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

    Gene ID: 1307, updated on 3-Nov-2024

    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; AllianceGenome:HGNC:2193
    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
    NEW
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    Genomic context

    See COL16A1 in Genome Data Viewer
    Location:
    1p35.2
    Exon count:
    74
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31652263..31704017, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31509912..31561650, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32117864..32169618, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32041927-32042647 Neighboring gene tubulointerstitial nephritis antigen like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 571 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:32070860-32072059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32080194-32080980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32083206-32083895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32090464-32090964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32090965-32091465 Neighboring gene hypocretin receptor 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32110207-32110977 Neighboring gene penta-EF-hand domain containing 1 Neighboring gene PEF1 and COL16A1 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32123622-32123860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32124291-32124792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32131402-32131941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32131942-32132480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32133021-32133558 Neighboring gene uncharacterized LOC101929444 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:32145564-32146763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32147039-32147911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32162063-32162572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32164717-32165470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32166977-32167729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 649 Neighboring gene Sharpr-MPRA regulatory region 11964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32181521-32182116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32189409-32189910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 573 Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32218779-32219393 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32219394-32220007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32220374-32220980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32221586-32222191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32222192-32222796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32227559-32228412 Neighboring gene uncharacterized LOC124903930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 576 Neighboring gene microRNA 4254

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-02-01)

    ClinGen Genome Curation Page
    Haploinsufficency

    Dosage sensitivity unlikely (Last evaluated 2021-02-01)

    ClinGen Genome Curation PagePubMed

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    part_of collagen type IX trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen type XVI trimer TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    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)

    NEW Try the new Transcript table

    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_001856.4NP_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, Q16593, Q59F89, Q71RG9
      Related
      ENSP00000362776.3, ENST00000373672.8
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      31652263..31704017 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047446435.1XP_047302391.1  collagen alpha-1(XVI) chain isoform X9

    2. XM_047446431.1XP_047302387.1  collagen alpha-1(XVI) chain isoform X7

    3. XM_017000339.2XP_016855828.1  collagen alpha-1(XVI) chain isoform X2

    4. XM_047446432.1XP_047302388.1  collagen alpha-1(XVI) chain isoform X8

    5. XM_011540724.2XP_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
    6. XM_011540723.2XP_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
    7. XM_005270481.2XP_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
    8. XM_017000338.2XP_016855827.1  collagen alpha-1(XVI) chain isoform X1

    9. XM_011540722.2XP_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
    10. XM_047446439.1XP_047302395.1  collagen alpha-1(XVI) chain isoform X10

    11. XM_011540727.3XP_011539029.1  collagen alpha-1(XVI) chain isoform X11

      Conserved Domains (1) summary
      pfam01391
      Location:454501
      Collagen; Collagen triple helix repeat (20 copies)
    12. XM_011540728.3XP_011539030.1  collagen alpha-1(XVI) chain isoform X13

      Conserved Domains (1) summary
      pfam01391
      Location:241288
      Collagen; Collagen triple helix repeat (20 copies)
    13. XM_017000340.3XP_016855829.1  collagen alpha-1(XVI) chain isoform X14

    14. XM_017000341.2XP_016855830.1  collagen alpha-1(XVI) chain isoform X17

    15. XM_047446440.1XP_047302396.1  collagen alpha-1(XVI) chain isoform X12

    16. XM_011540730.2XP_011539032.1  collagen alpha-1(XVI) chain isoform X16

      Related
      ENSP00000362772.3, ENST00000373668.7
      Conserved Domains (2) summary
      pfam01391
      Location:756803
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50231
      TSPN; Thrombospondin N-terminal -like domains
    17. XM_011540729.2XP_011539031.1  collagen alpha-1(XVI) chain isoform X15

      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_001736983.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      31509912..31561650 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334483.1XP_054190458.1  collagen alpha-1(XVI) chain isoform X9

    2. XM_054334481.1XP_054190456.1  collagen alpha-1(XVI) chain isoform X7

    3. XM_054334476.1XP_054190451.1  collagen alpha-1(XVI) chain isoform X2

    4. XM_054334482.1XP_054190457.1  collagen alpha-1(XVI) chain isoform X8

    5. XM_054334480.1XP_054190455.1  collagen alpha-1(XVI) chain isoform X6

    6. XM_054334479.1XP_054190454.1  collagen alpha-1(XVI) chain isoform X5

    7. XM_054334478.1XP_054190453.1  collagen alpha-1(XVI) chain isoform X4

    8. XM_054334475.1XP_054190450.1  collagen alpha-1(XVI) chain isoform X1

    9. XM_054334477.1XP_054190452.1  collagen alpha-1(XVI) chain isoform X3

    10. XM_054334484.1XP_054190459.1  collagen alpha-1(XVI) chain isoform X10

    11. XM_054334485.1XP_054190460.1  collagen alpha-1(XVI) chain isoform X11

    12. XM_054334487.1XP_054190462.1  collagen alpha-1(XVI) chain isoform X13

    13. XM_054334488.1XP_054190463.1  collagen alpha-1(XVI) chain isoform X14

    14. XM_054334491.1XP_054190466.1  collagen alpha-1(XVI) chain isoform X17

    15. XM_054334486.1XP_054190461.1  collagen alpha-1(XVI) chain isoform X12

    16. XM_054334490.1XP_054190465.1  collagen alpha-1(XVI) chain isoform X16

    17. XM_054334489.1XP_054190464.1  collagen alpha-1(XVI) chain isoform X15

    RNA

    1. XR_008485931.1 RNA Sequence