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] See more...

Aliases for COL28A1 Gene

Aliases for COL28A1 Gene

  • Collagen Type XXVIII Alpha 1 Chain 2 3 5
  • Collagen Alpha-1(XXVIII) Chain 3 4
  • Collagen, Type XXVIII, Alpha 1 2 3
  • 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 Chain) is a Protein Coding gene. Diseases associated with COL28A1 include Epididymis Disease. Among its related pathways are Collagen chain trimerization and Degradation of the extracellular matrix. Gene Ontology (GO) annotations related to this gene include serine-type endopeptidase inhibitor activity. An important paralog of this gene is COL4A4.

UniProtKB/Swiss-Prot Summary for COL28A1 Gene

Gene Wiki entry for COL28A1 Gene

Additional gene information for COL28A1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COL28A1 Gene

Genomics for COL28A1 Gene

GeneHancer (GH) Regulatory Elements for COL28A1 Gene

Promoters and enhancers for COL28A1 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
GH07J007562 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 520.5 -29.6 -29597 8.2 HNRNPK ZBTB40 ZNF217 SIN3A TCF12 POLR2G SP1 GTF2E2 PHF8 JUND ENSG00000272894 COL28A1 MIOS LOC101927391 NONHSAG046908.2 ZNF12 RPA3 LOC100421597 C7orf26 ZNF316
GH07J007535 Promoter/Enhancer 0.6 EPDnew Ensembl 500.7 +1.4 1376 0.2 NR3C1 COL28A1 lnc-RPA3-3
GH07J007577 Enhancer 0.7 Ensembl ENCODE 20.1 -40.6 -40624 1.8 POLR2A NBN SPI1 IKZF1 TBX21 NFIC MTA2 IKZF2 EED ZSCAN29 COL28A1 RPA3 MIOS ENSG00000272894 NONHSAG046908.2 piR-37972-602
GH07J007639 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 6.5 -103.7 -103694 3.9 FOXK2 ZBTB40 ZNF217 SIN3A NRF1 TCF12 POLR2G SP1 GTF2E2 PHF8 RPA3 ENSG00000283549 UMAD1 lnc-COL28A1-3 GLCCI1 COL28A1 ENSG00000272732 piR-31534-594
GH07J007581 Enhancer 0.7 Ensembl ENCODE 19.8 -44.3 -44324 1.2 MYC USF1 POLR2A YY1 TAF1 USF2 CHD2 MAX EZH2 COL28A1 ENSG00000272894 ENSG00000233108 GLCCI1 MIOS NONHSAG046908.2 piR-37972-602
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL28A1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COL28A1

Top Transcription factor binding sites by QIAGEN in the COL28A1 gene promoter:
  • CUTL1
  • HNF-1
  • HNF-1A
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c

Genomic Locations for COL28A1 Gene

Genomic Locations for COL28A1 Gene
chr7:7,338,549-7,537,277
(GRCh38/hg38)
Size:
198,729 bases
Orientation:
Minus strand
chr7:7,395,834-7,575,484
(GRCh37/hg19)
Size:
179,651 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

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

Protein Domains for COL28A1 Gene

Blocks:
  • Collagen triple helix repeat
  • Collagen helix repeat
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for COL28A1 Gene

GenScript: Design optimal peptide antigens:
  • Collagen alpha-1(XXVIII) chain (COSA1_HUMAN)

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.

Phenotypes From GWAS Catalog for COL28A1 Gene

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:0005201 extracellular matrix structural constituent IBA 21873635
GO:0030020 extracellular matrix structural constituent conferring tensile strength RCA 25037231
GO:0030414 peptidase inhibitor activity IEA --
genes like me logo Genes that share ontologies with COL28A1: view

Phenotypes for COL28A1 Gene

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

Clone 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
extracellular 4
endoplasmic reticulum 4
mitochondrion 2
cytoskeleton 1
cytosol 1
plasma membrane 0
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

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:0005615 extracellular space IBA 21873635
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

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 --
GO:0030198 extracellular matrix organization IBA 21873635
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

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

Clone 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

Expression for COL28A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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 and MOPED for COL28A1 Gene



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

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 31 30
  • 99.35 (n)
OneToOne
dog
(Canis familiaris)
Mammalia COL28A1 31 30
  • 88.67 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Col28a1 30
  • 86.8 (n)
mouse
(Mus musculus)
Mammalia Col28a1 17 31 30
  • 85.96 (n)
cow
(Bos Taurus)
Mammalia COL28A1 31
  • 79 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL28A1 31
  • 35 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 16 (a)
ManyToMany
chicken
(Gallus gallus)
Aves COL28A1 31 30
  • 62.53 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL28A1 31
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col28a1 30
  • 58.8 (n)
zebrafish
(Danio rerio)
Actinopterygii col28a1 31 30
  • 55.81 (n)
OneToMany
COL28A1 (2 of 3) 31
  • 46 (a)
OneToMany
col6a3 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for COL28A1: view image

Paralogs for COL28A1 Gene

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

  • COSA1_HUMAN
  • H7BZU0_HUMAN
  • H7C3P2_HUMAN
genes like me logo Genes that share paralogs with COL28A1: view

Variants for COL28A1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COL28A1 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
776204 Benign: not provided 7,373,261(-) T/A MISSENSE_VARIANT
776205 Benign: not provided 7,531,789(-) T/C SYNONYMOUS_VARIANT
787848 Benign: not provided 7,380,698(-) A/G INTRON_VARIANT
rs10486176 - p.Thr327Ser
rs10486180 - p.Ile239Val

Additional dbSNP identifiers (rs#s) for COL28A1 Gene

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)

Additional Variant Information 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

MalaCards: The human disease database

(1) MalaCards diseases for COL28A1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
epididymis disease
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for COL28A1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with COL28A1: view

No data available for 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 (The Journal of biological chemistry 2006) 2 3 4 23 54
  2. 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 54
  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 SD … DREAM investigators (Diabetes care 2010) 3 41 54
  4. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer SW … Tsui LC (Science (New York, N.Y.) 2003) 3 4 54
  5. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. (PMID: 29676528) Khanna R … Parnaik VK (The FEBS journal 2018) 3 54

Products for COL28A1 Gene

Sources for COL28A1 Gene