U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

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

    Gene ID: 1302, updated on 17-Jun-2024

    Summary

    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; AllianceGenome:HGNC:2187
    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; OSMEDA; OSMEDB
    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]
    Expression
    Broad expression in testis (RPKM 1.9), brain (RPKM 1.8) and 20 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL11A2 in Genome Data Viewer
    Location:
    6p21.32
    Exon count:
    72
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33162694..33193519, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32984047..33014927, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33130471..33160244, 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 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33131677-33132178 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33165434-33165634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:33168171-33168672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33168673-33169174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33169175-33169676 Neighboring gene retinoid X receptor beta Neighboring gene RNY4 pseudogene 10 Neighboring gene solute carrier family 39 member 7

    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

    EBI GWAS Catalog

    Description
    A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23.
    EBI GWAS Catalog
    Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis.
    EBI GWAS Catalog
    Genetically distinct subsets within ANCA-associated vasculitis.
    EBI GWAS Catalog
    Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cartilage development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in collagen fibril organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in roof of mouth development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory perception of sound IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in skeletal system development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in soft palate development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of collagen trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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-2(XI) chain
    Names
    collagen, type XI, alpha 2
    pro-a2 chain of collagen type XI

    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_011589.1 RefSeqGene

      Range
      5002..34775
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001163771.2NP_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/TrEMBL
      A0A140T9A1
      Related
      ENSP00000378620.1, ENST00000395194.1
      Conserved Domains (1) summary
      smart00210
      Location:31213
      TSPN; Thrombospondin N-terminal -like domains
    2. NM_001424108.1NP_001411037.1  collagen alpha-2(XI) chain isoform 5 preproprotein

      Status: REVIEWED

      Source sequence(s)
      AL645940
      UniProtKB/TrEMBL
      A0A140T9N1
    3. NM_001424109.1NP_001411038.1  collagen alpha-2(XI) chain isoform 6

      Status: REVIEWED

      Source sequence(s)
      AL645940
      UniProtKB/TrEMBL
      A0A1U9X7J8
    4. NM_001424110.1NP_001411039.1  collagen alpha-2(XI) chain isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL645940
    5. NM_001424111.1NP_001411040.1  collagen alpha-2(XI) chain isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL645940
    6. NM_001424112.1NP_001411041.1  collagen alpha-2(XI) chain isoform 8

      Status: REVIEWED

      Source sequence(s)
      AL645940
    7. NM_080679.3NP_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
      A0A0G2JL78, A0A140TA54
      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
    8. NM_080680.3NP_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/TrEMBL
      A0A0C4DFS1, A0A1U9X7J8
      Related
      ENSP00000339915.2, ENST00000341947.7
      Conserved Domains (5) 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
      cl26386
      Location:12641437
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
      cl28033
      Location:361703
      Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
    9. NM_080681.3NP_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/TrEMBL
      A0A140T9N1, Q4VXY6
      Related
      ENSP00000363840.4, ENST00000374708.8
      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

    RNA

    1. NR_187605.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL645940

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      33162694..33193519 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418183.1XP_047274139.1  collagen alpha-2(XI) chain isoform X7

      UniProtKB/TrEMBL
      A0A1U9X7J8
    2. XM_017010250.2XP_016865739.1  collagen alpha-2(XI) chain isoform X1

      UniProtKB/TrEMBL
      A0A0C4DFS1, A0A1U9X7J8
      Conserved Domains (5) 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
      cl26386
      Location:12641437
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
      cl28033
      Location:361703
      Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
    3. XM_011514300.3XP_011512602.1  collagen alpha-2(XI) chain isoform X4

      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
    4. XM_011514299.3XP_011512601.1  collagen alpha-2(XI) chain isoform X3

      See identical proteins and their annotated locations for XP_011512601.1

      UniProtKB/TrEMBL
      A0A1U9X7J8
      Conserved Domains (2) summary
      pfam01391
      Location:416472
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:13021497
      COLFI; Fibrillar collagens C-terminal domain
    5. XM_017010251.3XP_016865740.1  collagen alpha-2(XI) chain isoform X6

    6. XM_011514302.3XP_011512604.1  collagen alpha-2(XI) chain isoform X5

      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.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      4574202..4605026 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329736.1XP_054185711.1  collagen alpha-2(XI) chain isoform X8

      UniProtKB/Swiss-Prot
      A6NLX2, E7ER90, P13942, Q07751, Q13271, Q13272, Q13273, Q5JP94, Q5SUI8, Q7Z6C3, Q99866, Q9UIP9
      UniProtKB/TrEMBL
      A0A1U9X7J1

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      4406193..4437018 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330229.1XP_054186204.1  collagen alpha-2(XI) chain isoform X1

      UniProtKB/TrEMBL
      A0A0C4DFS1, A0A1U9X7J8
    2. XM_054330232.1XP_054186207.1  collagen alpha-2(XI) chain isoform X4

