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Aliases for COL11A1 Gene

Aliases for COL11A1 Gene

  • Collagen Type XI Alpha 1 Chain 2 3 5
  • Collagen XI, Alpha-1 Polypeptide 2 3
  • Collagen, Type XI, Alpha 1 2 3
  • COLL6 3 4
  • Collagen Alpha-1(XI) Chain 3
  • CO11A1 3
  • STL2 3

External Ids for COL11A1 Gene

Previous HGNC Symbols for COL11A1 Gene

  • COLL6

Previous GeneCards Identifiers for COL11A1 Gene

  • GC01M104172
  • GC01M102524
  • GC01M102633
  • GC01M102805
  • GC01M103055
  • GC01M103342
  • GC01M101474

Summaries for COL11A1 Gene

Entrez Gene Summary for COL11A1 Gene

  • 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]

GeneCards Summary for COL11A1 Gene

COL11A1 (Collagen Type XI Alpha 1 Chain) is a Protein Coding gene. Diseases associated with COL11A1 include Stickler Syndrome, Type Ii and Marshall Syndrome. Among its related pathways are ERK Signaling and Focal Adhesion. Gene Ontology (GO) annotations related to this gene include extracellular matrix structural constituent and extracellular matrix binding. An important paralog of this gene is COL5A1.

UniProtKB/Swiss-Prot for COL11A1 Gene

  • May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils.

Gene Wiki entry for COL11A1 Gene

Additional gene information for COL11A1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL11A1 Gene

Genomics for COL11A1 Gene

GeneHancer (GH) Regulatory Elements for COL11A1 Gene

Promoters and enhancers for COL11A1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J103106 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE 660.4 +0.2 153 4.9 CTCF ZNF654 SIN3A REST RAD21 POLR2A PRDM1 MAFK ZBTB17 COL11A1 SOD2P1 GC01M102950 GC01M102951
GH01J103515 Enhancer 0.4 ENCODE 10.7 -407.7 -407679 1.5 JUND JUNB AMY2B COL11A1 GC01M103511 RN7SKP285 LOC101928436 GC01M103512
GH01J102879 Enhancer 0.8 Ensembl ENCODE 4.5 +228.9 228896 1.8 SP1 JUND POLR2A JUN CREB1 FOSL2 FOS MAFK COL11A1 GC01M102855 ENSG00000230864
GH01J103180 Enhancer 0.4 ENCODE 7.7 -71.9 -71931 0.8 SP1 FOSL2 MAFK COL11A1 GC01P103125 GC01M103254 GC01M102950 GC01M102951
GH01J102897 Enhancer 0.6 ENCODE 4.4 +211.1 211130 1 JUN CEBPB EP300 FOXA1 SP1 JUND GATA3 POLR2A STAT3 FOS GC01M102855 COL11A1 GC01P102938
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL11A1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COL11A1 gene promoter:
  • PPAR-gamma1
  • Nkx2-5
  • HSF2
  • PPAR-gamma2
  • POU2F1a
  • POU2F1
  • Spz1
  • GCNF
  • GCNF-1
  • GCNF-2

Genomic Locations for COL11A1 Gene

Genomic Locations for COL11A1 Gene
232,406 bases
Minus strand
232,030 bases
Minus strand

Genomic View for COL11A1 Gene

Genes around COL11A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL11A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL11A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL11A1 Gene

Proteins for COL11A1 Gene

  • Protein details for COL11A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-1(XI) chain
    Protein Accession:
    Secondary Accessions:
    • B1ASK7
    • D3DT73
    • E9PCU0
    • Q14034
    • Q149N0
    • Q9UIT4
    • Q9UIT5
    • Q9UIT6

    Protein attributes for COL11A1 Gene

    1806 amino acids
    Molecular mass:
    181065 Da
    Quaternary structure:
    • Trimers composed of three different chains: alpha 1(XI), alpha 2(XI), and alpha 3(XI). Alpha 3(XI) is a post-translational modification of alpha 1(II). Alpha 1(V) can also be found instead of alpha 3(XI)=1(II).

    Alternative splice isoforms for COL11A1 Gene


neXtProt entry for COL11A1 Gene

Post-translational modifications for COL11A1 Gene

No data available for DME Specific Peptides for COL11A1 Gene

Domains & Families for COL11A1 Gene

Gene Families for COL11A1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry



  • The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity).
  • Belongs to the fibrillar collagen family.
  • The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity).
  • Belongs to the fibrillar collagen family.
genes like me logo Genes that share domains with COL11A1: view

Function for COL11A1 Gene

Molecular function for COL11A1 Gene

UniProtKB/Swiss-Prot Function:
May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils.
GENATLAS Biochemistry:
collagen type XI,alpha 1,fibril forming,expressed in hyaline cartilage,in the ocular vitreous, in the nucleus pulposus of the intervertebral disc and in the inner ear,playing an essential role in skeletal morphogenesis and in maitaining the interfibrillar spacing and fibril diameter of type II collagen

