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    EDC3 enhancer of mRNA decapping 3 [ Homo sapiens (human) ]

    Gene ID: 80153, updated on 10-Dec-2024

    Summary

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    Official Symbol
    EDC3provided by HGNC
    Official Full Name
    enhancer of mRNA decapping 3provided by HGNC
    Primary source
    HGNC:HGNC:26114
    See related
    Ensembl:ENSG00000179151 MIM:609842; AllianceGenome:HGNC:26114
    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
    YJDC; LSM16; MRT50; YJEFN2; hYjeF_N2-15q23
    Summary
    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]
    Expression
    Ubiquitous expression in testis (RPKM 14.2), ovary (RPKM 7.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EDC3 in Genome Data Viewer
    Location:
    15q24.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (74630558..74696024, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72500459..72565921, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74922899..74988365, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene AT-rich interaction domain 3B Neighboring gene uncharacterized LOC124903527 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74880397-74881182 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74881183-74881968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74886857-74887357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74889350-74889850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74890466-74891354 Neighboring gene uncharacterized LOC102723750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6654 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74908320-74908931 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74908932-74909542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74921666-74922166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9786 Neighboring gene CDC like kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9788 Neighboring gene CYP1A1 5' regulatory region Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:75021499-75022227 Neighboring gene cytochrome P450 family 1 subfamily A member 1 Neighboring gene CYP1A2 5' regulatory region Neighboring gene cytochrome P450 family 1 subfamily A member 2

    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. Structure of a Human 4E-T/DDX6/CNOT1 Complex Reveals the Different Interplay of DDX6-Binding Proteins with the CCR4-NOT Complex. Ozgur S, et al. Cell Rep, 2015 Oct 27. PMID 26489469
    2. Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability. Scheller U, et al. BMC Med Genomics, 2018 Apr 23. PMID 29685133, Free PMC Article
    3. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Brannan K, et al. Mol Cell, 2012 May 11. PMID 22483619, Free PMC Article
    4. Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment. Ahmed I, et al. Hum Mol Genet, 2015 Jun 1. PMID 25701870, Free PMC Article
    5. 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. Rudolph C, et al. Horm Metab Res, 2007 May. PMID 17533573

    See all (110) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. EDC3 might be preferentially involved in the degradation of long coding and non-coding RNAs
      Title: Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability.
    2. In vitro decapping assays showed that altered EDC3 is unable to enhance DCP2 decapping at low concentrations and even inhibits DCP2 decapping at high concentration.
      Title: Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment.
    3. Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B.
      Title: Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B.
    4. The dimerization interface of Edc3 is highly conserved in eukaryotes despite the overall low sequence homology across species; structure-based site-directed mutagenesis revealed dimerization is required for efficient RNA binding, P-body formation
      Title: Crystal structure of human Edc3 and its functional implications.
    5. The modular architecture enables EDC3 to interact with multiple components of the decapping machinery, including DCP1, DCP2, and Me31B.
      Title: A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting.
    Submit: New GeneRIF Correction

    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

    Associated conditions

    Description Tests
    Intellectual disability, autosomal recessive 50
    MedGen: C4225319 OMIM: 616460 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption.
    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)

    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

    • FLJ21128, FLJ31777

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in P-body assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in deadenylation-independent decapping of nuclear-transcribed mRNA IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    enhancer of mRNA-decapping protein 3
    Names
    LSM16 homolog (EDC3, S. cerevisiae)
    enhancer of mRNA decapping 3 homolog
    yjeF N-terminal domain-containing protein 2
    yjeF domain containing
    yjeF domain-containing protein 1

    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.

    Genomic

    1. NG_054910.1 RefSeqGene

      Range
      5022..70488
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001142443.3 → NP_001135915.1  enhancer of mRNA-decapping protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001135915.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1-4 encode the same isoform (1).
      Source sequence(s)
      AC091230, AL133447, BC021271, BM999594, CA440205
      Consensus CDS
      CCDS10267.1
      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797
      Related
      ENSP00000401343.3, ENST00000426797.7
      Conserved Domains (4) summary
      cd01737
      Location:2 → 66
      LSm16_N; Like-Sm protein 16, N-terminal domain
      pfam03853
      Location:302 → 455
      YjeF_N; YjeF-related protein N-terminus
      pfam09532
      Location:199 → 300
      FDF; FDF domain
      pfam16598
      Location:104 → 197
      Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

