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

    Gene ID: 1301, updated on 9-Dec-2024

    Summary

    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 MIM:120280; AllianceGenome:HGNC:2186
    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; DFNA37
    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]
    Expression
    Biased expression in placenta (RPKM 6.4), gall bladder (RPKM 1.9) and 4 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL11A1 in Genome Data Viewer
    Location:
    1p21.1
    Exon count:
    73
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (102876473..103108522, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (102725394..102957399, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (103342029..103574078, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268286 Neighboring gene uncharacterized LOC107985096 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:103344928-103346127 Neighboring gene superoxide dismutase 2 pseudogene 1 Neighboring gene uncharacterized LOC124904593 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:103698107-103698264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1412 Neighboring gene RNPC3 divergent transcript Neighboring gene RN7SK pseudogene 285

    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 Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Fibrochondrogenesis 1
    MedGen: C3278138 OMIM: 228520 GeneReviews: Not available
    Compare labs
    Hearing loss, autosomal dominant 37
    MedGen: C4760307 OMIM: 618533 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

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies protein quantitative trait loci (pQTLs).
    EBI GWAS Catalog
    Genome-wide association analyses identify three new susceptibility loci for primary angle closure glaucoma.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables extracellular matrix binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables extracellular matrix structural constituent NAS
    Non-traceable Author Statement
    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 heparan sulfate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables heparin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein-macromolecule adaptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cartilage condensation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in collagen fibril organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in detection of mechanical stimulus involved in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in embryonic skeletal system morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endodermal cell differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in extracellular matrix organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in inner ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proteoglycan metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in tendon development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ventricular cardiac muscle tissue morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of collagen type XI trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen type XI trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen type XI trimer NAS
    Non-traceable Author Statement
    more info
    PubMed 
    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 collagen-containing extracellular matrix NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(XI) chain
    Names
    collagen XI, alpha-1 polypeptide
    collagen, type XI, alpha 1
    deafness, autosomal dominant 37

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_008033.2 RefSeqGene

      Range
      4975..237024
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001190709.2NP_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
      Related
      ENSP00000302551.6, ENST00000353414.8
      Conserved Domains (3) summary
      pfam01391
      Location:802861
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:38229
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:15391765
      COLFI; Fibrillar collagen C-terminal domain
    2. NM_001854.4NP_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
      B1ASK7, D3DT73, E9PCU0, P12107, Q14034, Q149N0, Q9UIT4, Q9UIT5, Q9UIT6
      Related
      ENSP00000359114.3, ENST00000370096.9
      Conserved Domains (3) summary
      pfam01391
      Location:841900
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:38229
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:15781804
      COLFI; Fibrillar collagen C-terminal domain
    3. NM_080629.3NP_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
      Related
      ENSP00000351163.2, ENST00000358392.6
      Conserved Domains (3) summary
      pfam01391
      Location:853912
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:38229
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:15901816
      COLFI; Fibrillar collagen C-terminal domain
    4. NM_080630.4NP_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
      Related
      ENSP00000426533.1, ENST00000512756.5
      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_134980.2 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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      102876473..103108522 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017000335.2XP_016855824.1  collagen alpha-1(XI) chain isoform X2

    2. XM_017000334.2XP_016855823.1  collagen alpha-1(XI) chain isoform X1

    3. XM_017000337.2XP_016855826.1  collagen alpha-1(XI) chain isoform X4

    4. XM_017000336.2XP_016855825.1  collagen alpha-1(XI) chain isoform X3

    RNA

    1. XR_007085257.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      102725394..102957399 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334472.1XP_054190447.1  collagen alpha-1(XI) chain isoform X2

    2. XM_054334471.1XP_054190446.1  collagen alpha-1(XI) chain isoform X1

    3. XM_054334474.1XP_054190449.1  collagen alpha-1(XI) chain isoform X4

    4. XM_054334473.1XP_054190448.1  collagen alpha-1(XI) chain isoform X3

    RNA

    1. XR_008485930.1 RNA Sequence