Phenotypes From GWAS Catalog for COL11A1 Gene

Gene Ontology (GO) - Molecular Function for COL11A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005201 extracellular matrix structural constituent NAS 10486316
GO:0030674 protein binding, bridging NAS 10486316
GO:0046872 metal ion binding IEA --
GO:0050840 extracellular matrix binding NAS 3182841
genes like me logo Genes that share ontologies with COL11A1: view
genes like me logo Genes that share phenotypes with COL11A1: view

Human Phenotype Ontology for COL11A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for COL11A1 Gene

miRTarBase miRNAs that target COL11A1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for COL11A1 Gene

Localization for COL11A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL11A1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL11A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
cytoskeleton 3
mitochondrion 2
cytosol 2
plasma membrane 1
nucleus 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COL11A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer IEA --
GO:0005592 collagen type XI trimer NAS 10486316
GO:0005615 extracellular space IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL11A1: view

Pathways & Interactions for COL11A1 Gene

genes like me logo Genes that share pathways with COL11A1: view

Gene Ontology (GO) - Biological Process for COL11A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001502 cartilage condensation IEA --
GO:0001503 ossification IEA --
GO:0002063 chondrocyte development IEA --
GO:0003007 heart morphogenesis IEA --
GO:0006029 proteoglycan metabolic process IEA --
genes like me logo Genes that share ontologies with COL11A1: view

No data available for SIGNOR curated interactions for COL11A1 Gene

Drugs & Compounds for COL11A1 Gene

(1) Additional Compounds for COL11A1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with COL11A1: view

Transcripts for COL11A1 Gene

mRNA/cDNA for COL11A1 Gene

Unigene Clusters for COL11A1 Gene

Collagen, type XI, alpha 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL11A1 Gene

No ASD Table

Relevant External Links for COL11A1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL11A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL11A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for COL11A1 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (37.9) and Bone marrow stromal cell (20.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for COL11A1 Gene

NURSA nuclear receptor signaling pathways regulating expression of COL11A1 Gene:


SOURCE GeneReport for Unigene cluster for COL11A1 Gene:


mRNA Expression by UniProt/SwissProt for COL11A1 Gene:

Tissue specificity: Cartilage, placenta and some tumor or virally transformed cell lines. Isoforms using exon IIA or IIB are found in the cartilage while isoforms using only exon IIB are found in the tendon.

Evidence on tissue expression from TISSUES for COL11A1 Gene

  • Blood(4.1)
  • Bone(3.4)
  • Skin(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL11A1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • sinus
  • skull
  • tongue
  • tooth
  • chest wall
  • clavicle
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • abdominal wall
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • pelvis
  • placenta
  • uterus
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with COL11A1: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for COL11A1 Gene

Orthologs for COL11A1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL11A1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia COL11A1 34 33
  • 99.39 (n)
(Monodelphis domestica)
Mammalia COL11A1 34
  • 93 (a)
(Canis familiaris)
Mammalia COL11A1 34 33
  • 92.98 (n)
(Bos Taurus)
Mammalia COL11A1 34 33
  • 92.86 (n)
(Mus musculus)
Mammalia Col11a1 16 34 33
  • 87.29 (n)
(Rattus norvegicus)
Mammalia Col11a1 33
  • 86.92 (n)
(Ornithorhynchus anatinus)
Mammalia COL11A1 34
  • 85 (a)
(Gallus gallus)
Aves COL11A1 34 33
  • 81.8 (n)
(Anolis carolinensis)
Reptilia COL11A1 34
  • 88 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col5a3 33
  • 74.97 (n)
Str.13851 33
(Danio rerio)
Actinopterygii col11a1b 34
  • 75 (a)
col11a1a 34 33
  • 72.43 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 63 (a)
Species where no ortholog for COL11A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for COL11A1 Gene

Gene Tree for COL11A1 (if available)
Gene Tree for COL11A1 (if available)
Evolutionary constrained regions (ECRs) for COL11A1: view image

Paralogs for COL11A1 Gene

(13) SIMAP similar genes for COL11A1 Gene using alignment to 10 proteins:

  • D3DT71_HUMAN
  • D3DT72_HUMAN
  • H7C381_HUMAN
genes like me logo Genes that share paralogs with COL11A1: view

Variants for COL11A1 Gene

Sequence variations from dbSNP and Humsavar for COL11A1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1012281 benign, not specified, Marshall syndrome, Stickler Syndrome, Dominant, Fibrochondrogenesis 102,961,851(-) T/C intron_variant
rs1031820 benign, Fibrochondrogenesis, Marshall syndrome, Stickler Syndrome, Dominant 102,877,914(-) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1057518666 likely-pathogenic, pathogenic, Stickler syndrome, type 2, not provided 102,978,703(-) C/T intron_variant
rs11164663 benign, not specified, Fibrochondrogenesis, Stickler Syndrome, Dominant, Marshall syndrome 103,082,941(-) A/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs111841420 benign, likely-benign, not specified, Marshall syndrome, Fibrochondrogenesis, Stickler Syndrome, Dominant 103,004,635(-) T/C coding_sequence_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for COL11A1 Gene