    3. XM_054330231.1XP_054186206.1  collagen alpha-2(XI) chain isoform X3

      UniProtKB/TrEMBL
      A0A1U9X7J8
    4. XM_054330234.1XP_054186209.1  collagen alpha-2(XI) chain isoform X6

    5. XM_054330233.1XP_054186208.1  collagen alpha-2(XI) chain isoform X5

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      4582167..4613046 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330520.1XP_054186495.1  collagen alpha-2(XI) chain isoform X11

      UniProtKB/TrEMBL
      A0A140TA54
    2. XM_054330519.1XP_054186494.1  collagen alpha-2(XI) chain isoform X10

      UniProtKB/TrEMBL
      A0A140T9I7
    3. XM_054330517.1XP_054186492.1  collagen alpha-2(XI) chain isoform X1

      UniProtKB/TrEMBL
      A0A140TA43, A0A1U9X7J8
    4. XM_054330518.1XP_054186493.1  collagen alpha-2(XI) chain isoform X9

      UniProtKB/TrEMBL
      A0A1U9X7J8
    5. XM_054330522.1XP_054186497.1  collagen alpha-2(XI) chain isoform X4

    6. XM_054330521.1XP_054186496.1  collagen alpha-2(XI) chain isoform X3

      UniProtKB/TrEMBL
      A0A1U9X7J8
    7. XM_054330524.1XP_054186499.1  collagen alpha-2(XI) chain isoform X6

    8. XM_054330523.1XP_054186498.1  collagen alpha-2(XI) chain isoform X5

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      4598652..4629530 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330768.1XP_054186743.1  collagen alpha-2(XI) chain isoform X14

      UniProtKB/TrEMBL
      A0A140T9I7
    2. XM_054330766.1XP_054186741.1  collagen alpha-2(XI) chain isoform X13

      UniProtKB/TrEMBL
      A0A140T9I7
    3. XM_054330764.1XP_054186739.1  collagen alpha-2(XI) chain isoform X1

      UniProtKB/TrEMBL
      A0A0G2JL35, A0A1U9X7J8
    4. XM_054330765.1XP_054186740.1  collagen alpha-2(XI) chain isoform X12

      UniProtKB/TrEMBL
      A0A1U9X7J8
    5. XM_054330770.1XP_054186745.1  collagen alpha-2(XI) chain isoform X4

    6. XM_054330769.1XP_054186744.1  collagen alpha-2(XI) chain isoform X3

      UniProtKB/TrEMBL
      A0A1U9X7J8
    7. XM_054330772.1XP_054186747.1  collagen alpha-2(XI) chain isoform X6

    8. XM_054330771.1XP_054186746.1  collagen alpha-2(XI) chain isoform X5

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      4357098..4387977 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331004.1XP_054186979.1  collagen alpha-2(XI) chain isoform X17

      UniProtKB/TrEMBL
      A0A140T9I7
    2. XM_054331003.1XP_054186978.1  collagen alpha-2(XI) chain isoform X16

      UniProtKB/TrEMBL
      A0A140T9I7
    3. XM_054331001.1XP_054186976.1  collagen alpha-2(XI) chain isoform X1

      UniProtKB/TrEMBL
      A0A0G2JL35, A0A1U9X7J8
    4. XM_054331002.1XP_054186977.1  collagen alpha-2(XI) chain isoform X15

      UniProtKB/TrEMBL
      A0A1U9X7J8
    5. XM_054331006.1XP_054186981.1  collagen alpha-2(XI) chain isoform X4

    6. XM_054331005.1XP_054186980.1  collagen alpha-2(XI) chain isoform X3

      UniProtKB/TrEMBL
      A0A1U9X7J8
    7. XM_054331008.1XP_054186983.1  collagen alpha-2(XI) chain isoform X6

    8. XM_054331007.1XP_054186982.1  collagen alpha-2(XI) chain isoform X5

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      4611340..4639206 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      32984047..33014927 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354226.1XP_054210201.1  collagen alpha-2(XI) chain isoform X20

      UniProtKB/TrEMBL
      A0A140T9I7
    2. XM_054354224.1XP_054210199.1  collagen alpha-2(XI) chain isoform X19

      UniProtKB/TrEMBL
      A0A140T9I7
    3. XM_054354222.1XP_054210197.1  collagen alpha-2(XI) chain isoform X1

      UniProtKB/TrEMBL
      A0A0C4DFS1, A0A1U9X7J8
    4. XM_054354223.1XP_054210198.1  collagen alpha-2(XI) chain isoform X18

      UniProtKB/TrEMBL
      A0A1U9X7J8
    5. XM_054354228.1XP_054210203.1  collagen alpha-2(XI) chain isoform X4

    6. XM_054354227.1XP_054210202.1  collagen alpha-2(XI) chain isoform X3

      UniProtKB/TrEMBL
      A0A1U9X7J8
    7. XM_054354230.1XP_054210205.1  collagen alpha-2(XI) chain isoform X6

    8. XM_054354229.1XP_054210204.1  collagen alpha-2(XI) chain isoform X5