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

    Gene ID: 107581, updated on 27-Nov-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, Nov 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

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

      Status: VALIDATED

      Source sequence(s)
      AL606925

    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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