The protein encoded by this gene is an integrin ligand. It plays an important role in mediating angiogenesis and may be important in vessel wall remodeling and development. It also influences endothelial cell behavior. [provided by RefSeq, Jul 2008] See more...

Aliases for EDIL3 Gene

Aliases for EDIL3 Gene

  • EGF Like Repeats And Discoidin Domains 3 2 3 5
  • EGF-Like Repeat And Discoidin I-Like Domain-Containing Protein 3 3 4
  • Developmentally-Regulated Endothelial Cell Locus 1 Protein 3 4
  • EGF-Like Repeats And Discoidin I-Like Domains 3 2 3
  • Integrin-Binding Protein DEL1 3 4
  • DEL1 3 4
  • Developmental Endothelial Locus-1 3

External Ids for EDIL3 Gene

Previous GeneCards Identifiers for EDIL3 Gene

  • GC05M082056
  • GC05M083465
  • GC05M083277
  • GC05M083322
  • GC05M083320
  • GC05M083272
  • GC05M078445
  • GC05M083236

Summaries for EDIL3 Gene

Entrez Gene Summary for EDIL3 Gene

  • The protein encoded by this gene is an integrin ligand. It plays an important role in mediating angiogenesis and may be important in vessel wall remodeling and development. It also influences endothelial cell behavior. [provided by RefSeq, Jul 2008]

GeneCards Summary for EDIL3 Gene

EDIL3 (EGF Like Repeats And Discoidin Domains 3) is a Protein Coding gene. Diseases associated with EDIL3 include Anal Paget's Disease and Acute Pericementitis. Among its related pathways are MAPK-Erk Pathway and Integrins in angiogenesis. Gene Ontology (GO) annotations related to this gene include calcium ion binding and integrin binding. An important paralog of this gene is MFGE8.

UniProtKB/Swiss-Prot Summary for EDIL3 Gene

  • Promotes adhesion of endothelial cells through interaction with the alpha-v/beta-3 integrin receptor. Inhibits formation of vascular-like structures. May be involved in regulation of vascular morphogenesis of remodeling in embryonic development.

Additional gene information for EDIL3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for EDIL3 Gene

Genomics for EDIL3 Gene

GeneHancer (GH) Regulatory Elements for EDIL3 Gene

Promoters and enhancers for EDIL3 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
GH05J084381 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 506.8 +0.9 883 5.6 ZSCAN5C USF1 ZNF639 ZIC2 ZBTB10 ZNF423 ZBTB26 SAP30 KLF7 ZEB1 EDIL3 EDIL3-DT ENSG00000250320
GH05J084287 Enhancer 1.2 FANTOM5 Ensembl ENCODE 15 +96.0 95977 4.6 ZSCAN5C JUND FOS ZNF639 ZNF10 ZIC2 ATF2 ZEB1 ZNF341 OSR2 EDIL3 ENSG00000250320 RNU6-448P piR-55809-031 piR-31508-045
GH05J084411 Enhancer 0.6 Ensembl ENCODE 11.8 -27.2 -27182 0.3 FOS FEZF1 GLIS1 MYC EDIL3 ENSG00000250320 lnc-VCAN-5 EDIL3-DT
GH05J084292 Enhancer 0.9 FANTOM5 Ensembl 7.6 +91.6 91579 1 ZSCAN5C ZNF623 NFYB ZNF341 OSR2 BCL11A MYNN WT1 SP2 ZBTB17 EDIL3 piR-55809-031 piR-31508-045
GH05J084378 Enhancer 1.1 FANTOM5 Ensembl ENCODE dbSUPER 5.6 +6.0 5979 3.8 CTCF JUND ZNF664 RAD21 PRDM4 ZNF366 POLR2A SMC3 CEBPB EDIL3 ENSG00000250320 piR-50437-543
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EDIL3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for EDIL3

Top Transcription factor binding sites by QIAGEN in the EDIL3 gene promoter:
  • AREB6
  • CUTL1
  • FOXI1
  • HFH-3
  • Oct-B1
  • oct-B2
  • oct-B3
  • Pax-4a
  • Roaz

Genomic Locations for EDIL3 Gene

Genomic Locations for EDIL3 Gene
chr5:83,940,554-84,384,880
(GRCh38/hg38)
Size:
444,327 bases
Orientation:
Minus strand
chr5:83,236,373-83,680,611
(GRCh37/hg19)
Size:
444,239 bases
Orientation:
Minus strand

Genomic View for EDIL3 Gene

Genes around EDIL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EDIL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EDIL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EDIL3 Gene

Proteins for EDIL3 Gene

  • Protein details for EDIL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43854-EDIL3_HUMAN
    Recommended name:
    EGF-like repeat and discoidin I-like domain-containing protein 3
    Protein Accession:
    O43854
    Secondary Accessions:
    • B2R763
    • O43855
    • Q5D094
    • Q8N610

