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Aliases for COL28A1 Gene

Aliases for COL28A1 Gene

  • Collagen, Type XXVIII, Alpha 1 2 3
  • COL28 3 4
  • Collagen Alpha-1(XXVIII) Chain 3

External Ids for COL28A1 Gene

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 SCARA3.

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

Genomic Location for COL28A1 Gene

Start:
7,356,203 bp from pter
End:
7,535,853 bp from pter
Size:
179,651 bases
Orientation:
Minus strand

Genomic View for COL28A1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL28A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL28A1 Gene

Regulatory Elements 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

No Post-translational modifications

Other Protein References for COL28A1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for COL28A1 Gene

Domains for COL28A1 Gene

Gene Families for COL28A1 Gene

HGNC:

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
Domain:
  • Contains 1 BPTI/Kunitz inhibitor domain.:
    • Q2UY09
  • Contains 6 collagen-like domains.:
    • Q2UY09
  • Contains 2 VWFA domains.:
    • Q2UY09
Family:
  • Belongs to the VWA-containing collagen family.:
    • Q2UY09
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

Gene Ontology (GO) - Molecular Function for COL28A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004867 serine-type endopeptidase inhibitor activity IEA --
genes like me logo Genes that share ontologies with COL28A1: view

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting 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 4
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:0005576 extracellular region TAS --
GO:0005581 collagen trimer IEA --
GO:0005604 basement membrane IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL28A1: view

Pathways 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

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0010951 negative regulation of endopeptidase activity IEA --
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with COL28A1: view

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 (9.6).

Integrated Proteomics: protein expression 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 expressions with COL28A1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt 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
chimpanzee
(Pan troglodytes)
Mammalia COL28A1 35
  • 99.35 (n)
  • 99.02 (a)
COL28A1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia COL28A1 36
  • 79 (a)
OneToOne
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
oppossum
(Monodelphis domestica)
Mammalia COL28A1 36
  • 35 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 16 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Col28a1 35
  • 86.8 (n)
  • 86.2 (a)
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

Selected 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 MAF
rs720288 -- 7,529,213(-) CTCCC(G/T)GGTTC intron-variant
rs725933 -- 7,419,303(-) TAGGG(A/G)CATTT intron-variant
rs725934 -- 7,419,158(-) ATTCA(C/G)TTGCT intron-variant
rs758910 -- 7,361,188(+) TGTTT(C/G)ATATC intron-variant
rs758911 -- 7,369,747(+) GATCC(A/C/G)AATGT intron-variant

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

Relevant External Links for COL28A1 Gene

HapMap Linkage Disequilibrium report
COL28A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL28A1 Gene

Disorders for COL28A1 Gene

Relevant External Links for COL28A1

Genetic Association Database (GAD)
COL28A1
Human Genome Epidemiology (HuGE) Navigator
COL28A1
genes like me logo Genes that share disorders with COL28A1: view

No data available for UniProtKB/Swiss-Prot 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
  2. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer S.W. … Tsui L.-C. (Science 2003) 3 4
  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 48
  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 48
  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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