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    Col16a1 collagen type XVI alpha 1 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 366474, updated on 17-Aug-2024

    Summary

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    Official Symbol
    Col16a1provided by RGD
    Official Full Name
    collagen type XVI alpha 1 chainprovided by RGD
    Primary source
    RGD:1310982
    See related
    EnsemblRapid:ENSRNOG00000031475 AllianceGenome:RGD:1310982
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable integrin binding activity. Predicted to be an extracellular matrix structural constituent. Predicted to be involved in several processes, including cell adhesion mediated by integrin; integrin activation; and positive regulation of focal adhesion assembly. Predicted to act upstream of or within cellular response to amino acid stimulus. Predicted to be part of collagen type V trimer. Predicted to be active in extracellular matrix and extracellular space. Orthologous to human COL16A1 (collagen type XVI alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Uterus (RPKM 172.2), Lung (RPKM 121.7) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col16a1 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    75
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (147672559..147727007)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (142388376..142442825)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (148257030..148311645)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene SPOC domain containing 1 Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene uncharacterized LOC120102987 Neighboring gene penta-EF hand domain containing 1 Neighboring gene hypocretin receptor 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Collagen XVI induces expression of MMP9 via modulation of AP-1 transcription factors and facilitates invasion of oral squamous cell carcinoma. Bedal KB, et al. PLoS One, 2014. PMID 24466237, Free PMC Article
    2. Collagen XVI harbors an integrin alpha1 beta1 recognition site in its C-terminal domains. Eble JA, et al. J Biol Chem, 2006 Sep 1. PMID 16754661
    3. Difference in expression of hepatic microRNAs miR-29c, miR-34a, miR-155, and miR-200b is associated with strain-specific susceptibility to dietary nonalcoholic steatohepatitis in mice. Pogribny IP, et al. Lab Invest, 2010 Oct. PMID 20548288, Free PMC Article
    4. Extracellular matrix remodelling in response to venous hypertension: proteomics of human varicose veins. Barallobre-Barreiro J, et al. Cardiovasc Res, 2016 Jun 1. PMID 27068509, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC109452

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables integrin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell adhesion mediated by integrin ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cellular response to amino acid stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in integrin activation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of focal adhesion assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen type IX trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-1(XVI) chain
    Names
    collagen, type XVI, alpha 1
    procollagen, type XVI, alpha 1

    NCBI Reference Sequences (RefSeq)

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    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_001302967.1 → NP_001289896.1  collagen alpha-1(XVI) chain precursor

      See identical proteins and their annotated locations for NP_001289896.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A0A8I5Y198
      Related
      ENSRNOP00000077174.1, ENSRNOT00000114962.2
      Conserved Domains (2) summary
      pfam01391
      Location:1083 → 1136
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50 → 231
      TSPN; Thrombospondin N-terminal -like domains

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      147672559..147727007
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063288120.1 → XP_063144190.1  collagen alpha-1(XVI) chain isoform X1

    2. XM_063288121.1 → XP_063144191.1  collagen alpha-1(XVI) chain isoform X2

      UniProtKB/TrEMBL
      F1LND0

    3. XM_006238946.5 → XP_006239008.1  collagen alpha-1(XVI) chain isoform X1

      See identical proteins and their annotated locations for XP_006239008.1

      Conserved Domains (2) summary
      pfam01391
      Location:1104 → 1157
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:56 → 237
      TSPN; Thrombospondin N-terminal -like domains

    4. XM_039110476.2 → XP_038966404.1  collagen alpha-1(XVI) chain isoform X9

      Conserved Domains (3) summary
      smart00210
      Location:56 → 237
      TSPN; Thrombospondin N-terminal -like domains
      PRK07764
      Location:766 → 884
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam01391
      Location:1104 → 1157
      Collagen; Collagen triple helix repeat (20 copies)

    5. XM_006238948.5 → XP_006239010.1  collagen alpha-1(XVI) chain isoform X3

      Conserved Domains (2) summary
      pfam01391
      Location:1089 → 1142
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:56 → 237
      TSPN; Thrombospondin N-terminal -like domains

    6. XM_006238950.5 → XP_006239012.1  collagen alpha-1(XVI) chain isoform X5

      UniProtKB/TrEMBL
      A0A8I6A8Q5
      Conserved Domains (2) summary
      pfam01391
      Location:1088 → 1141
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:56 → 237
      TSPN; Thrombospondin N-terminal -like domains

    7. XM_039110473.2 → XP_038966401.1  collagen alpha-1(XVI) chain isoform X8

      Conserved Domains (3) summary
      smart00210
      Location:56 → 237
      TSPN; Thrombospondin N-terminal -like domains
      pfam09606
      Location:696 → 975
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam01391
      Location:1073 → 1126
      Collagen; Collagen triple helix repeat (20 copies)

    8. XM_039110472.2 → XP_038966400.1  collagen alpha-1(XVI) chain isoform X4

      Conserved Domains (3) summary
      smart00210
      Location:56 → 237
      TSPN; Thrombospondin N-terminal -like domains
      PRK07764
      Location:751 → 869
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam01391
      Location:1089 → 1142
      Collagen; Collagen triple helix repeat (20 copies)

    9. XM_006238947.5 → XP_006239009.1  collagen alpha-1(XVI) chain isoform X2

      UniProtKB/TrEMBL
      F1LND0
      Related
      ENSRNOP00000058947.4, ENSRNOT00000067663.4
      Conserved Domains (2) summary
      pfam01391
      Location:1098 → 1151
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50 → 231
      TSPN; Thrombospondin N-terminal -like domains

    10. XM_006238951.5 → XP_006239013.1  collagen alpha-1(XVI) chain isoform X6

      See identical proteins and their annotated locations for XP_006239013.1

      UniProtKB/TrEMBL
      A0A8I5Y198
      Conserved Domains (2) summary
      pfam01391
      Location:1083 → 1136
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50 → 231
      TSPN; Thrombospondin N-terminal -like domains

    11. XM_063288122.1 → XP_063144192.1  collagen alpha-1(XVI) chain isoform X7

      Related
      ENSRNOP00000089698.2, ENSRNOT00000100626.2

    12. XM_039110477.2 → XP_038966405.1  collagen alpha-1(XVI) chain isoform X10

      Conserved Domains (3) summary
      smart00210
      Location:56 → 237
      TSPN; Thrombospondin N-terminal -like domains
      PRK07764
      Location:766 → 884
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam01391
      Location:1104 → 1157
      Collagen; Collagen triple helix repeat (20 copies)

    13. XM_039110478.2 → XP_038966406.1  collagen alpha-1(XVI) chain isoform X11

      Conserved Domains (2) summary
      PRK07764
      Location:198 → 316
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam01391
      Location:536 → 589
      Collagen; Collagen triple helix repeat (20 copies)

    RNA

    1. XR_005504507.2 RNA Sequence

    2. XR_005504508.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001015033.2: Suppressed sequence

      Description
      NM_001015033.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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