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Col16a1 collagen, type XVI, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 107581, updated on 9-Dec-2024

Summary

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Official Symbol
Col16a1provided by MGI
Official Full Name
collagen, type XVI, alpha 1provided by MGI
Primary source
MGI:MGI:1095396
See related
Ensembl:ENSMUSG00000040690 AllianceGenome:MGI:1095396
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
CA1F; 2700007F12Rik; A530052M23Rik
Summary
Predicted to enable integrin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Acts upstream of or within cellular response to amino acid stimulus. Located in collagen-containing extracellular matrix. Is expressed in several structures, including genitourinary system; nervous system; retina layer; and trunk mesenchyme. Orthologous to human COL16A1 (collagen type XVI alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
Expression
Broad expression in limb E14.5 (RPKM 43.0), bladder adult (RPKM 17.7) and 16 other tissues See more
Orthologs
human all
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Genomic context

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See Col16a1 in Genome Data Viewer
Location:
4 D2.2; 4 63.43 cM
Exon count:
75
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (129941638..129993070)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (130047817..130099277)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_11515 Neighboring gene STARR-seq mESC enhancer starr_11516 Neighboring gene predicted gene, 54260 Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:129694658-129694811 Neighboring gene predicted gene 12963 Neighboring gene predicted gene, 46871 Neighboring gene STARR-positive B cell enhancer ABC_E1656 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:129785190-129785373 Neighboring gene predicted gene, 40258 Neighboring gene penta-EF hand domain containing 1 Neighboring gene hypocretin (orexin) receptor 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Tissue distribution and developmental expression of type XVI collagen in the mouse. Lai CH, et al. Tissue Cell, 1996 Apr. PMID 8650669
  2. Collagen XVI is a neural component of the developing and regenerating dorsal root ganglia extracellular matrix. Hubert T, et al. Matrix Biol, 2007 Apr. PMID 17169544
  3. 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
  4. The KMT2D Kabuki syndrome histone methylase controls neural crest cell differentiation and facial morphology. Shpargel KB, et al. Development, 2020 Jul 17. PMID 32541010, Free PMC Article
  5. Collagen XXVIII is a distinctive component of the peripheral nervous system nodes of ranvier and surrounds nonmyelinating glial cells. Grimal S, et al. Glia, 2010 Dec. PMID 20830809

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Data show tha collagen XVI is a neural component of the developing and regenerating dorsal root ganglia extracellular matrix.
    Title: Collagen XVI is a neural component of the developing and regenerating dorsal root ganglia extracellular matrix.
  2. there is a unique alpha1 beta1 integrin-binding site within collagen XVI located close to its C-terminal end
    Title: Collagen XVI harbors an integrin alpha1 beta1 recognition site in its C-terminal domains.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables integrin binding ISO
Inferred from Sequence Orthology
more info
  
enables integrin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in cell adhesion ISO
Inferred from Sequence Orthology
more info
  
involved_in cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell adhesion mediated by integrin IEA
Inferred from Electronic Annotation
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 IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in integrin activation IEA
Inferred from Electronic Annotation
more info
  
involved_in integrin activation ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of focal adhesion assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of focal adhesion assembly ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in basement membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
part_of collagen type IX trimer IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in collagen-containing extracellular matrix HDA PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
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
[a]1 (XVI) collagen
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_001404352.1 → NP_001391281.1  collagen alpha-1(XVI) chain isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AL606925
    UniProtKB/TrEMBL
    A3KFV7

  2. NM_001404353.1 → NP_001391282.1  collagen alpha-1(XVI) chain isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AL606925
    UniProtKB/TrEMBL
    A3KFV7

  3. NM_028266.6 → NP_082542.3  collagen alpha-1(XVI) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_082542.3

    Status: VALIDATED

    Source sequence(s)
    AL606925
    Consensus CDS
    CCDS38889.1
    UniProtKB/Swiss-Prot
    A3KFV5, Q8BLX7, Q9CZS2
    Related
    ENSMUSP00000035802.9, ENSMUST00000044565.15
    Conserved Domains (2) summary
    pfam01391
    Location:1074 → 1127
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains

RNA

  1. NR_175838.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL606925
    Related
    ENSMUST00000143432.8

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000070.7 Reference GRCm39 C57BL/6J

    Range
    129941638..129993070
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006502642.5 → XP_006502705.1  collagen alpha-1(XVI) chain isoform X2

    UniProtKB/TrEMBL
    A3KFV7
    Conserved Domains (3) summary
    pfam01391
    Location:1074 → 1127
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains
    PRK07764
    Location:644 → 867
    PRK07764; DNA polymerase III subunits gamma and tau; Validated

  2. XM_036163564.1 → XP_036019457.1  collagen alpha-1(XVI) chain isoform X4

    Conserved Domains (3) summary
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains
    PRK07764
    Location:644 → 867
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam01391
    Location:1058 → 1111
    Collagen; Collagen triple helix repeat (20 copies)

  3. XM_036163565.1 → XP_036019458.1  collagen alpha-1(XVI) chain isoform X5

    UniProtKB/TrEMBL
    E9Q0X4
    Conserved Domains (3) summary
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains
    PRK07764
    Location:644 → 867
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam01391
    Location:590 → 643
    Collagen; Collagen triple helix repeat (20 copies)

  4. XM_006502647.5 → XP_006502710.1  collagen alpha-1(XVI) chain isoform X7

    UniProtKB/TrEMBL
    E9Q0X4
    Related
    ENSMUST00000106001.8
    Conserved Domains (3) summary
    pfam01391
    Location:751 → 812
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains
    PRK07764
    Location:644 → 867
    PRK07764; DNA polymerase III subunits gamma and tau; Validated

  5. XM_006502648.5 → XP_006502711.1  collagen alpha-1(XVI) chain isoform X8

    Conserved Domains (3) summary
    pfam01391
    Location:751 → 812
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains
    PRK07764
    Location:644 → 867
    PRK07764; DNA polymerase III subunits gamma and tau; Validated

  6. XM_006502641.4 → XP_006502704.1  collagen alpha-1(XVI) chain isoform X1

    See identical proteins and their annotated locations for XP_006502704.1

    UniProtKB/TrEMBL
    A3KFV7
    Conserved Domains (3) summary
    pfam01391
    Location:1089 → 1142
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains
    PRK07764
    Location:644 → 867
    PRK07764; DNA polymerase III subunits gamma and tau; Validated

  7. XM_006502640.5 → XP_006502703.1  collagen alpha-1(XVI) chain isoform X1

    See identical proteins and their annotated locations for XP_006502703.1

    UniProtKB/TrEMBL
    A3KFV7
    Conserved Domains (3) summary
    pfam01391
    Location:1089 → 1142
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:50 → 231
    TSPN; Thrombospondin N-terminal -like domains
    PRK07764
    Location:644 → 867
    PRK07764; DNA polymerase III subunits gamma and tau; Validated

  8. XM_036163566.1 → XP_036019459.1  collagen alpha-1(XVI) chain isoform X6

    Related
    ENSMUSP00000120339.2, ENSMUST00000143577.2
    Conserved Domains (2) summary
    PRK07764
    Location:82 → 305
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam01391
    Location:527 → 580
    Collagen; Collagen triple helix repeat (20 copies)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8BLX7.2 GenPept UniProtKB/Swiss-Prot:Q8BLX7

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