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

    Gene ID: 1307, updated on 3-Oct-2018

    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; Vega:OTTHUMG00000003883
    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

    Genomic context

    See COL16A1 in Genome Data Viewer
    Location:
    1p35.2
    Exon count:
    74
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (31652247..31704167, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32117848..32169768, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene hypocretin receptor 1 Neighboring gene uncharacterized LOC107985471 Neighboring gene uncharacterized LOC105378628 Neighboring gene penta-EF-hand domain containing 1 Neighboring gene uncharacterized LOC101929444 Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene microRNA 4254 Neighboring gene SPOC domain containing 1

    Genomic regions, transcripts, and products

    Expression

    • 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
      Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
    • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
      Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
    • Collagen degradation, organism-specific biosystem (from REACTOME)
      Collagen degradation, organism-specific biosystemCollagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknow...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
      Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
    • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
      Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix structural constituent IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix structural constituent conferring tensile strength HDA PubMed 
    integrin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    integrin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell adhesion mediated by integrin IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell adhesion mediated by integrin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to amino acid stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    female pregnancy TAS
    Traceable Author Statement
    more info
    PubMed 
    integrin activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integrin-mediated signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of focal adhesion assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of focal adhesion assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    collagen type XVI trimer TAS
    Traceable Author Statement
    more info
    PubMed 
    collagen-containing extracellular matrix HDA PubMed 
    endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    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)

    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)

    1. NM_001856.3NP_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
      Related
      ENSP00000362776.3, OTTHUMP00000003955, ENST00000373672.7, OTTHUMT00000011057
      Conserved Domains (2) summary
      pfam01391
      Location:756803
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50231
      TSPN; Thrombospondin N-terminal -like domains

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

      Range
      31652247..31704167 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017000339.1XP_016855828.1  collagen alpha-1(XVI) chain isoform X2

    2. XM_011540724.1XP_011539026.1  collagen alpha-1(XVI) chain isoform X6

      Conserved Domains (2) summary
      pfam01391
      Location:685744
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50231
      TSPN; Thrombospondin N-terminal -like domains
    3. XM_011540723.1XP_011539025.1  collagen alpha-1(XVI) chain isoform X5

      Conserved Domains (2) summary
      pfam01391
      Location:756803
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50231
      TSPN; Thrombospondin N-terminal -like domains
    4. XM_005270481.1XP_005270538.1  collagen alpha-1(XVI) chain isoform X4

      Conserved Domains (2) summary
      pfam01391
      Location:756803
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50231
      TSPN; Thrombospondin N-terminal -like domains
    5. XM_017000338.1XP_016855827.1  collagen alpha-1(XVI) chain isoform X1

    6. XM_011540722.1XP_011539024.1  collagen alpha-1(XVI) chain isoform X3

      Conserved Domains (2) summary
      pfam01391
      Location:756803
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50231
      TSPN; Thrombospondin N-terminal -like domains
    7. XM_011540726.3XP_011539028.1  collagen alpha-1(XVI) chain isoform X7

      Conserved Domains (2) summary
      pfam01391
      Location:585632
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:160
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    8. XM_011540727.2XP_011539029.1  collagen alpha-1(XVI) chain isoform X8

      Conserved Domains (1) summary
      pfam01391
      Location:454501
      Collagen; Collagen triple helix repeat (20 copies)
    9. XM_017000340.2XP_016855829.1  collagen alpha-1(XVI) chain isoform X10

    10. XM_011540728.2XP_011539030.1  collagen alpha-1(XVI) chain isoform X9

      Conserved Domains (1) summary
      pfam01391
      Location:241288
      Collagen; Collagen triple helix repeat (20 copies)
    11. XM_017000341.1XP_016855830.1  collagen alpha-1(XVI) chain isoform X13

    12. XM_011540730.1XP_011539032.1  collagen alpha-1(XVI) chain isoform X12

      Related
      ENSP00000362772.3, OTTHUMP00000035638, ENST00000373668.7, OTTHUMT00000091413
      Conserved Domains (2) summary
      pfam01391
      Location:756803
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50231
      TSPN; Thrombospondin N-terminal -like domains
    13. XM_011540729.1XP_011539031.1  collagen alpha-1(XVI) chain isoform X11

      Conserved Domains (2) summary
      pfam01391
      Location:756803
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50231
      TSPN; Thrombospondin N-terminal -like domains

    RNA

    1. XR_946546.3 RNA Sequence

    2. XR_001736981.1 RNA Sequence

    3. XR_001736982.1 RNA Sequence

    4. XR_001736984.1 RNA Sequence

    5. XR_001736983.1 RNA Sequence

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