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Aliases for COL21A1 Gene

Aliases for COL21A1 Gene

  • Collagen, Type XXI, Alpha 1 2 3
  • Alpha 1 Chain-Like Collagen 3
  • Alpha 1 Type XXI Collagen 3
  • DJ682J15.1 3
  • DJ708F5.1 3
  • COLA1L 3
  • COL1AL 4
  • FP633 3

External Ids for COL21A1 Gene

Previous GeneCards Identifiers for COL21A1 Gene

  • GC06M055923
  • GC06M055968
  • GC06M055756

Summaries for COL21A1 Gene

Entrez Gene Summary for COL21A1 Gene

  • This gene encodes the alpha chain of type XXI collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Type XXI collagen is localized to tissues containing type I collagen so, like other members of this collagen family, it may serve to maintain the integrity of the extracellular matrix. An alternatively spliced transcript variant has been described, but its full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for COL21A1 Gene

COL21A1 (Collagen, Type XXI, Alpha 1) is a Protein Coding gene. Among its related pathways are Phospholipase-C Pathway and ERK Signaling. An important paralog of this gene is COL25A1.

No data available for UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL21A1 Gene

Genomics for COL21A1 Gene

Genomic Location for COL21A1 Gene

56,056,590 bp from pter
56,394,122 bp from pter
337,533 bases
Minus strand

Genomic View for COL21A1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL21A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL21A1 Gene

No data available for Regulatory Elements for COL21A1 Gene

Proteins for COL21A1 Gene

  • Protein details for COL21A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-1(XXI) chain
    Protein Accession:
    Secondary Accessions:
    • A6NIX5
    • B2R8J9
    • Q49A51
    • Q71RF4
    • Q8WXV8
    • Q9H0V3

    Protein attributes for COL21A1 Gene

    957 amino acids
    Molecular mass:
    99369 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH45597.1; Type=Frameshift; Positions=478; Evidence={ECO:0000305};

    Alternative splice isoforms for COL21A1 Gene


neXtProt entry for COL21A1 Gene

Proteomics data for COL21A1 Gene at MOPED

Post-translational modifications for COL21A1 Gene

  • Glycosylation at Asn 62
  • Modification sites at PhosphoSitePlus

Other Protein References for COL21A1 Gene

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for COL21A1

No data available for DME Specific Peptides for COL21A1 Gene

Domains & Families for COL21A1 Gene

Gene Families for COL21A1 Gene

Suggested Antigen Peptide Sequences for COL21A1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 7 collagen-like domains.
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
  • Contains 7 collagen-like domains.
  • Contains 1 laminin G-like domain.
  • Contains 1 VWFA domain.
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
genes like me logo Genes that share domains with COL21A1: view

Function for COL21A1 Gene

Molecular function for COL21A1 Gene

UniProtKB/Swiss-Prot Induction:
Stimulated by PDGF/platelet-derived growth factor.

Phenotypes for COL21A1 Gene

GenomeRNAi human phenotypes for COL21A1:
genes like me logo Genes that share phenotypes with COL21A1: view

Animal Model Products

CRISPR Products

miRNA for COL21A1 Gene

miRTarBase miRNAs that target COL21A1

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL21A1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for COL21A1 Gene

Localization for COL21A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL21A1 Gene

Secreted, extracellular space, extracellular matrix. Cytoplasm. Note=Found in the extracellular matrix component of blood vessel walls and in the cytoplasm of cultured human aortic smooth muscle.

Subcellular locations from

Jensen Localization Image for COL21A1 Gene COMPARTMENTS Subcellular localization image for COL21A1 gene
Compartment Confidence
endoplasmic reticulum 4
extracellular 4
cytoskeleton 2

Gene Ontology (GO) - Cellular Components for COL21A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005581 collagen trimer IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0031012 colocalizes_with extracellular matrix IDA 20551380
genes like me logo Genes that share ontologies with COL21A1: view

Pathways & Interactions for COL21A1 Gene

genes like me logo Genes that share pathways with COL21A1: view

Interacting Proteins for COL21A1 Gene

Gene Ontology (GO) - Biological Process for COL21A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with COL21A1: view

No data available for SIGNOR curated interactions for COL21A1 Gene

Drugs & Compounds for COL21A1 Gene

No Compound Related Data Available

Transcripts for COL21A1 Gene

Unigene Clusters for COL21A1 Gene

Collagen, type XXI, alpha 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL21A1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL21A1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b
SP1: -
SP2: -
SP4: - -
SP5: - - -

Relevant External Links for COL21A1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL21A1 Gene

mRNA expression in normal human tissues for COL21A1 Gene

mRNA differential expression in normal tissues according to GTEx for COL21A1 Gene

This gene is overexpressed in Artery - Aorta (x7.7) and Artery - Coronary (x4.7).

