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EDIL3 EGF like repeats and discoidin domains 3 [ Homo sapiens (human) ]

Gene ID: 10085, updated on 23-Mar-2024

Summary

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Official Symbol
EDIL3provided by HGNC
Official Full Name
EGF like repeats and discoidin domains 3provided by HGNC
Primary source
HGNC:HGNC:3173
See related
Ensembl:ENSG00000164176 MIM:606018; AllianceGenome:HGNC:3173
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DEL1
Summary
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]
Expression
Broad expression in brain (RPKM 53.2), gall bladder (RPKM 22.9) and 17 other tissues See more
Orthologs
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Genomic context

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See EDIL3 in Genome Data Viewer
Location:
5q14.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (83940554..84384880, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (84429063..84873508, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (83236373..83680698, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986386 Neighboring gene NANOG hESC enhancer GRCh37_chr5:83223051-83223552 Neighboring gene ZP3 pseudogene 1 Neighboring gene RNA, U6 small nuclear 448, pseudogene Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:83561430-83562113 Neighboring gene uncharacterized LOC124901223 Neighboring gene EDIL3 divergent transcript Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:83776469-83777065 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:83777066-83777661 Neighboring gene uncharacterized LOC105379059 Neighboring gene NANOG hESC enhancer GRCh37_chr5:83863995-83864551 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:83999549-84000393 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:84256683-84257184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:84257185-84257684 Neighboring gene peptidylprolyl isomerase A pseudogene 79

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Del-1 in Psoriasis Induced the Expression of αvβ3 and α5β1 in Endothelial Cells. Niu X, et al. Curr Mol Med, 2022. PMID 34325631
  2. Regulatory role of local tissue signal Del-1 in cancer and inflammation: a review. Li M, et al. Cell Mol Biol Lett, 2021 Jul 3. PMID 34217213, Free PMC Article
  3. Identification of a novel non-invasive biological marker to overcome the shortcomings of PSA in diagnosis and risk stratification for prostate cancer: Initial prospective study of developmental endothelial locus-1 protein. Chung JW, et al. PLoS One, 2021. PMID 33901217, Free PMC Article
  4. Overcoming Tamoxifen Resistance by Regulation of Del-1 in Breast Cancer. Lee J, et al. Oncology, 2019. PMID 31330520
  5. DEL1 protects against chondrocyte apoptosis through integrin binding. Wang Z, et al. J Surg Res, 2018 Nov. PMID 30278915

See all (64) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Epidermal Growth Factor-Like Repeats and Discoidin I-Like Domains 3 Deficiency Attenuates Dilated Cardiomyopathy by Inhibiting Ubiquitin Specific Peptidase 10 Dependent Smad4 Deubiquitination.
    Title: Epidermal Growth Factor-Like Repeats and Discoidin I-Like Domains 3 Deficiency Attenuates Dilated Cardiomyopathy by Inhibiting Ubiquitin Specific Peptidase 10 Dependent Smad4 Deubiquitination.
  2. Del-1 Plays a Protective Role against COPD Development by Inhibiting Inflammation and Apoptosis.
    Title: Del-1 Plays a Protective Role against COPD Development by Inhibiting Inflammation and Apoptosis.
  3. An IL-10/DEL-1 axis supports granulopoiesis and survival from sepsis in early life.
    Title: An IL-10/DEL-1 axis supports granulopoiesis and survival from sepsis in early life.
  4. Del1 Is a Growth Factor for Skeletal Progenitor Cells in the Fracture Callus.
    Title: Del1 Is a Growth Factor for Skeletal Progenitor Cells in the Fracture Callus.
  5. Del-1 in Psoriasis Induced the Expression of alphavbeta3 and alpha5beta1 in Endothelial Cells.
    Title: Del-1 in Psoriasis Induced the Expression of αvβ3 and α5β1 in Endothelial Cells.
  6. Obesity and altered angiogenic-related gene expression in endometrial cancer.
    Title: Obesity and altered angiogenic-related gene expression in endometrial cancer.
  7. Regulatory role of local tissue signal Del-1 in cancer and inflammation: a review.
    Title: Regulatory role of local tissue signal Del-1 in cancer and inflammation: a review.
  8. Identification of a novel non-invasive biological marker to overcome the shortcomings of PSA in diagnosis and risk stratification for prostate cancer: Initial prospective study of developmental endothelial locus-1 protein.
    Title: Identification of a novel non-invasive biological marker to overcome the shortcomings of PSA in diagnosis and risk stratification for prostate cancer: Initial prospective study of developmental endothelial locus-1 protein.
  9. Clinically confirmed DEL-1 as a myokine attenuates lipid-induced inflammation and insulin resistance in 3T3-L1 adipocytes via AMPK/HO-1- pathway.
    Title: Clinically confirmed DEL-1 as a myokine attenuates lipid-induced inflammation and insulin resistance in 3T3-L1 adipocytes via AMPK/HO-1- pathway.
  10. Del-1, an Endogenous Inhibitor of TGF-beta Activation, Attenuates Fibrosis.
    Title: Del-1, an Endogenous Inhibitor of TGF-β Activation, Attenuates Fibrosis.
Submit: New GeneRIF Correction See all GeneRIFs (38)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study in Han Chinese identifies new susceptibility loci for ankylosing spondylitis.
EBI GWAS Catalog
A genome-wide association study in the genetic analysis of idiopathic thrombophilia project suggests sex-specific regulation of mitochondrial DNA levels.
EBI GWAS Catalog
APOE and BCHE as modulators of cerebral amyloid deposition: a florbetapir PET genome-wide association study.
EBI GWAS Catalog
Chemerin, a novel adipokine in the regulation of angiogenesis.
EBI GWAS Catalog
Genome-wide association analysis identifies 11 risk variants associated with the asthma with hay fever phenotype.
EBI GWAS Catalog
Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ50929, MGC26287

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables extracellular matrix structural constituent RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables integrin binding TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell-substrate adhesion IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in collagen-containing extracellular matrix HDA PubMed 
located_in extracellular exosome HDA PubMed 
located_in extracellular vesicle HDA PubMed 

General protein information

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Preferred Names
EGF-like repeat and discoidin I-like domain-containing protein 3
Names
EGF-like repeats and discoidin I-like domains 3
developmental endothelial locus-1
developmentally-regulated endothelial cell locus 1 protein
integrin-binding protein DEL1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001278642.1 → NP_001265571.1  EGF-like repeat and discoidin I-like domain-containing protein 3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001265571.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AC093296, BC030828, BC053656, BQ101116, DB504385, ES308783
    Consensus CDS
    CCDS64195.1
    UniProtKB/Swiss-Prot
    O43854
    Related
    ENSP00000369483.3, ENST00000380138.3
    Conserved Domains (2) summary
    cd00054
    Location:109 → 145
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    cd00057
    Location:150 → 303
    FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.

  2. NM_005711.5 → NP_005702.3  EGF-like repeat and discoidin I-like domain-containing protein 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_005702.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC026440, AC093296, BC030828, BQ101116, ES308783, U70312
    Consensus CDS
    CCDS4062.1
    UniProtKB/Swiss-Prot
    B2R763, O43854, O43855, Q5D094, Q8N610
    Related
    ENSP00000296591.4, ENST00000296591.10
    Conserved Domains (3) summary
    smart00231
    Location:157 → 314
    FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain
    cd00054
    Location:119 → 155
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    cd00057
    Location:160 → 313
    FA58C; Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes.

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    83940554..84384880 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    84429063..84873508 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43854.1 GenPept UniProtKB/Swiss-Prot:O43854

Gene LinkOut

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