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    Col27a1 collagen, type XXVII, alpha 1 [ Mus musculus (house mouse) ]

    Gene ID: 373864, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Col27a1provided by MGI
    Official Full Name
    collagen, type XXVII, alpha 1provided by MGI
    Primary source
    MGI:MGI:2672118
    See related
    Ensembl:ENSMUSG00000045672 AllianceGenome:MGI:2672118
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    5730512J02Rik
    Summary
    This gene encodes the alpha-1 subunit of type XXVII collagen, one of the low abundance fibril-forming collagens found in cartilage. The encoded protein forms a homotrimeric triple helical procollagen that undergoes proteolytic processing during fibril formation. Transgenic mice lacking a portion of the collagenous domain in the encoded protein exhibit skeletal abnormalities, chondrodysplasia and die at birth because of a lung defect. [provided by RefSeq, Dec 2015]
    Expression
    Broad expression in limb E14.5 (RPKM 27.8), ovary adult (RPKM 7.1) and 17 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Col27a1 in Genome Data Viewer
    Location:
    4 B3; 4 33.96 cM
    Exon count:
    65
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (63132246..63253228)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (63214009..63334991)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene alpha 1 microglobulin/bikunin precursor Neighboring gene kinesin family member 12 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:62883492-62883675 Neighboring gene microRNA 455 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:62968523-62968632 Neighboring gene STARR-seq mESC enhancer starr_10435 Neighboring gene predicted gene, 52743 Neighboring gene orosomucoid 1 pseudogene Neighboring gene orosomucoid 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. Identification, characterization and expression analysis of a new fibrillar collagen gene, COL27A1. Pace JM, et al. Matrix Biol, 2003 Mar. PMID 12714037
    2. A novel and highly conserved collagen (pro(alpha)1(XXVII)) with a unique expression pattern and unusual molecular characteristics establishes a new clade within the vertebrate fibrillar collagen family. Boot-Handford RP, et al. J Biol Chem, 2003 Aug 15. PMID 12766169
    3. Collagen XXVII is developmentally regulated and forms thin fibrillar structures distinct from those of classical vertebrate fibrillar collagens. Plumb DA, et al. J Biol Chem, 2007 Apr 27. PMID 17331945, Free PMC Article
    4. The transcription factor Lc-Maf participates in Col27a1 regulation during chondrocyte maturation. Mayo JL, et al. Exp Cell Res, 2009 Aug 1. PMID 19414009, Free PMC Article
    5. Collagen XXVII organises the pericellular matrix in the growth plate. Plumb DA, et al. PLoS One, 2011. PMID 22206015, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Results suggest that Lc-Maf may affect the process of endochondral ossification by participating in the regulation of Col27a1 expression.
      Title: The transcription factor Lc-Maf participates in Col27a1 regulation during chondrocyte maturation.
    2. molecular cloning
      Title: Identification, characterization and expression analysis of a new fibrillar collagen gene, COL27A1.
    3. type XXVII collagen has unusual molecular features such as no minor helical domain, a major helical domain that is short and interrupted, and a short chain selection sequence within the NC1 domain (COLLAGEN TYPE XXVII)
      Title: A novel and highly conserved collagen (pro(alpha)1(XXVII)) with a unique expression pattern and unusual molecular characteristics establishes a new clade within the vertebrate fibrillar collagen family.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 
    • Targeted (2)  1 citation

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within extracellular matrix organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within growth plate cartilage chondrocyte development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of fibrillar collagen trimer IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    collagen alpha-1(XXVII) chain
    Names
    procollagen, type XXVII, 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_025685.3 → NP_079961.3  collagen alpha-1(XXVII) chain preproprotein

