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Aliases for COL21A1 Gene

Aliases for COL21A1 Gene

  • Collagen Type XXI Alpha 1 Chain 2 3 5
  • Collagen, Type XXI, Alpha 1 2 3
  • Alpha 1 Chain-Like Collagen 3
  • Collagen Alpha-1(XXI) Chain 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 (fibril-associated collagens with interrupted helices) collagen family. Type XXI collagen is localized to tissues containing type I collagen and maintains the integrity of the extracellular matrix. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

GeneCards Summary for COL21A1 Gene

COL21A1 (Collagen Type XXI Alpha 1 Chain) is a Protein Coding gene. Among its related pathways are Phospholipase-C Pathway and Collagen chain trimerization. An important paralog of this gene is COL4A5.

Additional gene information for COL21A1 Gene

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

Genomics for COL21A1 Gene

Regulatory Elements for COL21A1 Gene

Enhancers for COL21A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H056231 0.5 ENCODE 19.5 +162.8 162785 0.2 JUN NFE2 MAFK NFE2L2 COL21A1 GC06M056228 GC06P056252
GH06H056090 1.1 Ensembl ENCODE 8.7 +302.6 302611 1.6 ELF3 FOXA2 ATF1 ARID4B DMAP1 RARA SLC30A9 ZNF366 ATF7 CREM COL21A1 LOC105375100 GC06M056228
GH06H056100 0.9 Ensembl ENCODE 8.7 +292.9 292902 0.9 JUN CEBPB MAX DPF2 EP300 ZNF217 GATA3 JUND POLR2A STAT3 COL21A1 LOC105375100 GC06M056228
GH06H056245 0.8 ENCODE 8.9 +147.3 147281 2.5 CTCF KLF1 ZNF777 ZNF76 ZIC2 ZFHX2 ZSCAN5C PATZ1 ZNF600 PRDM10 COL21A1 GC06P056252 GC06M056228
GH06H056668 1.1 Ensembl ENCODE dbSUPER 5 -277.1 -277137 6.4 CTCF ATF2 NR2F2 ZNF121 ZNF585B SCRT2 ATF7 HNF4A PRDM1 KIAA1586 ZNF451 DST BEND6 COL21A1 LOC101930010 GC06P056616 GC06M056744
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL21A1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for COL21A1 Gene

Genomic Locations for COL21A1 Gene
337,533 bases
Minus strand

Genomic View for COL21A1 Gene

Genes around COL21A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL21A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL21A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

Post-translational modifications for COL21A1 Gene

  • Glycosylation at posLast=6262
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL21A1 Gene

Domains & Families for COL21A1 Gene

Gene Families for COL21A1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for COL21A1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
  • 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 From GWAS Catalog for COL21A1 Gene

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

miRNA for COL21A1 Gene

miRTarBase miRNAs that target COL21A1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , 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

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 COL21A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
cytosol 4
cytoskeleton 2
plasma membrane 1
mitochondrion 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

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:0005737 cytoplasm IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
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

Gene Ontology (GO) - Biological Process for COL21A1 Gene


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:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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

NURSA nuclear receptor signaling pathways regulating expression of COL21A1 Gene:


SOURCE GeneReport for Unigene cluster for COL21A1 Gene:


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.

Evidence on tissue expression from TISSUES for COL21A1 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with COL21A1: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia COL21A1 33 34
  • 99.55 (n)
(Canis familiaris)
Mammalia COL21A1 33 34
  • 91.54 (n)
(Bos Taurus)
Mammalia COL21A1 33 34
  • 88.77 (n)
(Monodelphis domestica)
Mammalia COL21A1 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia COL21A1 34
  • 77 (a)
(Gallus gallus)
Aves COL21A1 33 34
  • 74.92 (n)
(Anolis carolinensis)
Reptilia COL21A1 34
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col21a1 33
  • 68.34 (n)
(Danio rerio)
Actinopterygii LOC100333837 33
  • 61.76 (n)
COL21A1 34
  • 60 (a)
(Caenorhabditis elegans)
Secernentea col-135 34
  • 31 (a)
Species where no ortholog for COL21A1 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)
  • 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

Variants for COL21A1 Gene

Sequence variations from dbSNP and Humsavar for COL21A1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000000722 -- 56,159,366(+) CTTGC(G/T)CCGTC intron-variant
rs1000021275 -- 56,201,542(+) CCCAG(A/C)GTCAT intron-variant
rs1000024804 -- 56,069,162(+) TGCTT(A/G)TGAAA intron-variant
rs1000031319 -- 56,373,133(+) CTGTG(A/G)GCTGG intron-variant
rs1000033085 -- 56,158,933(+) GTAAT(C/T)CTAAT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv819041 CNV gain 19587683
nsv5313 CNV insertion 18451855
nsv526703 CNV loss 19592680
nsv477746 CNV novel sequence insertion 20440878
nsv349404 CNV deletion 16902084
nsv1140630 CNV deletion 24896259
nsv1117623 CNV deletion 24896259
nsv1074397 CNV deletion 25765185
nsv1034037 CNV gain 25217958
esv993486 CNV deletion 20482838
esv3609089 CNV loss 21293372
esv3609088 CNV loss 21293372
esv3571087 CNV loss 25503493
esv3571085 CNV loss 25503493
esv3539781 CNV deletion 23714750
esv2732119 CNV deletion 23290073
esv2732118 CNV deletion 23290073
esv27231 CNV loss 19812545
esv2427713 CNV deletion 19546169
esv1388199 CNV deletion 17803354

Variation tolerance for COL21A1 Gene

Residual Variation Intolerance Score: 58.6% 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

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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:

No disorders were found for COL21A1 Gene.

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 JF (FEBS letters 2001) 2 3 4 22 60
  2. Genomic organization and characterization of the human type XXI collagen (COL21A1) gene. (PMID: 11863369) Chou MY … Li HC (Genomics 2002) 3 4 22 60
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4 60

Products for COL21A1 Gene

Sources for COL21A1 Gene

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