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

Gene ID: 1301, updated on 27-Sep-2014
Official Symbol
COL11A1provided by HGNC
Official Full Name
collagen, type XI, alpha 1provided 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]
See COL11A1 in Epigenomics, MapViewer
Location:
1p21
Exon count:
68
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 1 NC_000001.11 (102876467..103108496, 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 ribosomal protein SA pseudogene 19 Neighboring gene DnaJ (Hsp40) homolog, subfamily A, member 1 pseudogene 5 Neighboring gene olfactomedin 3 Neighboring gene superoxide dismutase 2, mitochondrial pseudogene 1 Neighboring gene uncharacterized LOC101928436 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
  • Amoebiasis, organism-specific biosystem (from KEGG)
    Amoebiasis, organism-specific biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • Amoebiasis, conserved biosystem (from KEGG)
    Amoebiasis, conserved biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
  • 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...
  • ECM-receptor interaction, organism-specific biosystem (from KEGG)
    ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • ECM-receptor interaction, conserved biosystem (from KEGG)
    ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • 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...
  • Focal adhesion, organism-specific biosystem (from KEGG)
    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...
  • Focal adhesion, conserved biosystem (from KEGG)
    Focal adhesion, conserved 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...
  • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
    PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
    PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • Platelet activation, organism-specific biosystem (from KEGG)
    Platelet activation, organism-specific biosystemPlatelets play a key and beneficial role for primary hemostasis on the disruption of the integrity of vessel wall. Platelet adhesion and activation at sites of vascular wall injury is initiated by ad...
  • 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
 
extracellular matrix disassembly TAS
Traceable Author Statement
more info
 
extracellular matrix organization NAS
Non-traceable Author Statement
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
inner ear morphogenesis 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 alpha-1(XI) chain
collagen XI, alpha-1 polypeptide

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 

    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 proteins identical to 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 proteins identical to 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 proteins identical to 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
    Conserved Domains (3) summary
    pfam01391
    Location:725784
    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:14771688
    COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000001.11 

    Range
    102876467..103108496
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000133.1 

    Range
    101474202..101706091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 

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