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

Gene ID: 80153, updated on 6-Jan-2019

Summary

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
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

Genomic context

See EDC3 in Genome Data Viewer
Location:
15q24.1
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 15 NC_000015.10 (74630558..74696434, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74922899..74988386, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene AT-rich interaction domain 3B Neighboring gene VISTA enhancer hs1510 Neighboring gene uncharacterized LOC102723750 Neighboring gene CDC like kinase 3 Neighboring gene CYP1A1 5' regulatory region 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

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, autosomal recessive 50
MedGen: C4225319 OMIM: 616460 GeneReviews: Not available
not available

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Deadenylation-dependent mRNA decay, organism-specific biosystem (from REACTOME)
    Deadenylation-dependent mRNA decay, organism-specific biosystemAfter undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by...
  • Decapping complex, organism-specific biosystem (from KEGG)
    Decapping complex, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • Decapping complex, conserved biosystem (from KEGG)
    Decapping complex, conserved biosystemStructural complex; Genetic information processing; RNA processing
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • RNA degradation, organism-specific biosystem (from KEGG)
    RNA degradation, organism-specific biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • RNA degradation, conserved biosystem (from KEGG)
    RNA degradation, conserved biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • mRNA decay by 5' to 3' exoribonuclease, organism-specific biosystem (from REACTOME)
    mRNA decay by 5' to 3' exoribonuclease, organism-specific biosystemDegradation of mRNA from 5' to 3' occurs in three steps. First, the mRNA is bound at its 3' end by the Lsm1-7 complex. The bound Lsm1-7 may prevent nucleases from accessing the 3' end. Second, the 7-...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ21128, FLJ31777

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphodiesterase decapping endonuclease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
P-body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
membrane HDA PubMed 

General protein information

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)

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
    4993..70488
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142443.2NP_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
    Q96F86
    Related
    ENSP00000401343.3, ENST00000426797.7
    Conserved Domains (4) summary
    cd01737
    Location:266
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199300
    FDF; FDF domain
    pfam16598
    Location:104197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3
  2. NM_001142444.2NP_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)
    AC091230, AF193058, AK024781, AL133447, CA440205, DA168050, DB007958
    Consensus CDS
    CCDS10267.1
    UniProtKB/Swiss-Prot
    Q96F86
    Related
    ENSP00000455580.1, ENST00000568176.5
    Conserved Domains (4) summary
    cd01737
    Location:266
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199300
    FDF; FDF domain
    pfam16598
    Location:104197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3
  3. NM_001351378.1NP_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
    Related
    ENSP00000497737.1, ENST00000647659.1
    Conserved Domains (4) summary
    cd01737
    Location:266
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199300
    FDF; FDF domain
    pfam16598
    Location:104197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3
  4. NM_001351379.1NP_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:157310
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:54155
    FDF; FDF domain
    pfam16598
    Location:152
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3
  5. NM_025083.5NP_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
    Q96F86
    Related
    ENSP00000320503.4, ENST00000315127.8
    Conserved Domains (4) summary
    cd01737
    Location:266
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199300
    FDF; FDF domain
    pfam16598
    Location:104197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p12 Primary Assembly

    Range
    74630558..74696434 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (4) summary
    cd01737
    Location:266
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199300
    FDF; FDF domain
    pfam16598
    Location:104197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3
  2. XM_024450079.1XP_024305847.1  enhancer of mRNA-decapping protein 3 isoform X1

    Conserved Domains (4) summary
    cd01737
    Location:266
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199300
    FDF; FDF domain
    pfam16598
    Location:104197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3
  3. XM_024450078.1XP_024305846.1  enhancer of mRNA-decapping protein 3 isoform X1

    Conserved Domains (4) summary
    cd01737
    Location:266
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199300
    FDF; FDF domain
    pfam16598
    Location:104197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3
  4. XM_011522092.3XP_011520394.1  enhancer of mRNA-decapping protein 3 isoform X2

    Conserved Domains (3) summary
    pfam03853
    Location:119272
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:16117
    FDF; FDF domain
    pfam16598
    Location:114
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3
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