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Aliases for COL28A1 Gene

Aliases for COL28A1 Gene

  • Collagen Type XXVIII Alpha 1 2 3
  • Collagen, Type XXVIII, Alpha 1 2 3 5
  • COL28 3 4

External Ids for COL28A1 Gene

Previous GeneCards Identifiers for COL28A1 Gene

  • GC07M007364
  • GC07M007246

Summaries for COL28A1 Gene

Entrez Gene Summary for COL28A1 Gene

  • COL28A1 belongs to a class of collagens containing von Willebrand factor (VWF; MIM 613160) type A (VWFA) domains (Veit et al., 2006 [PubMed 16330543]).[supplied by OMIM, Nov 2010]

GeneCards Summary for COL28A1 Gene

COL28A1 (Collagen Type XXVIII Alpha 1) is a Protein Coding gene. Among its related pathways are Degradation of the extracellular matrix and Collagen biosynthesis and modifying enzymes. GO annotations related to this gene include serine-type endopeptidase inhibitor activity. An important paralog of this gene is COL6A1.

UniProtKB/Swiss-Prot for COL28A1 Gene

  • May act as a cell-binding protein.

Gene Wiki entry for COL28A1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL28A1 Gene

Genomics for COL28A1 Gene

Regulatory Elements for COL28A1 Gene

Enhancers for COL28A1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around COL28A1 on UCSC Golden Path with GeneCards custom track

Genomic Location for COL28A1 Gene

Chromosome:
7
Start:
7,338,549 bp from pter
End:
7,537,277 bp from pter
Size:
198,729 bases
Orientation:
Minus strand

Genomic View for COL28A1 Gene

Genes around COL28A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL28A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL28A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL28A1 Gene

Proteins for COL28A1 Gene

  • Protein details for COL28A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q2UY09-COSA1_HUMAN
    Recommended name:
    Collagen alpha-1(XXVIII) chain
    Protein Accession:
    Q2UY09
    Secondary Accessions:
    • A4D101
    • A4D106
    • A4D107
    • A8MVR2
    • B9EGX9
    • Q2UY07
    • Q2UY08

    Protein attributes for COL28A1 Gene

    Size:
    1125 amino acids
    Molecular mass:
    116657 Da
    Quaternary structure:
    • Trimer or homomer. Secreted as a 135 kDa monomer under reducing conditions and as a homotrimer under non-reducing conditions (By similarity).
    SequenceCaution:
    • Sequence=EAL24305.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=EAL24306.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=EAL24307.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for COL28A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL28A1 Gene

Proteomics data for COL28A1 Gene at MOPED

Post-translational modifications for COL28A1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for COL28A1 Gene

No data available for DME Specific Peptides for COL28A1 Gene

Domains & Families for COL28A1 Gene

Gene Families for COL28A1 Gene

Protein Domains for COL28A1 Gene

Suggested Antigen Peptide Sequences for COL28A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q2UY09

UniProtKB/Swiss-Prot:

COSA1_HUMAN :
  • Contains 1 BPTI/Kunitz inhibitor domain.
  • Belongs to the VWA-containing collagen family.
Domain:
  • Contains 1 BPTI/Kunitz inhibitor domain.
  • Contains 6 collagen-like domains.
  • Contains 2 VWFA domains.
Family:
  • Belongs to the VWA-containing collagen family.
genes like me logo Genes that share domains with COL28A1: view

Function for COL28A1 Gene

Molecular function for COL28A1 Gene

UniProtKB/Swiss-Prot Function:
May act as a cell-binding protein.

Phenotypes for COL28A1 Gene

GenomeRNAi human phenotypes for COL28A1:
genes like me logo Genes that share phenotypes with COL28A1: view

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for COL28A1 Gene

Localization for COL28A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL28A1 Gene

Secreted, extracellular space, extracellular matrix, basement membrane.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL28A1 Gene COMPARTMENTS Subcellular localization image for COL28A1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 4
mitochondrion 3
cytosol 2
peroxisome 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for COL28A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL28A1: view

Pathways & Interactions for COL28A1 Gene

genes like me logo Genes that share pathways with COL28A1: view

Pathways by source for COL28A1 Gene

Interacting Proteins for COL28A1 Gene

Gene Ontology (GO) - Biological Process for COL28A1 Gene

None

No data available for SIGNOR curated interactions for COL28A1 Gene

Drugs & Compounds for COL28A1 Gene

No Compound Related Data Available

Transcripts for COL28A1 Gene

mRNA/cDNA for COL28A1 Gene

(10) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for COL28A1 Gene

Collagen, type XXVIII, alpha 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for COL28A1 Gene

No ASD Table

Relevant External Links for COL28A1 Gene

GeneLoc Exon Structure for
COL28A1
ECgene alternative splicing isoforms for
COL28A1

Expression for COL28A1 Gene

mRNA expression in normal human tissues for COL28A1 Gene

mRNA differential expression in normal tissues according to GTEx for COL28A1 Gene

This gene is overexpressed in Nerve - Tibial (x9.6).

