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    COL11A1 collagen type XI alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1301, updated on 8-Aug-2016
    Official Symbol
    COL11A1provided by HGNC
    Official Full Name
    collagen type XI alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2186
    See related
    Ensembl:ENSG00000060718 HPRD:00375; MIM:120280; Vega:OTTHUMG00000010872
    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
    STL2; COLL6; CO11A1
    Summary
    This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in this gene is also associated with susceptibility to lumbar disc herniation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]
    Orthologs
    Location:
    1p21
    Exon count:
    71
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 1 NC_000001.11 (102876467..103108580, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (103342023..103574052, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378874 Neighboring gene uncharacterized LOC107985096 Neighboring gene superoxide dismutase 2, mitochondrial pseudogene 1 Neighboring gene uncharacterized LOC101928436 Neighboring gene RNA, 7SK small nuclear pseudogene 285 Neighboring gene RNA binding region (RNP1, RRM) containing 3 Neighboring gene amylase, alpha 2B (pancreatic)

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Fibrochondrogenesis
    MedGen: C0265282 OMIM: 228520 GeneReviews: Not available
    Compare labs
    Intervertebral disc disorder
    MedGen: C0158252 OMIM: 603932 GeneReviews: Not available
    Compare labs
    Marshall syndrome
    MedGen: C0265235 OMIM: 154780 GeneReviews: Not available
    Compare labs
    Stickler syndrome, type 2
    MedGen: C1858084 OMIM: 604841 GeneReviews: Stickler Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2011-10-19)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated (2011-10-19)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    A genome-wide association study identifies protein quantitative trait loci (pQTLs).
    NHGRI GWA Catalog
    Genome-wide association analyses identify three new susceptibility loci for primary angle closure glaucoma.
    NHGRI GWA Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    NHGRI GWA Catalog
    • 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 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...
    • Focal Adhesion, organism-specific biosystem (from WikiPathways)
      Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • 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...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    extracellular matrix structural constituent NAS
    Non-traceable Author Statement
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding, bridging NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    cartilage condensation IEA
    Inferred from Electronic Annotation
    more info
     
    chondrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    collagen catabolic process TAS
    Traceable Author Statement
    more info
     
    collagen fibril organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    detection of mechanical stimulus involved in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic skeletal system morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    endodermal cell differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    extracellular matrix organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    inner ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    ossification IEA
    Inferred from Electronic Annotation
    more info
     
    proteoglycan metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    tendon development IEA
    Inferred from Electronic Annotation
    more info
     
    ventricular cardiac muscle tissue morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    visual perception IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    collagen type XI trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    collagen type XI trimer NAS
    Non-traceable Author Statement
    more info
    PubMed 
    endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    extracellular region TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    collagen alpha-1(XI) chain
    Names
    collagen XI, alpha-1 polypeptide
    collagen, type XI, alpha 1

    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_008033.1 RefSeqGene

      Range
      5001..237030
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001190709.1NP_001177638.1  collagen alpha-1(XI) chain isoform E preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (E, previously referred to as C) does not utilize either alternate exon 6A or 6B. The encoded isoform (E, previously referred to as C) is shorter than isoform A. There are no publicly available transcripts representing this variant; it is supported by mRNA annotation on DNA accession AF101112.1, protein AAF04724.1, submitted by the authors of PMID:10486316.
      Source sequence(s)
      AB208844, AC093150, AC099567, BU159588, BX476821, CA448616, J04177
      Consensus CDS
      CCDS53348.1
      UniProtKB/Swiss-Prot
      P12107
      UniProtKB/TrEMBL
      Q59HB5
      Related
      ENSP00000302551, ENST00000353414
      Conserved Domains (3) summary
      pfam01391
      Location:802861
      Collagen; Collagen triple helix repeat (20 copies)
      cd00110
      Location:73225
      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 ...
      pfam01410
      Location:15541765
      COLFI; Fibrillar collagen C-terminal domain
    2. NM_001854.3NP_001845.3  collagen alpha-1(XI) chain isoform A preproprotein

      See identical proteins and their annotated locations for NP_001845.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (A) utilizes alternate exon 6, designated exon 6A. The encoded isoform (A) has a 39 aa region specified by exon 6A, that differs from the corresponding 51 aa region encoded by exon 6B in isoform B.
      Source sequence(s)
      AB208844, AC093150, AC099567, BU159588, BX476821, J04177
      Consensus CDS
      CCDS778.1
      UniProtKB/Swiss-Prot
      P12107
      UniProtKB/TrEMBL
      Q59HB5
      Related
      ENSP00000359114, OTTHUMP00000012567, ENST00000370096, OTTHUMT00000029997
      Conserved Domains (3) summary
      pfam01391
      Location:841900
      Collagen; Collagen triple helix repeat (20 copies)
      cd00110
      Location:73225
      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 ...
      pfam01410
      Location:15931804
      COLFI; Fibrillar collagen C-terminal domain
    3. NM_080629.2NP_542196.2  collagen alpha-1(XI) chain isoform B preproprotein

      See identical proteins and their annotated locations for NP_542196.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (B) utilizes alternate exon 6, designated exon 6B, and encodes the longest isoform (B). There are no publicly available transcripts representing this variant; it is supported by mRNA annotation on DNA accession AF101112.1, protein AAF04726.1, submitted by the authors of PMID:10486316.
      Source sequence(s)
      AB208844, AC093150, AC099567, BU159588, BX476821, J04177
      UniProtKB/Swiss-Prot
      P12107
      UniProtKB/TrEMBL
      Q59HB5
      Related
      ENSP00000351163, ENST00000358392
      Conserved Domains (3) summary
      pfam01391
      Location:853912
      Collagen; Collagen triple helix repeat (20 copies)
      cd00110
      Location:73225
      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 ...
      pfam01410
      Location:16051816
      COLFI; Fibrillar collagen C-terminal domain
    4. NM_080630.3NP_542197.3  collagen alpha-1(XI) chain isoform C preproprotein

      See identical proteins and their annotated locations for NP_542197.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (C, previously referred to as D) includes alternate exon 6A but lacks two other alternate exons, resulting in the loss of an in-frame segment in the coding region, compared to variant A. The encoded isoform (C, previously referred to as D) is shorter than isoform A.
      Source sequence(s)
      AC093150, AC099567, BC117697, CA448616
      Consensus CDS
      CCDS780.2
      UniProtKB/Swiss-Prot
      P12107
      Related
      ENSP00000426533, OTTHUMP00000218241, ENST00000512756, OTTHUMT00000360666
      Conserved Domains (3) summary
      pfam01391
      Location:725784
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:38229
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:14621688
      COLFI; Fibrillar collagen C-terminal domain

    RNA

    1. NR_134980.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (F) contains an alternate internal exon compared to variant A. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB208844, AC093150, AC099567, BC117697, CA448616

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p7 Primary Assembly

      Range
      102876467..103108580 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017000334.1XP_016855823.1  

    2. XM_017000335.1XP_016855824.1  

    3. XM_017000337.1XP_016855826.1  

    4. XM_017000336.1XP_016855825.1  

    Alternate CHM1_1.1

    Genomic

    1. NC_018912.2 Alternate CHM1_1.1

      Range
      103456836..103688896 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)