Variant ID Type Subtype PubMed ID
dgv25n27 CNV loss 19166990
dgv386n54 CNV loss 21841781
dgv387n54 CNV loss 21841781
dgv388n54 CNV loss 21841781
dgv389n54 CNV loss 21841781
dgv66e212 CNV loss 25503493
esv2323749 CNV deletion 18987734
esv24564 CNV gain 19812545
esv2670279 CNV deletion 23128226
esv3336359 CNV duplication 20981092
esv3578030 CNV loss 25503493
esv3578031 CNV loss 25503493
esv3578032 CNV loss 25503493
esv3578033 CNV loss 25503493
esv3578034 CNV loss 25503493
esv3578037 CNV loss 25503493
esv3587002 CNV loss 21293372
nsv462739 CNV loss 19166990
nsv462750 CNV loss 19166990
nsv462772 CNV loss 19166990
nsv476094 CNV novel sequence insertion 20440878
nsv506951 OTHER sequence alteration 20534489
nsv522922 CNV loss 19592680
nsv546931 CNV loss 21841781
nsv546932 CNV loss 21841781
nsv546934 CNV loss 21841781
nsv830882 CNV loss 17160897
nsv830893 CNV loss 17160897

Variation tolerance for COL11A1 Gene

Residual Variation Intolerance Score: 5.09% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 18.07; 98.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COL11A1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL11A1 Gene

Disorders for COL11A1 Gene

MalaCards: The human disease database

(27) MalaCards diseases for COL11A1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • Stickler syndrome 2 (STL2) [MIM:604841]: An autosomal dominant form of Stickler syndrome, an inherited disorder that associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders and sensorineural deafness. Ocular disorders may include juvenile cataract, myopia, strabismus, vitreoretinal or chorioretinal degeneration, retinal detachment, and chronic uveitis. Pierre Robin sequence includes an opening in the roof of the mouth (a cleft palate), a large tongue (macroglossia), and a small lower jaw (micrognathia). Bones are affected by slight platyspondylisis and large, often defective epiphyses. Juvenile joint laxity is followed by early signs of arthrosis. The degree of hearing loss varies among affected individuals and may become more severe over time. Syndrome expressivity is variable. {ECO:0000269 PubMed:10486316, ECO:0000269 PubMed:20513134, ECO:0000269 PubMed:8872475}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Marshall syndrome (MRSHS) [MIM:154780]: An autosomal dominant disorder characterized by ocular abnormalities, deafness, craniofacial anomalies, and anhidrotic ectodermal dysplasia. Clinical features include short stature; flat or retruded midface with short, depressed nose, flat nasal bridge and anteverted nares; cleft palate with or without the Pierre Robin sequence; appearance of large eyes with ocular hypertelorism; cataracts, either congenital or juvenile; esotropia; high myopia; sensorineural hearing loss; spondyloepiphyseal abnormalities; calcification of the falx cerebri; ectodermal abnormalities, including defects in sweating and dental structures. {ECO:0000269 PubMed:10486316}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Fibrochondrogenesis 1 (FBCG1) [MIM:228520]: A severe short-limbed skeletal dysplasia characterized by broad long-bone metaphyses, pear-shaped vertebral bodies, and characteristic morphology of the growth plate, in which the chondrocytes have a fibroblastic appearance and there are regions of fibrous cartilage extracellular matrix. Clinical features include a flat midface with a small nose and anteverted nares, significant shortening of all limb segments but relatively normal hands and feet, and a small bell-shaped thorax with a protuberant abdomen. {ECO:0000269 PubMed:21035103}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for COL11A1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with COL11A1: view

No data available for Genatlas for COL11A1 Gene

Publications for COL11A1 Gene

  1. Stickler syndrome and the vitreous phenotype: mutations in COL2A1 and COL11A1. (PMID: 20513134) Richards AJ … Snead MP (Human mutation 2010) 3 4 22 58
  2. Associations of 25 structural, degradative, and inflammatory candidate genes with lumbar disc desiccation, bulging, and height narrowing. (PMID: 19180518) Videman T … Battié MC (Arthritis and rheumatism 2009) 3 22 44 58
  3. Introduction of cytogenetic tests in colorectal cancer screening. (PMID: 19337631) Suceveanu AI … Adam T (Journal of gastrointestinal and liver diseases : JGLD 2009) 3 22 44 58
  4. A functional polymorphism in COL11A1, which encodes the alpha 1 chain of type XI collagen, is associated with susceptibility to lumbar disc herniation. (PMID: 17999364) Mio F … Ikegawa S (American journal of human genetics 2007) 3 22 44 58
  5. The role of sequence variations within the genes encoding collagen II, IX and XI in non-syndromic, early-onset osteoarthritis. (PMID: 15922184) Jakkula E … Ala-Kokko L (Osteoarthritis and cartilage 2005) 3 22 44 58

Products for COL11A1 Gene

Sources for COL11A1 Gene

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