    2. NM_001142444.3 → NP_001135916.1  enhancer of mRNA-decapping protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001135916.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-4 encode the same isoform (1).
      Source sequence(s)
      AF193058, AK024781, AL133447, CA440205, DA168050, DB007958
      Consensus CDS
      CCDS10267.1
      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797
      Related
      ENSP00000455580.1, ENST00000568176.5
      Conserved Domains (4) summary
      cd01737
      Location:2 → 66
      LSm16_N; Like-Sm protein 16, N-terminal domain
      pfam03853
      Location:302 → 455
      YjeF_N; YjeF-related protein N-terminus
      pfam09532
      Location:199 → 300
      FDF; FDF domain
      pfam16598
      Location:104 → 197
      Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

    3. NM_001351378.2 → NP_001338307.1  enhancer of mRNA-decapping protein 3 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1-4 encode the same isoform (1).
      Source sequence(s)
      AC091230, AC100835, BC011534
      Consensus CDS
      CCDS10267.1
      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797
      Related
      ENSP00000497737.1, ENST00000647659.1
      Conserved Domains (4) summary
      cd01737
      Location:2 → 66
      LSm16_N; Like-Sm protein 16, N-terminal domain
      pfam03853
      Location:302 → 455
      YjeF_N; YjeF-related protein N-terminus
      pfam09532
      Location:199 → 300
      FDF; FDF domain
      pfam16598
      Location:104 → 197
      Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

    4. NM_001351379.2 → NP_001338308.1  enhancer of mRNA-decapping protein 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AC091230, AC100835, BC011534
      Conserved Domains (3) summary
      pfam03853
      Location:157 → 310
      YjeF_N; YjeF-related protein N-terminus
      pfam09532
      Location:54 → 155
      FDF; FDF domain
      pfam16598
      Location:1 → 52
      Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

    5. NM_025083.5 → NP_079359.2  enhancer of mRNA-decapping protein 3 isoform 1

      See identical proteins and their annotated locations for NP_079359.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-4 encode the same isoform (1).
      Source sequence(s)
      AC091230, BC011534
      Consensus CDS
      CCDS10267.1
      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797
      Related
      ENSP00000320503.4, ENST00000315127.9
      Conserved Domains (4) summary
      cd01737
      Location:2 → 66
      LSm16_N; Like-Sm protein 16, N-terminal domain
      pfam03853
      Location:302 → 455
      YjeF_N; YjeF-related protein N-terminus
      pfam09532
      Location:199 → 300
      FDF; FDF domain
      pfam16598
      Location:104 → 197
      Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      74630558..74696024 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450077.2 → XP_024305845.1  enhancer of mRNA-decapping protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797
      Conserved Domains (4) summary
      cd01737
      Location:2 → 66
      LSm16_N; Like-Sm protein 16, N-terminal domain
      pfam03853
      Location:302 → 455
      YjeF_N; YjeF-related protein N-terminus
      pfam09532
      Location:199 → 300
      FDF; FDF domain
      pfam16598
      Location:104 → 197
      Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

    2. XM_047433143.1 → XP_047289099.1  enhancer of mRNA-decapping protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797

    3. XM_024450079.2 → XP_024305847.1  enhancer of mRNA-decapping protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797
      Conserved Domains (4) summary
      cd01737
      Location:2 → 66
      LSm16_N; Like-Sm protein 16, N-terminal domain
      pfam03853
      Location:302 → 455
      YjeF_N; YjeF-related protein N-terminus
      pfam09532
      Location:199 → 300
      FDF; FDF domain
      pfam16598
      Location:104 → 197
      Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

    4. XM_011522092.4 → XP_011520394.1  enhancer of mRNA-decapping protein 3 isoform X2

      Conserved Domains (3) summary
      pfam03853
      Location:119 → 272
      YjeF_N; YjeF-related protein N-terminus
      pfam09532
      Location:16 → 117
      FDF; FDF domain
      pfam16598
      Location:1 → 14
      Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      72500459..72565921 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378917.1 → XP_054234892.1  enhancer of mRNA-decapping protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797

    2. XM_054378918.1 → XP_054234893.1  enhancer of mRNA-decapping protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797

    3. XM_054378919.1 → XP_054234894.1  enhancer of mRNA-decapping protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KPH0, D3DW61, Q96F86, Q9H797

    4. XM_054378920.1 → XP_054234895.1  enhancer of mRNA-decapping protein 3 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96F86.1 GenPept UniProtKB/Swiss-Prot:Q96F86

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