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

Summary

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. 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 intellectual developmental disorder 50. Orthologous to human EDC3 (enhancer of mRNA decapping 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 25

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	25	NC_007136.7 (20668640..20691082, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	25	NC_007136.6 (20570978..20593428, complement)

Chromosome 25 - NC_007136.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

fb82d07.x1 (e-PCR)
- UniSTS:191681

fj94e06.y1 (e-PCR)
- UniSTS:200399

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)

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: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007136.7 Reference GRCz11 Primary Assembly

Range

20668640..20691082 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005163054.4 → 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
XM_005163053.4 → 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