Protein differential expression in normal tissues from HIPED for COL21A1 Gene

This gene is overexpressed in Spinal cord (14.9), Placenta (13.0), and Pancreatic juice (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL21A1 Gene

SOURCE GeneReport for Unigene cluster for COL21A1 Gene Hs.47629

mRNA Expression by UniProt/SwissProt for COL21A1 Gene

Tissue specificity: Highly expressed in lymph node, jejunum, pancreas, stomach, trachea, testis, uterus and placenta; moderately expressed in brain, colon, lung, prostate, spinal cord, salivary gland and vascular smooth-muscle cells and very weakly expressed in heart, liver, kidney, bone marrow, spleen, thymus, skeletal muscle, adrenal gland and peripheral leukocytes. Expression in heart was higher in the right ventricle and atrium than in the left ventricle and atrium.
genes like me logo Genes that share expression patterns with COL21A1: view

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

In Situ Assay Products

No data available for Protein tissue co-expression partners for COL21A1 Gene

Orthologs for COL21A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL21A1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia COL21A1 35
  • 88.77 (n)
  • 89.76 (a)
COL21A1 36
  • 90 (a)
(Canis familiaris)
Mammalia COL21A1 35
  • 91.54 (n)
  • 92.27 (a)
COL21A1 36
  • 92 (a)
(Pan troglodytes)
Mammalia COL21A1 35
  • 99.55 (n)
  • 99.69 (a)
COL21A1 36
  • 99 (a)
(Monodelphis domestica)
Mammalia COL21A1 36
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia COL21A1 36
  • 77 (a)
(Gallus gallus)
Aves COL21A1 35
  • 74.92 (n)
  • 77.32 (a)
COL21A1 36
  • 77 (a)
(Anolis carolinensis)
Reptilia COL21A1 36
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col21a1 35
  • 68.34 (n)
  • 66.25 (a)
(Danio rerio)
Actinopterygii LOC100333837 35
  • 61.76 (n)
  • 61.04 (a)
COL21A1 36
  • 60 (a)
(Caenorhabditis elegans)
Secernentea col-135 36
  • 31 (a)
Species with no ortholog for COL21A1:
  • 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)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for COL21A1 Gene

Gene Tree for COL21A1 (if available)
Gene Tree for COL21A1 (if available)

Paralogs for COL21A1 Gene

Paralogs for COL21A1 Gene

genes like me logo Genes that share paralogs with COL21A1: view

Variants for COL21A1 Gene

Sequence variations from dbSNP and Humsavar for COL21A1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs1480 -- 56,096,191(+) TGCCT(A/G)CAGCC intron-variant
rs140848 -- 56,223,920(-) GGAAA(-/TAAGA)TAAGA intron-variant
rs140863 -- 56,215,086(+) AAAAC(-/TG)AGAAA intron-variant
rs724677 -- 56,255,923(-) TGTTG(C/T)GGTTC intron-variant
rs724678 -- 56,255,496(-) GGCCT(A/G)ATTTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL21A1 Gene

Variant ID Type Subtype PubMed ID
nsv885911 CNV Loss 21882294
nsv526703 CNV Loss 19592680
nsv819041 CNV Gain 19587683
esv27231 CNV Loss 19812545
esv2427713 CNV Deletion 19546169
esv2732118 CNV Deletion 23290073
esv2732119 CNV Deletion 23290073
esv993486 CNV Deletion 20482838
nsv349404 CNV Loss 16902084
esv1388199 CNV Deletion 17803354
nsv5313 CNV Insertion 18451855

Variation tolerance for COL21A1 Gene

Residual Variation Intolerance Score: 58.59% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.82; 79.19% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL21A1 Gene

HapMap Linkage Disequilibrium report

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL21A1 Gene

Disorders for COL21A1 Gene

Relevant External Links for COL21A1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with COL21A1: view

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for COL21A1 Gene

Publications for COL21A1 Gene

  1. A new FACIT of the collagen family: COL21A1. (PMID: 11566190) Fitzgerald J. … Bateman J.F. (FEBS Lett. 2001) 2 23 67
  2. Assembly of homotrimeric type XXI minicollagen by coexpression of prolyl 4-hydroxylase in stably transfected Drosophila melanogaster S2 cells. (PMID: 16115607) Li H.C. … Chou M.Y. (Biochem. Biophys. Res. Commun. 2005) 23 67
  3. Genomic organization and characterization of the human type XXI collagen (COL21A1) gene. (PMID: 11863369) Chou M.-Y. … Li H.-C. (Genomics 2002) 23 67
  4. Extracellular matrix proteins expression profiling in chemoresistant variants of the A2780 ovarian cancer cell line. (PMID: 24804215) Januchowski R. … Zabel M. (Biomed Res Int 2014) 67
  5. Genome-wide association study of atypical psychosis. (PMID: 24132900) Kanazawa T. … Yoneda H. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2013) 67

Products for COL21A1 Gene

Sources for COL21A1 Gene

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