      See identical proteins and their annotated locations for NP_079961.3

      Status: REVIEWED

      Source sequence(s)
      AK157951, AL683828, AL691496, AY167568
      Consensus CDS
      CCDS18250.1
      UniProtKB/Swiss-Prot
      Q5QNQ9, Q69Z83, Q80UA8
      Related
      ENSMUSP00000043816.7, ENSMUST00000036300.13
      Conserved Domains (3) summary
      pfam01391
      Location:679 → 737
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:1646 → 1844
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:43 → 221
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    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
      63132246..63253228
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030253629.1 → XP_030109489.1  collagen alpha-1(XXVII) chain isoform X2

      Conserved Domains (4) summary
      pfam01391
      Location:679 → 737
      Collagen; Collagen triple helix repeat (20 copies)
      pfam05109
      Location:269 → 567
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl02436
      Location:1647 → 1845
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:43 → 221
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    2. XM_030253631.2 → XP_030109491.1  collagen alpha-1(XXVII) chain isoform X5

      Conserved Domains (3) summary
      pfam01391
      Location:679 → 737
      Collagen; Collagen triple helix repeat (20 copies)
      pfam05109
      Location:269 → 567
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl22861
      Location:43 → 221
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    3. XM_011250057.4 → XP_011248359.1  collagen alpha-1(XXVII) chain isoform X6

      Conserved Domains (3) summary
      pfam01391
      Location:679 → 737
      Collagen; Collagen triple helix repeat (20 copies)
      pfam05109
      Location:269 → 567
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl22861
      Location:43 → 221
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    4. XM_006538039.5 → XP_006538102.1  collagen alpha-1(XXVII) chain isoform X9

      Conserved Domains (3) summary
      pfam01391
      Location:679 → 737
      Collagen; Collagen triple helix repeat (20 copies)
      pfam05109
      Location:269 → 567
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl22861
      Location:43 → 221
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    5. XM_011250058.4 → XP_011248360.1  collagen alpha-1(XXVII) chain isoform X8

      Conserved Domains (3) summary
      pfam01391
      Location:679 → 737
      Collagen; Collagen triple helix repeat (20 copies)
      pfam05109
      Location:269 → 567
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl22861
      Location:43 → 221
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    6. XM_006538035.5 → XP_006538098.1  collagen alpha-1(XXVII) chain isoform X1

      Conserved Domains (4) summary
      pfam01391
      Location:679 → 737
      Collagen; Collagen triple helix repeat (20 copies)
      pfam05109
      Location:269 → 567
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl02436
      Location:1647 → 1845
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:43 → 221
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    7. XM_036164207.1 → XP_036020100.1  collagen alpha-1(XXVII) chain isoform X3

      Conserved Domains (5) summary
      PRK12678
      Location:1265 → 1445
      PRK12678; transcription termination factor Rho; Provisional
      pfam05109
      Location:269 → 567
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam01391
      Location:745 → 801
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:1629 → 1827
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:43 → 221
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    8. XM_030253630.2 → XP_030109490.1  collagen alpha-1(XXVII) chain isoform X4

      Conserved Domains (3) summary
      pfam01391
      Location:509 → 567
      Collagen; Collagen triple helix repeat (20 copies)
      pfam05109
      Location:99 → 397
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl02436
      Location:1477 → 1675
      COLFI; Fibrillar collagen C-terminal domain

    9. XM_030253632.1 → XP_030109492.1  collagen alpha-1(XXVII) chain isoform X7

      Conserved Domains (2) summary
      pfam01391
      Location:609 → 666
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:889 → 1087
      COLFI; Fibrillar collagen C-terminal domain

    10. XM_030253634.1 → XP_030109494.1  collagen alpha-1(XXVII) chain isoform X10

      Conserved Domains (2) summary
      pfam01391
      Location:457 → 514
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:737 → 935
      COLFI; Fibrillar collagen C-terminal domain

    RNA

    1. XR_390328.4 RNA Sequence

    2. XR_003954978.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5QNQ9.1 GenPept UniProtKB/Swiss-Prot:Q5QNQ9

    Gene LinkOut

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