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Aliases for COL21A1 Gene

Aliases for COL21A1 Gene

  • Collagen Type XXI Alpha 1 2 3
  • Collagen, Type XXI, Alpha 1 2 3 5
  • Alpha 1 Chain-Like Collagen 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) is a Protein Coding gene. Among its related pathways are Degradation of the extracellular matrix and ERK Signaling. An important paralog of this gene is COL9A2.

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

Chromosome:
6
Start:
56,056,590 bp from pter
End:
56,394,122 bp from pter
Size:
337,533 bases
Orientation:
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

No data available for Regulatory Elements for COL21A1 Gene

Proteins for COL21A1 Gene

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

    Protein Symbol:
    Q96P44-COLA1_HUMAN
    Recommended name:
    Collagen alpha-1(XXI) chain
    Protein Accession:
    Q96P44
    Secondary Accessions:
    • A6NIX5
    • B2R8J9
    • Q49A51
    • Q71RF4
    • Q8WXV8
    • Q9H0V3

    Protein attributes for COL21A1 Gene

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

    Alternative splice isoforms for COL21A1 Gene

    UniProtKB/Swiss-Prot:

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

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

Q96P44

UniProtKB/Swiss-Prot:

COLA1_HUMAN :
  • Contains 7 collagen-like domains.
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
Domain:
  • Contains 7 collagen-like domains.
  • Contains 1 laminin G-like domain.
  • Contains 1 VWFA domain.
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.
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

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

COMPARTMENTS
Jensen Localization Image for COL21A1 Gene COMPARTMENTS Subcellular localization image for COL21A1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
cytoskeleton 2
lysosome 1
mitochondrion 1
plasma membrane 1
vacuole 1

Gene Ontology (GO) - Cellular Components for COL21A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
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

None

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:

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: -
SP3:
SP4: - -
SP5: - - -
SP6:
SP7:

Relevant External Links for COL21A1 Gene

GeneLoc Exon Structure for
COL21A1
ECgene alternative splicing isoforms for
COL21A1

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

Q96P44-COLA1_HUMAN
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

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
chimpanzee
(Pan troglodytes)
Mammalia COL21A1 36
  • 99 (a)
OneToOne
COL21A1 35
  • 99.55 (n)
  • 99.69 (a)
cow
(Bos Taurus)
Mammalia COL21A1 35
  • 88.77 (n)
  • 89.76 (a)
COL21A1 36
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL21A1 36
  • 92 (a)
OneToOne
COL21A1 35
  • 91.54 (n)
  • 92.27 (a)
oppossum
(Monodelphis domestica)
Mammalia COL21A1 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL21A1 36
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL21A1 35
  • 74.92 (n)
  • 77.32 (a)
COL21A1 36
  • 77 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL21A1 36
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col21a1 35
  • 68.34 (n)
  • 66.25 (a)
zebrafish
(Danio rerio)
Actinopterygii COL21A1 36
  • 60 (a)
OneToOne
LOC100333837 35
  • 61.76 (n)
  • 61.04 (a)
worm
(Caenorhabditis elegans)
Secernentea col-135 36
  • 31 (a)
OneToMany
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

ENSEMBL:
Gene Tree for COL21A1 (if available)
TreeFam:
Gene Tree for COL21A1 (if available)

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
rs2764043 - 56,170,845(-) AGGTC(C/T)TCCTC nc-transcript-variant, reference, missense, utr-variant-5-prime
rs35471617 - 56,168,296(+) ACAAC(A/G)TCTAC nc-transcript-variant, reference, missense, utr-variant-5-prime
rs35583895 - 56,141,934(+) CTTGT(A/G)TTCCT nc-transcript-variant, reference, missense
rs9382581 - 56,124,265(+) GAAGC(C/T)AGCAT nc-transcript-variant, reference, missense
rs9464337 - 56,061,003(+) CAATG(G/T)CACCT nc-transcript-variant, reference, missense

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: 58.6% 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

HapMap Linkage Disequilibrium report
COL21A1

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)
COL21A1
Human Genome Epidemiology (HuGE) Navigator
COL21A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL21A1

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 J.F. (FEBS Lett. 2001) 2 3 4 23 67
  2. Genomic organization and characterization of the human type XXI collagen (COL21A1) gene. (PMID: 11863369) Chou M.-Y. … Li H.-C. (Genomics 2002) 3 23
  3. 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) 3
  4. Genome-wide association study of atypical psychosis. (PMID: 24132900) Kanazawa T. … Yoneda H. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2013) 3
  5. Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization. (PMID: 23817571) BA … . (Nat. Genet. 2013) 3

Products for COL21A1 Gene

Sources for COL21A1 Gene

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