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Aliases for COL28A1 Gene

Aliases for COL28A1 Gene

  • Collagen Type XXVIII Alpha 1 Chain 2 3 5
  • Collagen, Type XXVIII, Alpha 1 2 3
  • COL28 3 4
  • Collagen Alpha-1(XXVIII) Chain 3

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 Chain) is a Protein Coding gene. Among its related pathways are Collagen chain trimerization and Degradation of the extracellular matrix. GO annotations related to this gene include serine-type endopeptidase inhibitor activity. An important paralog of this gene is COL6A2.

UniProtKB/Swiss-Prot for COL28A1 Gene

  • May act as a cell-binding protein.

Gene Wiki entry for COL28A1 Gene

No data available for CIViC summary , 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 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
GH07G007562 2 FANTOM5 Ensembl ENCODE dbSUPER 20.5 -29.6 -29619 8.2 HNRNPUL1 HDGF PKNOX1 FOXA2 CREB3L1 WRNIP1 SIN3A FEZF1 YBX1 ZNF2 ENSG00000272894 COL28A1 RPA3 LOC100421597 C7orf26 MIOS ENSG00000198580 ZNF316 ENSG00000272732
GH07G007553 1 Ensembl ENCODE 13.6 -17.3 -17250 2.4 FOXA2 NFIB FEZF1 ZBTB40 YY1 SCRT2 KLF8 TCF7L2 ZNF362 NFIA COL28A1 ENSG00000272894 C1GALT1 RPA3 ENSG00000272732 LOC101927391
GH07G007639 1.4 ENCODE dbSUPER 6.5 -103.7 -103749 3.8 CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC TBX21 ZNF610 RPA3 COL28A1 ENSG00000272732 ENSG00000283549
GH07G007581 0.4 ENCODE 19.8 -44.5 -44455 0.5 MAX EZH2 COL28A1 GLCCI1 LOC100505921 ENSG00000272894 GC07P007610
GH07G007718 1.2 Ensembl ENCODE 5.1 -182.6 -182628 2.8 TBP PKNOX1 RFX5 ZNF366 CBX5 RCOR1 RELB FOS IKZF2 CREM RPA3 UMAD1 COL28A1 ENSG00000272894 LOC100533631
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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

Post-translational modifications for COL28A1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for COL28A1 Gene

Domains & Families for COL28A1 Gene

Gene Families 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 :
  • Belongs to the VWA-containing collagen family.
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.

Gene Ontology (GO) - Molecular Function for COL28A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004867 serine-type endopeptidase inhibitor activity IEA --
GO:0030414 peptidase inhibitor activity IEA --
genes like me logo Genes that share ontologies with COL28A1: view

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

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , 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
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 COL28A1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 4
mitochondrion 3
cytosol 2
plasma membrane 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for COL28A1 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:0005604 basement membrane IEA --
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

Gene Ontology (GO) - Biological Process for COL28A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0010466 negative regulation of peptidase activity IEA --
GO:0010951 negative regulation of endopeptidase activity IEA --
genes like me logo Genes that share ontologies with COL28A1: view

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

(12) 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:

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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



NURSA nuclear receptor signaling pathways regulating expression of COL28A1 Gene:

COL28A1

SOURCE GeneReport for Unigene cluster for COL28A1 Gene:

Hs.491104

Evidence on tissue expression from TISSUES for COL28A1 Gene

  • Lung(4.1)
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 , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34 35
  • 99.35 (n)
dog
(Canis familiaris)
Mammalia COL28A1 34 35
  • 88.67 (n)
rat
(Rattus norvegicus)
Mammalia Col28a1 34
  • 86.8 (n)
mouse
(Mus musculus)
Mammalia Col28a1 34 16 35
  • 85.96 (n)
cow
(Bos Taurus)
Mammalia COL28A1 35
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL28A1 35
  • 35 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 16 (a)
ManyToMany
chicken
(Gallus gallus)
Aves COL28A1 34 35
  • 62.53 (n)
lizard
(Anolis carolinensis)
Reptilia COL28A1 35
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col28a1 34
  • 58.8 (n)
zebrafish
(Danio rerio)
Actinopterygii col28a1 34 35
  • 55.81 (n)
COL28A1 (2 of 3) 35
  • 46 (a)
OneToMany
col6a3 35
  • 3 (a)
OneToMany
Species where no ortholog for COL28A1 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)
  • 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
rs1000011177 -- 7,388,905(+) TTTGT(C/G)AGATG intron-variant
rs1000016604 -- 7,405,633(+) GGACT(A/T)CTCTC intron-variant
rs1000025654 -- 7,440,403(+) GCCTT(C/T)CAAAG intron-variant
rs1000061357 -- 7,440,180(+) TTACC(A/G)GGACA intron-variant
rs1000068846 -- 7,391,090(+) ATCTT(C/T)CCCAC intron-variant

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

Variant ID Type Subtype PubMed ID
dgv1254e214 CNV loss 21293372
dgv221e55 CNV loss 17911159
dgv3487n106 CNV deletion 24896259
dgv6249n100 CNV gain 25217958
dgv6251n100 CNV loss 25217958
dgv6252n100 CNV loss 25217958
esv2413938 CNV deletion 18987734
esv2589325 CNV deletion 19546169
esv2673536 CNV deletion 23128226
esv2677948 CNV deletion 23128226
esv2678207 CNV deletion 23128226
esv2733936 CNV deletion 23290073
esv2733937 CNV deletion 23290073
esv2733938 CNV deletion 23290073
esv2752174 CNV gain 17911159
esv2759505 CNV loss 17122850
esv2761144 CNV gain+loss 21179565
esv29197 CNV loss 19812545
esv3541130 CNV deletion 23714750
esv3541131 CNV deletion 23714750
esv3571613 CNV loss 25503493
esv3571614 CNV loss 25503493
esv3576289 CNV gain 25503493
esv3612073 CNV loss 21293372
esv3612074 CNV gain 21293372
esv3612075 CNV loss 21293372
esv3612076 CNV loss 21293372
esv3612077 CNV loss 21293372
esv3612078 CNV loss 21293372
esv3612079 CNV gain 21293372
esv3612081 CNV gain 21293372
esv3612083 CNV loss 21293372
esv3612084 CNV loss 21293372
esv3612085 CNV gain 21293372
esv3612086 CNV loss 21293372
esv3612087 CNV loss 21293372
esv3612088 CNV loss 21293372
esv3612089 CNV loss 21293372
esv3891032 CNV gain 25118596
esv3891035 CNV gain 25118596
esv3891036 CNV gain 25118596
nsv1020181 CNV loss 25217958
nsv1023133 CNV gain 25217958
nsv1074483 CNV deletion 25765185
nsv1114916 CNV deletion 24896259
nsv366841 CNV deletion 16902084
nsv437531 CNV loss 16327808
nsv464301 CNV gain 19166990
nsv469770 CNV loss 16826518
nsv477033 CNV novel sequence insertion 20440878
nsv522393 CNV loss 19592680
nsv527573 CNV loss 19592680
nsv606035 CNV gain 21841781
nsv606039 CNV loss 21841781
nsv606041 CNV loss 21841781
nsv606042 CNV gain 21841781
nsv606043 CNV loss 21841781
nsv958399 CNV deletion 24416366

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)

Relevant External Links for COL28A1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
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
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 22 64
  2. 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 46 64
  3. 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 46 64
  4. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer S.W. … Tsui L.-C. (Science 2003) 3 4 64
  5. 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 64

Products for COL28A1 Gene

Sources for COL28A1 Gene

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