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

Gene ID: 1302, updated on 3-Mar-2019

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
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

Genomic context

See COL11A2 in Genome Data Viewer
Location:
6p21.32
Exon count:
70
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 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 FunctionsWhat's a GeneRIF?

Phenotypes

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

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

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...
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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 NAS
Non-traceable Author Statement
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
 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cartilage development IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen fibril organization IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
roof of mouth development IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound IBA
Inferred from Biological aspect of Ancestor
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 trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type XI trimer NAS
Non-traceable Author Statement
more info
PubMed 
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 

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)

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
    ENSP00000378620.1, ENST00000395194.1
    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
    ENSP00000355123.1, ENST00000361917.5
    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
    ENSP00000339915.2, ENST00000341947.6
    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
  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
    ENSP00000363840.4, 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

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_000006.12 Reference GRCh38.p12 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 (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
  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_017010251.2XP_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.p12 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p12 ALT_REF_LOCI_2

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

Reference GRCh38.p12 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p12 ALT_REF_LOCI_3

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

Reference GRCh38.p12 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p12 ALT_REF_LOCI_4

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

Reference GRCh38.p12 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p12 ALT_REF_LOCI_5

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

Reference GRCh38.p12 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p12 ALT_REF_LOCI_6

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

Reference GRCh38.p12 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p12 ALT_REF_LOCI_7

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