Protein differential expression in normal tissues from HIPED for COL28A1 Gene

This gene is overexpressed in Gallbladder (15.5), Spinal cord (15.1), and Urinary Bladder (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL28A1 Gene



SOURCE GeneReport for Unigene cluster for COL28A1 Gene Hs.491104

genes like me logo Genes that share expression patterns with COL28A1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for COL28A1 Gene

Orthologs for COL28A1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL28A1 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia COL28A1 35
  • 88.67 (n)
  • 86.92 (a)
COL28A1 36
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col28a1 35
  • 85.96 (n)
  • 86.46 (a)
Col28a1 16
Col28a1 36
  • 85 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia COL28A1 35
  • 99.35 (n)
  • 99.02 (a)
COL28A1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col28a1 35
  • 86.8 (n)
  • 86.2 (a)
cow
(Bos Taurus)
Mammalia COL28A1 36
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL28A1 36
  • 35 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 16 (a)
ManyToMany
chicken
(Gallus gallus)
Aves COL28A1 35
  • 62.53 (n)
  • 54.69 (a)
COL28A1 36
  • 53 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL28A1 36
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col28a1 35
  • 58.8 (n)
  • 52.82 (a)
zebrafish
(Danio rerio)
Actinopterygii col28a1 35
  • 55.81 (n)
  • 48.1 (a)
col28a1 36
  • 45 (a)
OneToMany
COL28A1 (2 of 3) 36
  • 46 (a)
OneToMany
col6a3 36
  • 3 (a)
OneToMany
Species with no ortholog for COL28A1:
  • 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 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)
  • worm (Caenorhabditis elegans)

Evolution for COL28A1 Gene

ENSEMBL:
Gene Tree for COL28A1 (if available)
TreeFam:
Gene Tree for COL28A1 (if available)

Paralogs for COL28A1 Gene

Paralogs for COL28A1 Gene

(16) SIMAP similar genes for COL28A1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with COL28A1: view

Variants for COL28A1 Gene

Sequence variations from dbSNP and Humsavar for COL28A1 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs7804532 - 7,531,463(+) AAAGT(C/G)CAATG nc-transcript-variant, reference, missense
rs10486180 - 7,521,949(+) ACAAA(A/C/T)CTTGC nc-transcript-variant, reference, missense
rs10486176 - 7,506,060(+) GTCCA(C/G)TAATT nc-transcript-variant, reference, missense
rs6952195 - 7,474,604(+) ACCTT(C/G)TCCCC nc-transcript-variant, reference, missense
rs17167927 - 7,453,466(+) TCCTG(A/C/G/T)GGGCC nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for COL28A1 Gene

Variant ID Type Subtype PubMed ID
esv2752174 CNV Gain 17911159
dgv2052e1 CNV Complex 17122850
nsv464301 CNV Gain 19166990
nsv469770 CNV Loss 16826518
dgv2053e1 CNV Complex 17122850
dgv7158n71 CNV Gain 21882294
dgv2054e1 CNV Complex 17122850
nsv437531 CNV Loss 16327808
esv29197 CNV Loss 19812545
nsv522393 CNV Loss 19592680
dgv221e55 CNV Loss 17911159
esv2677948 CNV Deletion 23128226
esv2678207 CNV Deletion 23128226
nsv887473 CNV Loss 21882294
esv2733936 CNV Deletion 23290073
esv2673536 CNV Deletion 23128226
dgv7159n71 CNV Gain 21882294
nsv887477 CNV Gain 21882294
esv2589325 CNV Deletion 19546169
esv2413938 CNV Deletion 18987734
esv2733937 CNV Deletion 23290073
nsv366841 CNV Loss 16902084
esv2733938 CNV Deletion 23290073
nsv527573 CNV Loss 19592680

Variation tolerance for COL28A1 Gene

Residual Variation Intolerance Score: 93.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.69; 97.86% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for COL28A1 Gene

Disorders for COL28A1 Gene

Relevant External Links for COL28A1

Genetic Association Database (GAD)
COL28A1
Human Genome Epidemiology (HuGE) Navigator
COL28A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL28A1

No disorders were found for COL28A1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for COL28A1 Gene

Publications for COL28A1 Gene

  1. Collagen XXVIII, a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain. (PMID: 16330543) Veit G. … Wagener R. (J. Biol. Chem. 2006) 2 3 4 23 67
  2. Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. (PMID: 22610502) Kennedy R.B. … Poland G.A. (Hum. Genet. 2012) 3
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3
  5. A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. (PMID: 20889312) Wang K.S. … Aragam N. (Schizophr. Res. 2010) 3

Products for COL28A1 Gene

Sources for COL28A1 Gene

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