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

    Gene ID: 10085, updated on 2-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (83940554..84384880, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (84429063..84873508, complement)
    RS_2024_09 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 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. In silico analysis of DEL-1 and inflammation-related genes in lung squamous cell carcinoma. Ilikci-Sagkan R, et al. Immunobiology, 2024 Sep. PMID 39089131
    2. Downregulation of developmentally regulated endothelial cell locus-1 inhibits the growth of colon cancer. Zou X, et al. J Biomed Sci, 2009. PMID 19292890, Free PMC Article
    3. High expression level of EDIL3 in HCC predicts poor prognosis of HCC patients. Sun JC, et al. World J Gastroenterol, 2010 Sep 28. PMID 20857535, Free PMC Article
    4. The RGD finger of Del-1 is a unique structural feature critical for integrin binding. Schürpf T, et al. FASEB J, 2012 Aug. PMID 22601780, Free PMC Article
    5. Del-1 overexpression potentiates lung cancer cell proliferation and invasion. Lee SH, et al. Biochem Biophys Res Commun, 2015 Dec 4-11. PMID 26545781

    See all (77) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. In silico analysis of DEL-1 and inflammation-related genes in lung squamous cell carcinoma.
      Title: In silico analysis of DEL-1 and inflammation-related genes in lung squamous cell carcinoma.
    2. Analysis of ANO6, HAPLN1, and EDIL3 Polymorphisms in Patients with Ankylosing Spondylitis in a Chinese Han Population: A Case-Control Study.
      Title: Analysis of ANO6, HAPLN1, and EDIL3 Polymorphisms in Patients with Ankylosing Spondylitis in a Chinese Han Population: A Case-Control Study.
    3. Exploration of MELK as a downstream of Del-1 and druggable targets in triple-negative breast cancer.
      Title: Exploration of MELK as a downstream of Del-1 and druggable targets in triple-negative breast cancer.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. Obesity and altered angiogenic-related gene expression in endometrial cancer.
      Title: Obesity and altered angiogenic-related gene expression in endometrial cancer.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (41)

    Phenotypes

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    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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    NEW Try the new Transcript table

    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_2024_08

    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

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