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    COL11A2 collagen type XI alpha 2 chain [ Homo sapiens (human) ]

    Gene ID: 1302, updated on 25-Mar-2017
    Official Symbol
    COL11A2provided by HGNC
    Official Full Name
    collagen type XI alpha 2 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2187
    See related
    Ensembl:ENSG00000204248 MIM:120290; Vega:OTTHUMG00000031036
    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
    HKE5; PARP; STL3; FBCG2; DFNA13; DFNB53
    Summary
    This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. It is located on chromosome 6 very close to but separate from the gene for retinoid X receptor beta. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Proteolytic processing of this type XI chain produces PARP, a proline/arginine-rich protein that is an amino terminal domain. Mutations in this gene are associated with type III Stickler syndrome, otospondylomegaepiphyseal dysplasia (OSMED syndrome), Weissenbacher-Zweymuller syndrome, autosomal dominant non-syndromic sensorineural type 13 deafness (DFNA13), and autosomal recessive non-syndromic sensorineural type 53 deafness (DFNB53). Alternative splicing results in multiple transcript variants. A related pseudogene is located nearby on chromosome 6. [provided by RefSeq, Jul 2009]
    Orthologs
    Location:
    6p21.32
    Exon count:
    70
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (33162692..33193009, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33130469..33160245, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375021 Neighboring gene major histocompatibility complex, class II, DP alpha 3 (pseudogene) Neighboring gene HLA complex group 24 (non-protein coding) Neighboring gene retinoid X receptor beta Neighboring gene RNA, Ro-associated Y4 pseudogene 10 Neighboring gene solute carrier family 39 member 7

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Deafness, autosomal dominant 13 Compare labs
    Deafness, autosomal recessive 53
    MedGen: C1864746 OMIM: 609706 GeneReviews: Not available
    Compare labs
    Fibrochondrogenesis 2
    MedGen: C3281128 OMIM: 614524 GeneReviews: Not available
    Compare labs
    Otospondylomegaepiphyseal dysplasia
    MedGen: C0432210 OMIM: 215150 GeneReviews: Not available
    Compare labs
    Stickler syndrome, type 3
    MedGen: C1861481 OMIM: 184840 GeneReviews: Stickler Syndrome
    Compare labs
    Weissenbacher-Zweymuller syndrome
    MedGen: C1848488 OMIM: 277610 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23.
    NHGRI GWA Catalog
    Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis.
    NHGRI GWA Catalog
    Genetically distinct subsets within ANCA-associated vasculitis.
    NHGRI GWA Catalog
    Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
    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 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...
    • 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...
    • Neural Crest Differentiation, organism-specific biosystem (from WikiPathways)
      Neural Crest Differentiation, organism-specific biosystemGene regulatory network model of cranial neural crest cell (CNCC) development, adaped from PMID: 19575671. Most interactions in the model are proposed to regulate transcription of core factors involv...
    • 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 structural constituent conferring tensile strength NAS
    Non-traceable Author Statement
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding, bridging NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    collagen catabolic process TAS
    Traceable Author Statement
    more info
     
    collagen fibril organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    palate development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    skeletal system development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    soft palate development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    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-2(XI) chain
    Names
    collagen, type XI, alpha 2
    pro-a2 chain of collagen type XI

    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_011589.1 RefSeqGene

      Range
      5001..34777
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001163771.1NP_001157243.1  collagen alpha-2(XI) chain isoform 4 precursor

