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Aliases for EDC3 Gene

Aliases for EDC3 Gene

  • Enhancer Of MRNA Decapping 3 2 3 5
  • YjeF N-Terminal Domain-Containing Protein 2 3 4
  • LSM16 Homolog (EDC3, S. Cerevisiae) 2 3
  • YjeF Domain-Containing Protein 1 3 4
  • YJEFN2 3 4
  • LSM16 3 4
  • YJDC 3 4
  • Enhancer Of MRNA Decapping 3 Homolog (S. Cerevisiae) 2
  • Enhancer Of MRNA Decapping 3 Homolog 3
  • Enhancer Of MRNA-Decapping Protein 3 3
  • YjeF Domain Containing (E.Coli) 2
  • YjeF Domain Containing 3
  • HYjeF_N2-15q23 3
  • LSM16 Homolog 4
  • HYjeF_N2 4
  • YjeF_N2 4
  • MRT50 3

External Ids for EDC3 Gene

Previous HGNC Symbols for EDC3 Gene

  • YJDC

Previous GeneCards Identifiers for EDC3 Gene

  • GC15M072712
  • GC15M074922
  • GC15M051721

Summaries for EDC3 Gene

Entrez Gene Summary for EDC3 Gene

  • This gene encodes a protein that is important in mRNA degradation. The encoded protein is a component of a decapping complex that promotes efficient removal of the monomethylguanosine (m7G) cap from mRNAs, as part of the 5' to 3' mRNA decay pathway. Mutations in this gene have been identified in human patients with an autosomal recessive form of intellectual disability. [provided by RefSeq, May 2017]

GeneCards Summary for EDC3 Gene

EDC3 (Enhancer Of MRNA Decapping 3) is a Protein Coding gene. Diseases associated with EDC3 include Mental Retardation, Autosomal Recessive 50 and Autosomal Recessive Non-Syndromic Intellectual Disability. Among its related pathways are Translational Control and Deadenylation-dependent mRNA decay. Gene Ontology (GO) annotations related to this gene include identical protein binding and RNA binding.

UniProtKB/Swiss-Prot for EDC3 Gene

  • Binds single-stranded RNA. Involved in the process of mRNA degradation and in the positive regulation of mRNA decapping. May play a role in spermiogenesis and oogenesis.

Gene Wiki entry for EDC3 Gene

Additional gene information for EDC3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EDC3 Gene

Genomics for EDC3 Gene

GeneHancer (GH) Regulatory Elements for EDC3 Gene

Promoters and enhancers for EDC3 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
GH15J074694 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 660.7 +0.4 407 2 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 YY1 EDC3 SIN3A MAN2C1 PML ENSG00000260274 CLK3 ENSG00000203392 GOLGA6D LOC732265 SNX33
GH15J075366 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 71.1 -672.5 -672463 3.8 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 MAN2C1 ENSG00000260274 SIN3A DNM1P35 EDC3 LOC441728 FBXO22 SNUPN CLK3 COMMD4
GH15J074412 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 55.3 +272.1 272109 22.6 HDGF PKNOX1 SMAD1 FOXA2 ARID4B SIN3A ZNF2 YY1 POLR2B ZNF207 SEMA7A ENSG00000260274 MAN2C1 EDC3 CLK3 LOC101929333 PML COMMD4 ENSG00000212279 UBL7-AS1
GH15J074380 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 58.2 +303.6 303632 24.1 ZFP64 IRF4 SLC30A9 E2F8 ZNF143 ZNF263 SP3 NFYC ZC3H11A MEF2D CYP11A1 EDC3 ENSG00000260274 CLK3 MAN2C1 COMMD4 LOC101929333 SEMA7A ENSG00000212279 LOXL1
GH15J075624 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 56.2 -929.9 -929938 3.8 MLX DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 ZNF610 SNUPN ENSG00000260235 SIN3A MAN2C1 ENSG00000260274 EDC3 FBXO22 COMMD4 DNM1P35 TYRO3P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EDC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EDC3 gene promoter:
  • Evi-1

Genomic Locations for EDC3 Gene

Genomic Locations for EDC3 Gene
chr15:74,630,558-74,696,292
(GRCh38/hg38)
Size:
65,735 bases
Orientation:
Minus strand
chr15:74,922,899-74,988,633
(GRCh37/hg19)
Size:
65,735 bases
Orientation:
Minus strand

Genomic View for EDC3 Gene

Genes around EDC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EDC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EDC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EDC3 Gene

Proteins for EDC3 Gene

  • Protein details for EDC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96F86-EDC3_HUMAN
    Recommended name:
    Enhancer of mRNA-decapping protein 3
    Protein Accession:
    Q96F86
    Secondary Accessions:
    • B3KPH0
    • D3DW61
    • Q9H797

    Protein attributes for EDC3 Gene

    Size:
    508 amino acids
    Molecular mass:
    56078 Da
    Quaternary structure:
    • Homodimer (via YjeF N-terminal domain). Forms a complex with DCP1A, DCP2, DDX6 and EDC4/HEDLS, within this complex directly interacts with DCP1A and DDX6. Interacts with ZFP36.