    Protein attributes for EDIL3 Gene

    Size:
    480 amino acids
    Molecular mass:
    53765 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for EDIL3 Gene

    Alternative splice isoforms for EDIL3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EDIL3 Gene

Post-translational modifications for EDIL3 Gene

  • Glycosylation at Thr73, Thr88, Asn140, and Thr336
  • Ubiquitination at Lys244
  • Modification sites at PhosphoSitePlus

Other Protein References for EDIL3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EDIL3 Gene

Domains & Families for EDIL3 Gene

Gene Families for EDIL3 Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for EDIL3 Gene

Blocks:
  • Aspartic acid and asparagine hydroxylation site
  • EGF-like calcium-binding
  • Coagulation factor 5/8 type C domain (FA58C)
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for EDIL3 Gene

GenScript: Design optimal peptide antigens:
  • Integrin-binding protein DEL1 (EDIL3_HUMAN)
  • EGF-like repeats and discoidin I-like domains 3 (Q8N610_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O43854

UniProtKB/Swiss-Prot:

EDIL3_HUMAN :
  • EGF2 and EGF3 form a rigid rod via an interdomain calcium ion binding site, while the long linker between EGF1 and EGF2 lends considerable flexibility to EGF1.
Domain:
  • EGF2 and EGF3 form a rigid rod via an interdomain calcium ion binding site, while the long linker between EGF1 and EGF2 lends considerable flexibility to EGF1.
genes like me logo Genes that share domains with EDIL3: view

Function for EDIL3 Gene

Molecular function for EDIL3 Gene

UniProtKB/Swiss-Prot Function:
Promotes adhesion of endothelial cells through interaction with the alpha-v/beta-3 integrin receptor. Inhibits formation of vascular-like structures. May be involved in regulation of vascular morphogenesis of remodeling in embryonic development.
GENATLAS Biochemistry:
EGF-like repeats and discoidin I-like domains 3,homolog to mouse Del1,initially expressed in the endothelial progenitor and in embryonic mesenchymal cells,promoting the adhesion of endothelial cells through interaction with the AVB3 integrin receptor,putative regulator of vascular morphogenesis or remodeling in embryonic development

Phenotypes From GWAS Catalog for EDIL3 Gene

Gene Ontology (GO) - Molecular Function for EDIL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005178 integrin binding IEA --
GO:0005201 extracellular matrix structural constituent RCA 23979707
GO:0005509 calcium ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with EDIL3: view
genes like me logo Genes that share phenotypes with EDIL3: view

Animal Models for EDIL3 Gene

MGI Knock Outs for EDIL3:

Animal Model Products

  • Taconic Biosciences Mouse Models for EDIL3

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EDIL3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for EDIL3 Gene

Localization for EDIL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EDIL3 Gene

Secreted.

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 EDIL3 gene
Compartment Confidence
extracellular 5
plasma membrane 3
cytoskeleton 2
nucleus 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for EDIL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0062023 collagen-containing extracellular matrix HDA 23979707
GO:0070062 extracellular exosome HDA 21362503
GO:1903561 extracellular vesicle HDA 24769233
genes like me logo Genes that share ontologies with EDIL3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for EDIL3 Gene

Pathways & Interactions for EDIL3 Gene

genes like me logo Genes that share pathways with EDIL3: view

Pathways by source for EDIL3 Gene

1 BioSystems pathway for EDIL3 Gene

Gene Ontology (GO) - Biological Process for EDIL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007275 multicellular organism development IEA --
GO:0010811 positive regulation of cell-substrate adhesion IEA --
genes like me logo Genes that share ontologies with EDIL3: view

No data available for SIGNOR curated interactions for EDIL3 Gene

Drugs & Compounds for EDIL3 Gene

No Compound Related Data Available

Transcripts for EDIL3 Gene

mRNA/cDNA for EDIL3 Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
4 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 EDIL3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for EDIL3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11
SP1:
SP2: -

Relevant External Links for EDIL3 Gene

GeneLoc Exon Structure for
EDIL3

Expression for EDIL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EDIL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for EDIL3 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x7.8) and Brain - Substantia nigra (x4.5).

