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Edc3 enhancer of mRNA decapping 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 315708, updated on 6-Jun-2024

Summary

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Official Symbol
Edc3provided by RGD
Official Full Name
enhancer of mRNA decapping 3provided by RGD
Primary source
RGD:1306898
See related
Ensembl:ENSRNOG00000019579 AllianceGenome:RGD:1306898
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Lsm16; RGD1306898
Summary
Predicted to enable identical protein binding activity; mRNA binding activity; and phosphodiesterase decapping endonuclease activity. Predicted to be involved in P-body assembly and deadenylation-independent decapping of nuclear-transcribed mRNA. Predicted to be located in cytoplasmic ribonucleoprotein granule. Predicted to be active in P-body. Human ortholog(s) of this gene implicated in autosomal recessive non-syndromic intellectual disability. Orthologous to human EDC3 (enhancer of mRNA decapping 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 92.1), Lung (RPKM 79.2) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Edc3 in Genome Data Viewer
Location:
8q24
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (67002032..67047563)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (58106147..58151685)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (62482126..62527665)

Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene cytochrome P450, family 1, subfamily a, polypeptide 2 Neighboring gene cytochrome P450, family 1, subfamily a, polypeptide 1 Neighboring gene U6 spliceosomal RNA Neighboring gene CDC-like kinase 3 Neighboring gene single stranded DNA binding protein 1, pseudogene 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. 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
  2. Crystal structure of human Edc3 and its functional implications. Ling SH, et al. Mol Cell Biol, 2008 Oct. PMID 18678652, Free PMC Article
  3. The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Jonas S, et al. Genes Dev, 2013 Dec 15. PMID 24352420, Free PMC Article
  4. Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth. Mertz J, et al. Mol Cell Proteomics, 2015 Jul. PMID 25931508, Free PMC Article
  5. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Chen S, et al. Nat Genet, 2018 Jul. PMID 29892012, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in P-body assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in biological_process ND
No biological Data available
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 ISO
Inferred from Sequence Orthology
more info
  

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

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.

mRNA and Protein(s)

  1. NM_001399316.1 → NP_001386245.1  enhancer of mRNA-decapping protein 3

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000008
    UniProtKB/TrEMBL
    F1M7Z1
    Related
    ENSRNOP00000026492.8, ENSRNOT00000026492.8
    Conserved Domains (4) summary
    cd01737
    Location:2 → 64
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam09532
    Location:197 → 298
    FDF; FDF domain
    pfam03853
    Location:300 → 453
    YjeF_N; YjeF-related protein N-terminus
    pfam16598
    Location:100 → 195
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086026.1 Reference GRCr8

    Range
    67002032..67047563
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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