    Three dimensional structures from OCA and Proteopedia for EDC3 Gene

neXtProt entry for EDC3 Gene

Post-translational modifications for EDC3 Gene

  • Ubiquitination at isoforms=426
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for EDC3 Gene

Domains & Families for EDC3 Gene

Gene Families for EDC3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for EDC3 Gene

Suggested Antigen Peptide Sequences for EDC3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96F86

UniProtKB/Swiss-Prot:

EDC3_HUMAN :
  • The DFDF domain is unstructured by itself. It assumes a helical fold upon interaction with DDX6.
  • Belongs to the EDC3 family.
Domain:
  • The DFDF domain is unstructured by itself. It assumes a helical fold upon interaction with DDX6.
Family:
  • Belongs to the EDC3 family.
genes like me logo Genes that share domains with EDC3: view

Function for EDC3 Gene

Molecular function for EDC3 Gene

UniProtKB/Swiss-Prot Function:
Binds single-stranded RNA. Involved in the process of mRNA degradation and in the positive regulation of mRNA decapping. May play a role in spermiogenesis and oogenesis.

Phenotypes From GWAS Catalog for EDC3 Gene

Gene Ontology (GO) - Molecular Function for EDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0003729 mRNA binding IBA,IEA --
GO:0005515 protein binding IPI 15161933
GO:0042802 identical protein binding IPI 18678652
GO:1990174 phosphodiesterase decapping endonuclease activity IMP 25701870
genes like me logo Genes that share ontologies with EDC3: view
genes like me logo Genes that share phenotypes with EDC3: view

Human Phenotype Ontology for EDC3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

  • Addgene plasmids for EDC3

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for EDC3 Gene

Localization for EDC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EDC3 Gene

Cytoplasm, P-body. Note=Processing bodies (PB).

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 EDC3 gene
Compartment Confidence
cytosol 5
nucleus 3
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytoplasmic bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IBA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0016020 membrane HDA 19946888
GO:0036464 cytoplasmic ribonucleoprotein granule IDA --
genes like me logo Genes that share ontologies with EDC3: view

Pathways & Interactions for EDC3 Gene

genes like me logo Genes that share pathways with EDC3: view

Pathways by source for EDC3 Gene

1 KEGG pathway for EDC3 Gene
1 Cell Signaling Technology pathway for EDC3 Gene

Gene Ontology (GO) - Biological Process for EDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA IBA,IEA --
GO:0033962 cytoplasmic mRNA processing body assembly IBA --
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS --
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic IEA --
genes like me logo Genes that share ontologies with EDC3: view

No data available for SIGNOR curated interactions for EDC3 Gene

Drugs & Compounds for EDC3 Gene

No Compound Related Data Available

Transcripts for EDC3 Gene

Unigene Clusters for EDC3 Gene

Enhancer of mRNA decapping 3 homolog (S. cerevisiae):
Representative Sequences:

Clone Products

  • Addgene plasmids for EDC3

Alternative Splicing Database (ASD) splice patterns (SP) for EDC3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c · 8d · 8e ^ 9 ^ 10a · 10b ^ 11 ^ 12a ·
SP1: - - - - - - - -
SP2: - - - - - - - - - -
SP3: - - - - - - - - - - - -
SP4: - - - - - - -
SP5: - - - - - - - - - -
SP6: - - - - - - - - - - - - - - - - - -
SP7: - - - - - - - - -
SP8: -
SP9:
SP10: - - - - - -
SP11: - - - - - - -
SP12: - - -
SP13:

ExUns: 12b · 12c ^ 13a · 13b · 13c · 13d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for EDC3 Gene

GeneLoc Exon Structure for
EDC3
ECgene alternative splicing isoforms for
EDC3

Expression for EDC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EDC3 Gene

Protein differential expression in normal tissues from HIPED for EDC3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (17.1), Testis (15.2), and CD8 Tcells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for EDC3 Gene



Protein tissue co-expression partners for EDC3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of EDC3 Gene:

EDC3

SOURCE GeneReport for Unigene cluster for EDC3 Gene:

Hs.96852

mRNA Expression by UniProt/SwissProt for EDC3 Gene:

Q96F86-EDC3_HUMAN
Tissue specificity: Expressed in theca and granulosa cells in ovary, and in spermatids of the meiotic division part II and apical membrane of Sertoli cells in testis (at protein level). Also expressed in brain and mammary gland.

