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

Gene ID: 1301, updated on 21-Mar-2023

Summary

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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
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Genomic context

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See COL11A1 in Genome Data Viewer
Location:
1p21.1
Exon count:
73
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (102876473..103108522, complement)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (102725394..102957399, complement)
105.20220307 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 RNPC3 divergent transcript Neighboring gene RN7SK pseudogene 285

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. COL11A1 as an novel biomarker for breast cancer with machine learning and immunohistochemistry validation. Shi W, et al. Front Immunol, 2022. PMID 36389832, Free PMC Article
  2. COL11A1 as a potential prognostic target for oral squamous cell carcinoma. Di YB, et al. Medicine (Baltimore), 2022 Oct 7. PMID 36221427, Free PMC Article
  3. COL11A1 is Downregulated by miR-339-5p and Promotes Colon Carcinoma Progression. Liu W, et al. Can J Gastroenterol Hepatol, 2022. PMID 35669376, Free PMC Article
  4. COL11A1-Driven Epithelial-Mesenchymal Transition and Stemness of Pancreatic Cancer Cells Induce Cell Migration and Invasion by Modulating the AKT/GSK-3β/Snail Pathway. Wang H, et al. Biomolecules, 2022 Mar 2. PMID 35327583, Free PMC Article
  5. Collagen XI Alpha 1 (COL11A1) Expression in the Tumor Microenvironment Drives Neuroblastoma Dissemination. Truong DQ, et al. Pediatr Dev Pathol, 2022 Mar-Apr. PMID 34460335

See all (141) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic associations in CHAT and COL11A1 with primary angle-closure glaucoma susceptibility: A systematic review and meta-analysis.
    Title: Genetic associations in CHAT and COL11A1 with primary angle-closure glaucoma susceptibility: A systematic review and meta-analysis.
  2. The Association of Variants within Types V and XI Collagen Genes with Knee Joint Laxity Measurements.
    Title: The Association of Variants within Types V and XI Collagen Genes with Knee Joint Laxity Measurements.
  3. COL11A1 as an novel biomarker for breast cancer with machine learning and immunohistochemistry validation.
    Title: COL11A1 as an novel biomarker for breast cancer with machine learning and immunohistochemistry validation.
  4. COL11A1 as a potential prognostic target for oral squamous cell carcinoma.
    Title: COL11A1 as a potential prognostic target for oral squamous cell carcinoma.
  5. An investigation on the c-MYC, AXIN1, and COL11A1 gene expression in colorectal cancer.
    Title: An investigation on the c-MYC, AXIN1, and COL11A1 gene expression in colorectal cancer.
  6. Hearing Outcomes in Stickler Syndrome: Variation Due to COL2A1 and COL11A1.
    Title: Hearing Outcomes in Stickler Syndrome: Variation Due to COL2A1 and COL11A1.
  7. COL11A1 is Downregulated by miR-339-5p and Promotes Colon Carcinoma Progression.
    Title: COL11A1 is Downregulated by miR-339-5p and Promotes Colon Carcinoma Progression.
  8. Mutually Exclusive Expression of COL11A1 by CAFs and Tumour Cells in a Large panCancer and a Salivary Gland Carcinoma Cohort.
    Title: Mutually Exclusive Expression of COL11A1 by CAFs and Tumour Cells in a Large panCancer and a Salivary Gland Carcinoma Cohort.
  9. Collagen XI Alpha 1 (COL11A1) Expression in the Tumor Microenvironment Drives Neuroblastoma Dissemination.
    Title: Collagen XI Alpha 1 (COL11A1) Expression in the Tumor Microenvironment Drives Neuroblastoma Dissemination.
  10. COL11A1-Driven Epithelial-Mesenchymal Transition and Stemness of Pancreatic Cancer Cells Induce Cell Migration and Invasion by Modulating the AKT/GSK-3beta/Snail Pathway.
    Title: COL11A1-Driven Epithelial-Mesenchymal Transition and Stemness of Pancreatic Cancer Cells Induce Cell Migration and Invasion by Modulating the AKT/GSK-3β/Snail Pathway.
Submit: New GeneRIF Correction See all GeneRIFs (93)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables extracellular matrix structural constituent NAS
Non-traceable Author Statement
more info
 PubMed 
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 IEA
Inferred from Electronic Annotation
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
 PubMed 
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
 PubMed 
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 
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
  
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 

General protein information

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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)

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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_001190709.2 → NP_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
    ENSP00000302551.6, ENST00000353414.8
    Conserved Domains (3) summary
    pfam01391
    Location:802 → 861
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:38 → 229
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:1539 → 1765
    COLFI; Fibrillar collagen C-terminal domain

  2. NM_001854.4 → NP_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
    P12107, Q9UIT6
    UniProtKB/TrEMBL
    Q59HB5
    Related
    ENSP00000359114.3, ENST00000370096.9
    Conserved Domains (3) summary
    pfam01391
    Location:841 → 900
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:38 → 229
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:1578 → 1804
    COLFI; Fibrillar collagen C-terminal domain

  3. NM_080629.3 → NP_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
    UniProtKB/Swiss-Prot
    P12107
    UniProtKB/TrEMBL
    Q59HB5
    Related
    ENSP00000351163.2, ENST00000358392.6
    Conserved Domains (3) summary
    pfam01391
    Location:853 → 912
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:38 → 229
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:1590 → 1816
    COLFI; Fibrillar collagen C-terminal domain

  4. NM_080630.4 → NP_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
    UniProtKB/Swiss-Prot
    P12107
    Related
    ENSP00000426533.1, ENST00000512756.5
    Conserved Domains (3) summary
    pfam01391
    Location:725 → 784
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:38 → 229
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:1462 → 1688
    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_2023_03

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_017000335.2 → XP_016855824.1  collagen alpha-1(XI) chain isoform X2

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

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

  4. XM_017000336.2 → XP_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_054334472.1 → XP_054190447.1  collagen alpha-1(XI) chain isoform X2

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

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

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

RNA

  1. XR_008485930.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P12107.4 GenPept UniProtKB/Swiss-Prot:P12107

Gene LinkOut

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