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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
  • YjeF Domain-Containing Protein 1 3 4
  • HYjeF_N2 3 4
  • YjeF_N2 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
  • LSM16 Homolog (EDC3, S. Cerevisiae) 3
  • YjeF Domain Containing (E.Coli) 2
  • YjeF Domain Containing 3
  • LSM16 Homolog (EDC3 2
  • S. Cerevisiae) 2
  • HYjeF_N2-15q23 3
  • LSM16 Homolog 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

  • EDC3 is associated with an mRNA-decapping complex required for removal of the 5-prime cap from mRNA prior to its degradation from the 5-prime end (Fenger-Gron et al., 2005 [PubMed 16364915]).[supplied by OMIM, Mar 2008]

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 Deadenylation-dependent mRNA decay and Gene Expression. 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

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

Genomics for EDC3 Gene

Regulatory Elements for EDC3 Gene

Enhancers for EDC3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around EDC3 on UCSC Golden Path with GeneCards custom track

Promoters for EDC3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around EDC3 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the EDC3 gene promoter:

Genomic Location for EDC3 Gene

Chromosome:
15
Start:
74,630,558 bp from pter
End:
74,696,292 bp from pter
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

Proteomics data for EDC3 Gene at MOPED

Post-translational modifications for EDC3 Gene

  • Ubiquitination at Lys 426
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for EDC3 Gene

Domains & Families for EDC3 Gene

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.
  • Contains 1 DFDF domain.
  • Contains 1 YjeF N-terminal domain.
Family:
  • Belongs to the EDC3 family.
genes like me logo Genes that share domains with EDC3: view

No data available for Gene Families for EDC3 Gene

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.

Gene Ontology (GO) - Molecular Function for EDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003729 mRNA binding IBA --
GO:0005515 protein binding IPI 16364915
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

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
Jensen Localization Image for EDC3 Gene COMPARTMENTS Subcellular localization image for EDC3 gene
Compartment Confidence
cytosol 5
nucleus 3
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for EDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IDA 19946888
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 Cell Signaling Technology pathway for EDC3 Gene
1 KEGG pathway for EDC3 Gene

Gene Ontology (GO) - Biological Process for EDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010467 gene expression TAS --
GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA IBA --
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS --
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:

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 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, PaxDb, MOPED, and MaxQB for EDC3 Gene



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.
genes like me logo Genes that share expression patterns with EDC3: view

Protein tissue co-expression partners for EDC3 Gene

- Elite partner

Primer Products

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
cow
(Bos Taurus)
Mammalia EDC3 35
  • 91.59 (n)
  • 92.79 (a)
FLJ21128 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia EDC3 35
  • 91.73 (n)
  • 96.46 (a)
EDC3 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Edc3 35
  • 89.63 (n)
  • 95.67 (a)
Edc3 16
Edc3 36
  • 96 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia EDC3 35
  • 98.36 (n)
  • 98.65 (a)
EDC3 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Edc3 35
  • 89.17 (n)
  • 96.24 (a)
oppossum
(Monodelphis domestica)
Mammalia EDC3 36
  • 93 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia EDC3 36
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves EDC3 35
  • 80.76 (n)
  • 88.74 (a)
EDC3 36
  • 89 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 88 (a)
OneToMany
-- 36
  • 87 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia edc3 35
  • 71.32 (n)
  • 77.84 (a)
Str.3735 35
zebrafish
(Danio rerio)
Actinopterygii Dr.5350 35
edc3 35
  • 66.27 (n)
  • 70.4 (a)
edc3 36
  • 69 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003131 35
  • 47.27 (n)
  • 39.13 (a)
fruit fly
(Drosophila melanogaster)
Insecta Edc3 35
  • 47.49 (n)
  • 41.18 (a)
Edc3 36
  • 25 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 46 (a)
OneToOne
Species with no ortholog for EDC3:
  • 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)

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 Sequence Context AA Info Type
VAR_073963 Mental retardation, autosomal recessive 50 (MRT50)
rs11858916 -- 74,686,394(+) aggca(A/G)gggag intron-variant
rs7161903 -- 74,647,929(+) AGAAT(A/G)ACATC intron-variant
rs950323 -- 74,674,188(+) CAGTC(A/T)CCAAC intron-variant
rs7166524 -- 74,653,679(+) GCTAA(A/G)GACCA intron-variant

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

Variant ID Type Subtype PubMed ID
nsv904379 CNV Loss 21882294
nsv904380 CNV Loss 21882294
nsv457204 CNV Loss 19166990
nsv817698 CNV Gain 17921354
esv28499 CNV Gain 19812545
nsv833055 CNV Loss 17160897

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)

Relevant External Links for EDC3 Gene

Human Gene Mutation Database (HGMD)
EDC3

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

Disorders for EDC3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for EDC3 Gene - From: OMIM, Orphanet, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, autosomal recessive 50
  • mrt50
autosomal recessive non-syndromic intellectual disability
  • autosomal recessive mental retardation
- 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.

Relevant External Links for EDC3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. (Horm. Metab. Res. 2007) 2 3 4 67
  2. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. (PMID: 22483619) Brannan K. … Bentley D.L. (Mol. Cell 2012) 2 3
  3. Novel Sm-like proteins with long C-terminal tails and associated methyltransferases. (PMID: 15225602) Albrecht M. … Lengauer T. (FEBS Lett. 2004) 2 3
  4. Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment. (PMID: 25701870) Ahmed I. … Jamra R.A. (Hum. Mol. Genet. 2015) 3
  5. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3

Products for EDC3 Gene

Sources for EDC3 Gene

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