Evidence on tissue expression from TISSUES for EDC3 Gene

  • Eye(4.1)
  • Liver(4.1)
  • Nervous system(3.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for EDC3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tooth
Thorax:
  • chest wall
  • heart
Abdomen:
  • abdominal wall
Limb:
  • foot
  • lower limb
General:
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
genes like me logo Genes that share expression patterns with EDC3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for EDC3 Gene

Orthologs for EDC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for EDC3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EDC3 34 33
  • 98.36 (n)
OneToOne
cow
(Bos Taurus)
Mammalia FLJ21128 34
  • 97 (a)
OneToOne
EDC3 33
  • 91.59 (n)
oppossum
(Monodelphis domestica)
Mammalia EDC3 34
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia EDC3 34 33
  • 91.73 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Edc3 16 34 33
  • 89.63 (n)
rat
(Rattus norvegicus)
Mammalia Edc3 33
  • 89.17 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia EDC3 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves EDC3 34 33
  • 80.76 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 88 (a)
OneToMany
-- 34
  • 87 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia edc3 33
  • 71.32 (n)
Str.3735 33
zebrafish
(Danio rerio)
Actinopterygii edc3 34 33
  • 66.27 (n)
OneToOne
Dr.5350 33
fruit fly
(Drosophila melanogaster)
Insecta Edc3 34 33
  • 47.49 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003131 33
  • 47.27 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
OneToOne
Species where no ortholog for EDC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 EDC3 Gene

ENSEMBL:
Gene Tree for EDC3 (if available)
TreeFam:
Gene Tree for EDC3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EDC3: view image

Paralogs for EDC3 Gene

No data available for Paralogs for EDC3 Gene

Variants for EDC3 Gene

Sequence variations from dbSNP and Humsavar for EDC3 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1057517676 pathogenic, Mental retardation, autosomal recessive 50, retardation, autosomal recessive 50 (MRT50) [MIM:616460] 74,674,964(-) A/G coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs1000089853 -- 74,680,563(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000101298 -- 74,655,371(-) T/A intron_variant
rs1000198387 -- 74,645,344(-) G/T intron_variant
rs1000199067 -- 74,638,024(-) A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for EDC3 Gene

Variant ID Type Subtype PubMed ID
esv28499 CNV gain 19812545
nsv1121512 CNV deletion 24896259
nsv457204 CNV loss 19166990
nsv569991 CNV loss 21841781
nsv817698 CNV gain 17921354
nsv833055 CNV loss 17160897
nsv951994 CNV deletion 24416366

Variation tolerance for EDC3 Gene

Residual Variation Intolerance Score: 27.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.28; 25.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EDC3 Gene

Human Gene Mutation Database (HGMD)
EDC3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
EDC3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EDC3 Gene

Disorders for EDC3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for EDC3 Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, autosomal recessive 50
  • mrt50
autosomal recessive non-syndromic intellectual disability
  • autosomal recessive mental retardation
syringomyelia
gliosarcoma
  • glioblastoma with sarcomatous component
- elite association - COSMIC cancer census association via MalaCards
Search EDC3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

EDC3_HUMAN
  • Mental retardation, autosomal recessive 50 (MRT50) [MIM:616460]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT50 patients show mild intellectual disability and microcephaly. {ECO:0000269 PubMed:25701870}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for EDC3

genes like me logo Genes that share disorders with EDC3: view

No data available for Genatlas for EDC3 Gene

Publications for EDC3 Gene

  1. ApoA-I-binding protein (AI-BP) and its homologues hYjeF_N2 and hYjeF_N3 comprise the YjeF_N domain protein family in humans with a role in spermiogenesis and oogenesis. (PMID: 17533573) Rudolph C … Schmitz G (Hormone and metabolic research = Hormon- und Stoffwechselforschung = Hormones et metabolisme 2007) 2 3 4 58
  2. Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment. (PMID: 25701870) Ahmed I … Jamra RA (Human molecular genetics 2015) 3 4 58
  3. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. (PMID: 22483619) Brannan K … Bentley DL (Molecular cell 2012) 2 3 58
  4. Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B. (PMID: 19285948) Tritschler F … Weichenrieder O (Molecular cell 2009) 3 4 58
  5. Crystal structure of human Edc3 and its functional implications. (PMID: 18678652) Ling SH … Song H (Molecular and cellular biology 2008) 3 4 58

Products for EDC3 Gene

Sources for EDC3 Gene