      See identical proteins and their annotated locations for NP_001157243.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks several exons at the 3' end and has a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is considerably shorter than isoform 1.
      Source sequence(s)
      AL645940, BC053886
      Consensus CDS
      CCDS54992.1
      UniProtKB/Swiss-Prot
      P13942
      Related
      ENSP00000378620, OTTHUMP00000178607, ENST00000395194, OTTHUMT00000276187
      Conserved Domains (1) summary
      smart00210
      Location:31213
      TSPN; Thrombospondin N-terminal -like domains
    2. NM_080679.2NP_542410.2  collagen alpha-2(XI) chain isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_542410.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks three alternate in-frame exons, compared to variant 1, resulting in a shorter protein (isoform 3), compared to isoform 1. There are no publicly available human transcripts representing the full-length exon combination of this variant, but the region of variation is supported by experimental data in PMIDs 8663204 and 8838804, by homology data in mouse, and the full-length sequence is represented in accession U32169.1:AAC50215.1.
      Source sequence(s)
      AL645940
      UniProtKB/TrEMBL
      H0YIS1
      Related
      ENSP00000355123, ENST00000361917
      Conserved Domains (3) summary
      pfam01391
      Location:547603
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:14331628
      COLFI; Fibrillar collagens C-terminal domain
      smart00210
      Location:31213
      TSPN; Thrombospondin N-terminal -like domains
    3. NM_080680.2NP_542411.2  collagen alpha-2(XI) chain isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_542411.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). There are no publicly available human transcripts representing the full-length exon combination of this variant, but the region of variation is supported by experimental data in PMIDs 8663204 and 8838804, by homology data in mouse, and the full-length sequence is represented in accession U32169.1:AAC50214.1.
      Source sequence(s)
      AL645940
      UniProtKB/Swiss-Prot
      P13942
      UniProtKB/TrEMBL
      A0A0C4DFS1
      Related
      ENSP00000339915, ENST00000341947
      Conserved Domains (3) summary
      pfam01391
      Location:654710
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:15401735
      COLFI; Fibrillar collagens C-terminal domain
      smart00210
      Location:31213
      TSPN; Thrombospondin N-terminal -like domains
    4. NM_080681.2NP_542412.2  collagen alpha-2(XI) chain isoform 2 preproprotein

      See identical proteins and their annotated locations for NP_542412.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1. There are no publicly available human transcripts representing the full-length exon combination of this variant, but the region of variation is supported by experimental data in PMIDs 8663204 and 8838804, by homology data in mouse, and the full-length sequence is represented in accession U32169.1:AAC50213.1.
      Source sequence(s)
      AL645940
      Consensus CDS
      CCDS43452.1
      UniProtKB/Swiss-Prot
      P13942
      UniProtKB/TrEMBL
      Q4VXY6
      Related
      ENSP00000363840, OTTHUMP00000029040, ENST00000374708, OTTHUMT00000076032
      Conserved Domains (3) summary
      pfam01391
      Location:568624
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:14541649
      COLFI; Fibrillar collagens C-terminal domain
      smart00210
      Location:31213
      TSPN; Thrombospondin N-terminal -like domains

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p7 Primary Assembly

      Range
      33162692..33193009 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017010250.1XP_016865739.1  collagen alpha-2(XI) chain isoform X1

      UniProtKB/Swiss-Prot
      P13942
      UniProtKB/TrEMBL
      A0A0C4DFS1
      Conserved Domains (3) summary
      pfam01391
      Location:654710
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:15401735
      COLFI; Fibrillar collagens C-terminal domain
      smart00210
      Location:31213
      TSPN; Thrombospondin N-terminal -like domains
    2. XM_011514300.2XP_011512602.1  collagen alpha-2(XI) chain isoform X3

      See identical proteins and their annotated locations for XP_011512602.1

      Conserved Domains (2) summary
      pfam01391
      Location:356412
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:12421437
      COLFI; Fibrillar collagens C-terminal domain
    3. XM_011514299.2XP_011512601.1  collagen alpha-2(XI) chain isoform X2

      See identical proteins and their annotated locations for XP_011512601.1

      Conserved Domains (2) summary
      pfam01391
      Location:416472
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:13021497
      COLFI; Fibrillar collagens C-terminal domain
    4. XM_017010251.1XP_016865740.1  collagen alpha-2(XI) chain isoform X5

    5. XM_011514302.2XP_011512604.1  collagen alpha-2(XI) chain isoform X4

      See identical proteins and their annotated locations for XP_011512604.1

      Conserved Domains (2) summary
      pfam01391
      Location:283339
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:11691364
      COLFI; Fibrillar collagens C-terminal domain

    Reference GRCh38.p7 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p7 ALT_REF_LOCI_2

      Range
      4574200..4603975 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p7 ALT_REF_LOCI_3

      Range
      4406191..4435967 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p7 ALT_REF_LOCI_4

      Range
      4582165..4611940 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p7 ALT_REF_LOCI_5

      Range
      4598650..4628424 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p7 ALT_REF_LOCI_6

      Range
      4357096..4386871 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p7 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p7 ALT_REF_LOCI_7

      Range
      4611338..4638116 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018917.2 Alternate CHM1_1.1

      Range
      33132343..33162118 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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