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] See more...

Aliases for COL21A1 Gene

Aliases for COL21A1 Gene

  • Collagen Type XXI Alpha 1 Chain 2 3 5
  • Collagen, Type XXI, Alpha 1 2 3
  • Collagen Alpha-1(XXI) Chain 3 4
  • Alpha 1 Chain-Like Collagen 3
  • COL21A1 5
  • COLA1L 3
  • COL1AL 4
  • FP633 3

External Ids for COL21A1 Gene

Previous GeneCards Identifiers for COL21A1 Gene

  • GC06M055923
  • GC06M055968
  • GC06M056029
  • 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 Integrin Pathway and Collagen chain trimerization. An important paralog of this gene is COL18A1.

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COL21A1 Gene

Genomics for COL21A1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for COL21A1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J056245 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 608.9 +147.3 147326 2.8 CTCF TEAD4 PRDM10 PRDM1 ZIC2 PATZ1 ZNF501 ZNF600 KLF9 ZBTB20 COL21A1 HSALNG0050778 L13714-388 BMP5
GH06J056394 Promoter 0.6 EPDnew 600.7 0.0 -20 0.1 MGA ZFHX2 EGR2 COL21A1 RCC2P7 DST
GH06J056231 Enhancer 0.6 Ensembl ENCODE 19.5 +162.5 162508 3.2 NFE2 MAFK JUN NFE2L2 CEBPB COL21A1 KIAA1586 HSALNG0050778 L13714-388 BMP5
GH06J056220 Enhancer 0.7 Ensembl ENCODE 14.7 +173.7 173727 1.6 SP1 CTBP1 PKNOX1 ZNF217 FOSL2 DPF2 FOXA1 ZNF843 FEZF1 FOS RF00017-5603 COL21A1 piR-55036-083 BMP5
GH06J056090 Promoter/Enhancer 1.1 Ensembl ENCODE 8.7 +302.6 302616 1.6 CEBPG GATAD2A ATF7 PRDM10 TFE3 FOXA1 RXRB CEBPA KMT2B SOX13 lnc-BMP5-2 COL21A1 piR-38351-399 BMP5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL21A1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COL21A1

Genomic Locations for COL21A1 Gene

Genomic Locations for COL21A1 Gene
chr6:56,056,590-56,394,128
(GRCh38/hg38)
Size:
337,539 bases
Orientation:
Minus strand
chr6:55,921,388-56,258,892
(GRCh37/hg19)
Size:
337,505 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

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; Evidence={ECO:0000305};

    Alternative splice isoforms for COL21A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL21A1 Gene

Post-translational modifications for COL21A1 Gene

  • Glycosylation at Asn62
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for COL21A1 Gene

Domains & Families for COL21A1 Gene

Gene Families for COL21A1 Gene

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

Protein Domains for COL21A1 Gene

InterPro:
Blocks:
  • Collagen triple helix repeat
  • Collagen helix repeat
  • Von Willebrand factor type A domain signature
  • Thrombospondin, N-terminal
ProtoNet:

Suggested Antigen Peptide Sequences for COL21A1 Gene

GenScript: Design optimal peptide antigens:
  • Collagen type XXI alpha 1 (A6PVD8_HUMAN)
  • COL21A1 protein (B7ZLK3_HUMAN)
  • Collagen alpha-1(XXI) chain (COLA1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96P44

UniProtKB/Swiss-Prot:

COLA1_HUMAN :
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
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

Gene Ontology (GO) - Molecular Function for COL21A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030020 extracellular matrix structural constituent conferring tensile strength RCA 20551380
genes like me logo Genes that share ontologies with COL21A1: view
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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL21A1

No data available for Enzyme Numbers (IUBMB) , 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
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 4
cytosol 4
cytoskeleton 2
plasma membrane 1
mitochondrion 1
nucleus 1
lysosome 0

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:0005581 collagen trimer IEA --
GO:0005615 extracellular space IBA 21873635
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

PathCards logo

SuperPathways for COL21A1 Gene

SuperPathway Contained pathways
1 Collagen chain trimerization
.48
.46
2 Integrin Pathway
.67
.67
.56
.56
.50
.38
3 ERK Signaling
.61
.61
.58
.51
.49
4 Phospholipase-C Pathway
.56
.56
5 Degradation of the extracellular matrix
genes like me logo Genes that share pathways with COL21A1: view

Pathways by source for COL21A1 Gene

15 Qiagen pathways for COL21A1 Gene
  • Blood Coagulation Cascade
  • ERK Signaling
  • FAK1 Signaling
  • GnRH Signaling
  • ILK Signaling

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

mRNA/cDNA for COL21A1 Gene

5 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL21A1

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

Expression for COL21A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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 and MOPED for COL21A1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COL21A1

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.

Evidence on tissue expression from TISSUES for COL21A1 Gene

  • Nervous system(4.4)
  • Muscle(2.4)
  • Heart(2.2)
genes like me logo Genes that share expression patterns with COL21A1: view

Primer Products

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
Chimpanzee
(Pan troglodytes)
Mammalia COL21A1 30 31
  • 99.55 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia COL21A1 30 31
  • 91.54 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia COL21A1 30 31
  • 88.77 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia COL21A1 31
  • 84 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia COL21A1 31
  • 77 (a)
OneToOne
Chicken
(Gallus gallus)
Aves COL21A1 30 31
  • 74.92 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia COL21A1 31
  • 75 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia col21a1 30
  • 68.34 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC100333837 30
  • 61.76 (n)
COL21A1 31
  • 60 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea col-135 31
  • 31 (a)
OneToMany
Species where no ortholog for COL21A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for COL21A1: view image

Paralogs for COL21A1 Gene

(31) SIMAP similar genes for COL21A1 Gene using alignment to 6 proteins:

  • COLA1_HUMAN
  • A6PVD9_HUMAN
  • B7ZLK3_HUMAN
  • F5GZK2_HUMAN
  • H0Y4C9_HUMAN
  • H0YDH6_HUMAN
genes like me logo Genes that share paralogs with COL21A1: view

Variants for COL21A1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COL21A1 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
771399 Benign: not provided 56,059,169(-) G/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
771715 Benign: not provided 56,124,072(-) G/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs12209452 - p.Leu821Pro
rs1555131 - p.Pro827Ala
rs2764043 - p.Leu277Pro

Additional dbSNP identifiers (rs#s) for COL21A1 Gene

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

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

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)

Additional Variant Information for COL21A1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL21A1

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

Disorders for COL21A1 Gene

Additional Disease Information for COL21A1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform

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 23
  2. Genomic organization and characterization of the human type XXI collagen (COL21A1) gene. (PMID: 11863369) Chou MY … Li HC (Genomics 2002) 3 4 23
  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 41
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  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

Products for COL21A1 Gene

  • Biorbyt antibodies for COL21A1

Sources for COL21A1 Gene