTCT 1 -- ds50010--------
    rs743583331,2
    C--32117709(+) CTTGAG/CAGAAG 1 -- ds50012Minor allele frequency- C:0.04NA EA 122
    rs21395391,2
    C,F,O,A,H--32117779(+) GATCCC/TGAGGA 1 -- ds500130Minor allele frequency- T:0.30NA NS EA CSA WA 2918
    rs1818423911,2
    C--32117807(+) GCCCCC/TATCCA 1 -- ds50010--------
    rs1414423621,2
    C--32117822(+) AATCT-/CACAGCA 1 -- ds50010--------
    rs1861871901,2
    --32117826(+) TCACAC/GCACCA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for COL16A1 (32117848 - 32169920 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for COL16A1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv528364CNV Loss19592680
    nsv818123CNV Loss17921354
    dgv209n71CNV Loss21882294
    nsv470708CNV Loss18288195
    nsv461028CNV Loss19166990
    nsv870517CNV Loss21882294
    dgv46e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL16A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL16A1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 120326    OMIM disorders: --


    Find genes that share disorders with COL16A1           About GenesLikeMe

    Genetic Association Database (GAD): COL16A1
    Human Genome Epidemiology (HuGE) Navigator: COL16A1 (3 documents)

    Export disorders for COL16A1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for COL16A1 gene, integrated from 10 sources (see all 19):
    (articles sorted by number of sources associating them with COL16A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and chromosomal location of human alpha 1(XVI) collagen. (PubMed id 1631157)1, 2, 3 Pan T.-C.... Chu M.-L. (Proc. Natl. Acad. Sci. U.S.A. 1992)
    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. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
    4. Collagen XVI harbors an integrin alpha1 beta1 recognition site in its C-terminal domains. (PubMed id 16754661)1, 2 Eble J.A.... Grassel S. (J. Biol. Chem. 2006)
    5. Molecular structure and interaction of recombinant human type XVI collagen. (PubMed id 15165854)1, 2 Kassner A.... Grassel S. (J. Mol. Biol. 2004)
    6. Discrete integration of collagen XVI into tissue-specific collagen fibrils or beaded microfibrils. (PubMed id 12782140)1, 2 Kassner A.... Grassel S. (Matrix Biol. 2003)
    7. Biosynthesis and processing of type XVI collagen in human fibroblasts and smooth muscle cells. (PubMed id 9022684)1, 2 Grassel S.... Chu M.-L. (Eur. J. Biochem. 1996)
    8. Recombinant analysis of human alpha 1 (XVI) collagen. Evidence for processing of the N-terminal globular domain. (PubMed id 7882999)1, 2 Tillet E.... Timpl R. (Eur. J. Biochem. 1995)
    9. Molecular cloning and partial characterization of a novel collagen chain, alpha 1(XVI), consisting of repetitive collagenous domains and cysteine-containing non-collagenous segments. (PubMed id 1284248)1, 2 Yamaguchi N.... Nagai Y. (J. Biochem. 1992)
    10. Collagen XVI in health and disease. (PubMed id 23149016)1 GrAossel S. and Bauer R.J. (Matrix Biol. 2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1307 HGNC: 2193 AceView: COL16A1 Ensembl:ENSG00000084636 euGenes: HUgn1307
    ECgene: COL16A1 H-InvDB: COL16A1

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for COL16A1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for COL16A1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for COL16A1 gene:
    Search GeneIP for patents involving COL16A1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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