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

Gene ID: 366474, updated on 4-Jan-2025

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 involved in 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. Orthologous to human COL16A1 (collagen type XVI alpha 1 chain). [provided by Alliance of Genome Resources, Jan 2025]
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
  • 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 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 integrin activation ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of focal adhesion assembly ISO
Inferred from Sequence Orthology
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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