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    COL27A1 collagen type XXVII alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 85301, updated on 15-Apr-2019

    Summary

    Official Symbol
    COL27A1provided by HGNC
    Official Full Name
    collagen type XXVII alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:22986
    See related
    Ensembl:ENSG00000196739 MIM:608461
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    STLS
    Summary
    This gene encodes a member of the fibrillar collagen family, and plays a role during the calcification of cartilage and the transition of cartilage to bone. The encoded protein product is a preproprotein. It includes an N-terminal signal peptide, which is followed by an N-terminal propetide, mature peptide and a C-terminal propeptide. The N-terminal propeptide contains thrombospondin N-terminal-like and laminin G-like domains. The mature peptide is a major triple-helical region. The C-terminal propeptide, also known as COLFI domain, plays crucial roles in tissue growth and repair. Mutations in this gene cause Steel syndrome. Alternatively spliced transcript variants have been found, but the full-length nature of some variants has not been determined. [provided by RefSeq, Sep 2014]
    Expression
    Ubiquitous expression in endometrium (RPKM 17.8), prostate (RPKM 8.1) and 23 other tissues See more
    Orthologs

    Genomic context

    See COL27A1 in Genome Data Viewer
    Location:
    9q32
    Exon count:
    66
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (114154271..114312516)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (116918231..117072975)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene kinesin family member 12 Neighboring gene uncharacterized LOC105376225 Neighboring gene microRNA 455 Neighboring gene uncharacterized LOC105376224 Neighboring gene orosomucoid 1 Neighboring gene orosomucoid 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Steel syndrome
    MedGen: C3554594 OMIM: 615155 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Genome-wide association study of Tourette's syndrome.
    NHGRI GWA Catalog
    Many sequence variants affecting diversity of adult human height.
    NHGRI GWA Catalog
    Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
      Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
    • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
      Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
    • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
      Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
    • Protein digestion and absorption, organism-specific biosystem (from KEGG)
      Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Protein digestion and absorption, conserved biosystem (from KEGG)
      Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ11895, KIAA1870, MGC11337

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix structural constituent IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular matrix structural constituent conferring tensile strength IEA
    Inferred from Electronic Annotation
    more info
    PubMed 
    extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    growth plate cartilage chondrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    collagen-containing extracellular matrix HDA PubMed 
    endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    fibrillar collagen trimer IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(XXVII) chain
    Names
    collagen, type XXVII, alpha 1

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_034260.1 RefSeqGene

      Range
      5001..161972
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_032888.4NP_116277.2  collagen alpha-1(XXVII) chain preproprotein

      See identical proteins and their annotated locations for NP_116277.2

      Status: REVIEWED

      Source sequence(s)
      AI808820, AL356796, AL445543, AY149237, BC035728, BU076480
      Consensus CDS
      CCDS6802.1
      UniProtKB/Swiss-Prot
      Q8IZC6
      Related
      ENSP00000348385.3, ENST00000356083.8
      Conserved Domains (3) summary
      pfam01391
      Location:694752
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:16611859
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:45220
      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: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

      Range
      114154271..114312516
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011519138.2XP_011517440.1  collagen alpha-1(XXVII) chain isoform X1

      Conserved Domains (3) summary
      pfam01391
      Location:692750
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:16591857
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:43218
      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_011519142.3XP_011517444.1  collagen alpha-1(XXVII) chain isoform X4

      Conserved Domains (2) summary
      pfam01391
      Location:694752
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:45220
      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_017015239.1XP_016870728.1  collagen alpha-1(XXVII) chain isoform X7

    4. XM_011519143.2XP_011517445.1  collagen alpha-1(XXVII) chain isoform X5

      Conserved Domains (2) summary
      pfam01391
      Location:694752
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:45220
      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_011519144.2XP_011517446.1  collagen alpha-1(XXVII) chain isoform X6

      Conserved Domains (2) summary
      pfam01391
      Location:694752
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:45220
      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_011519140.1XP_011517442.1  collagen alpha-1(XXVII) chain isoform X2

      Conserved Domains (3) summary
      pfam01391
      Location:694752
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:16431841
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:45220
      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_006717308.2XP_006717371.1  collagen alpha-1(XXVII) chain isoform X3

      Conserved Domains (3) summary
      pfam01391
      Location:676734
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:16431841
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:45220
      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_006717310.3XP_006717373.1  collagen alpha-1(XXVII) chain isoform X8

      Conserved Domains (2) summary
      pfam01391
      Location:603660
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:8881086
      COLFI; Fibrillar collagen C-terminal domain
    9. XM_011519145.3XP_011517447.1  collagen alpha-1(XXVII) chain isoform X9

      Conserved Domains (2) summary
      pfam01391
      Location:565622
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:8501048
      COLFI; Fibrillar collagen C-terminal domain

    RNA

    1. XR_001746405.1 RNA Sequence

    2. XR_929861.2 RNA Sequence

    3. XR_929862.1 RNA Sequence

    4. XR_929863.1 RNA Sequence

    5. XR_929860.3 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_032161.1: Suppressed sequence

      Description
      NM_032161.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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