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edc3 enhancer of mRNA decapping 3 homolog (S. cerevisiae) [ Danio rerio (zebrafish) ]

Gene ID: 504054, updated on 27-Mar-2024

Summary

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Official Symbol
edc3provided by ZNC
Official Full Name
enhancer of mRNA decapping 3 homolog (S. cerevisiae)provided by ZNC
Primary source
ZFIN:ZDB-GENE-050522-287
See related
Ensembl:ENSDARG00000051931 AllianceGenome:ZFIN:ZDB-GENE-050522-287
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
yjdc; lsm16; im:7151288; wu:fb82d07; zgc:112006
Summary
Predicted to enable 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 cytoplasm. 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]
Orthologs
human mouse all
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Genomic context

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See edc3 in Genome Data Viewer
Location:
chromosome: 25
Exon count:
7
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 25 NC_007136.7 (20668634..20691086, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 25 NC_007136.6 (20570978..20593428, complement)

Chromosome 25 - NC_007136.7Genomic Context describing neighboring genes Neighboring gene complexin 3a Neighboring gene C-terminal Src kinase Neighboring gene KxDL motif containing 1 Neighboring gene ERGIC and golgi 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Coherent but overlapping expression of microRNAs and their targets during vertebrate development. Shkumatava A, et al. Genes Dev, 2009 Feb 15. PMID 19240133, Free PMC Article
  2. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
  3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mRNA binding IEA
Inferred from Electronic Annotation
more info
  
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
  
acts_upstream_of_or_within deadenylation-independent decapping of nuclear-transcribed mRNA IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in P-body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in P-body IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
enhancer of mRNA-decapping protein 3
Names
LSM16 homolog (EDC3, S. cerevisiae)
LSM16 protein homolog
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.

mRNA and Protein(s)

  1. NM_001018126.2 → NP_001018136.2  enhancer of mRNA-decapping protein 3

    Status: VALIDATED

    Source sequence(s)
    BX323018
    UniProtKB/Swiss-Prot
    Q502M5
    UniProtKB/TrEMBL
    A0A8M1N5W4, F1QL27
    Related
    ENSDARP00000067372.3, ENSDART00000067373.5
    Conserved Domains (4) summary
    cd01737
    Location:2 → 66
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:300 → 455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:197 → 298
    FDF; FDF domain
    pfam16598
    Location:104 → 193
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007136.7 Reference GRCz11 Primary Assembly

    Range
    20668634..20691086 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005163054.3 → XP_005163111.1  enhancer of mRNA-decapping protein 3 isoform X2

    UniProtKB/Swiss-Prot
    Q502M5
    UniProtKB/TrEMBL
    A0A8M2BA31
    Conserved Domains (4) summary
    cd01737
    Location:2 → 66
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:278 → 433
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:175 → 276
    FDF; FDF domain
    pfam16598
    Location:104 → 171
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

  2. XM_005163053.3 → XP_005163110.1  enhancer of mRNA-decapping protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q502M5
    UniProtKB/TrEMBL
    A0A8M2BAE2
    Conserved Domains (4) summary
    cd01737
    Location:2 → 66
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:280 → 435
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:177 → 278
    FDF; FDF domain
    pfam16598
    Location:104 → 173
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q502M5.1 GenPept UniProtKB/Swiss-Prot:Q502M5

Gene LinkOut

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