Protein differential expression in normal tissues from HIPED for EDIL3 Gene

This gene is overexpressed in Amniocyte (55.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for EDIL3 Gene



Protein tissue co-expression partners for EDIL3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for EDIL3

SOURCE GeneReport for Unigene cluster for EDIL3 Gene:

Hs.482730

Evidence on tissue expression from TISSUES for EDIL3 Gene

  • Nervous system(4.9)
  • Lung(4.3)
  • Heart(2.2)
genes like me logo Genes that share expression patterns with EDIL3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EDIL3 Gene

Orthologs for EDIL3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for EDIL3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EDIL3 31 30
  • 99.58 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia EDIL3 31
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia EDIL3 31
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia EDIL3 31 30
  • 92.57 (n)
OneToOne
dog
(Canis familiaris)
Mammalia EDIL3 31 30
  • 92.08 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Edil3 17 31 30
  • 89.79 (n)
rat
(Rattus norvegicus)
Mammalia Edil3 30
  • 89.07 (n)
chicken
(Gallus gallus)
Aves EDIL3 31 30
  • 82.01 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia EDIL3 31
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia edil3 30
  • 78.96 (n)
MGC75581 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.7387 30
zebrafish
(Danio rerio)
Actinopterygii edil3 31 30
  • 78.37 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2640 31
  • 29 (a)
OneToMany
Species where no ortholog for EDIL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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 EDIL3 Gene

ENSEMBL:
Gene Tree for EDIL3 (if available)
TreeFam:
Gene Tree for EDIL3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EDIL3: view image

Paralogs for EDIL3 Gene

(5) SIMAP similar genes for EDIL3 Gene using alignment to 1 proteins:

  • EDIL3_HUMAN
genes like me logo Genes that share paralogs with EDIL3: view

Variants for EDIL3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for EDIL3 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
709768 Benign: not provided 84,066,493(-) C/G MISSENSE_VARIANT
721262 Benign: not provided 84,254,221(-) T/TA INTRON_VARIANT
722058 Likely Benign: not provided 84,064,787(-) T/C MISSENSE_VARIANT
737422 Likely Benign: not provided 84,060,294(-) C/T INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for EDIL3 Gene

Structural Variations from Database of Genomic Variants (DGV) for EDIL3 Gene

Variant ID Type Subtype PubMed ID
dgv200n6 CNV deletion 16902084
dgv3116n106 CNV deletion 24896259
dgv5709n100 CNV loss 25217958
esv2120037 CNV deletion 18987734
esv2657400 CNV deletion 23128226
esv2658431 CNV deletion 23128226
esv2661836 CNV deletion 23128226
esv2676239 CNV deletion 23128226
esv2730404 CNV deletion 23290073
esv2730405 CNV deletion 23290073
esv3566201 CNV deletion 23714750
esv3566206 CNV deletion 23714750
esv3605642 CNV loss 21293372
esv3605643 CNV loss 21293372
esv3605644 CNV loss 21293372
esv3605646 CNV loss 21293372
esv3605647 CNV loss 21293372
esv3605648 CNV loss 21293372
esv7439 CNV gain 19470904
nsv1015852 CNV gain 25217958
nsv1074314 CNV deletion 25765185
nsv1123967 CNV deletion 24896259
nsv1125846 CNV tandem duplication 24896259
nsv329064 CNV deletion 16902084
nsv4905 CNV insertion 18451855
nsv520830 CNV gain 19592680
nsv525596 CNV loss 19592680
nsv598786 CNV loss 21841781
nsv823108 CNV loss 20364138
nsv830368 CNV loss 17160897
nsv830369 CNV loss 17160897
nsv830371 CNV gain 17160897

Variation tolerance for EDIL3 Gene

Residual Variation Intolerance Score: 38.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.66; 31.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EDIL3 Gene

Human Gene Mutation Database (HGMD)
EDIL3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
EDIL3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EDIL3 Gene

Disorders for EDIL3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for EDIL3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
anal paget's disease
  • anal paget disease
acute pericementitis
  • acute periodontitis
anus adenocarcinoma
  • adenocarcinoma of anus
- elite association - COSMIC cancer census association via MalaCards
Search EDIL3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for EDIL3

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 EDIL3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EDIL3 Gene

Publications for EDIL3 Gene

  1. Cloning and characterization of developmental endothelial locus-1: an embryonic endothelial cell protein that binds the alphavbeta3 integrin receptor. (PMID: 9420328) Hidai C … Quertermous T (Genes & development 1998) 2 3 4 54
  2. The RGD finger of Del-1 is a unique structural feature critical for integrin binding. (PMID: 22601780) Schürpf T … Wang JH (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2012) 3 4 54
  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 54
  4. A genome-wide study reveals copy number variants exclusive to childhood obesity cases. (PMID: 20950786) Glessner JT … Grant SF (American journal of human genetics 2010) 3 41 54
  5. Chemerin, a novel adipokine in the regulation of angiogenesis. (PMID: 20237162) Bozaoglu K … Jowett JB (The Journal of clinical endocrinology and metabolism 2010) 3 41 54

Products for EDIL3 Gene

Sources for EDIL3 Gene