upf3a UPF3A regulator of nonsense mediated mRNA decay [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: upf3aprovided by ZNC
Official Full Name: UPF3A regulator of nonsense mediated mRNA decayprovided by ZNC
Primary source: ZFIN:ZDB-GENE-060721-2
See related: Ensembl:ENSDARG00000069297 AllianceGenome:ZFIN:ZDB-GENE-060721-2
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: si:dkey-21o13.6
Summary: Predicted to enable telomeric DNA binding activity. Predicted to be involved in positive regulation of translation. Predicted to act upstream of or within mRNA transport and nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Part of protein-containing complex. Orthologous to human UPF3A (UPF3A regulator of nonsense mediated mRNA decay). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 9

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	9	NC_007120.7 (34902137..34915395, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (35092952..35108843, complement)

Chromosome 9 - NC_007120.7 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?

mRNA bearing a premature termination codon (PTC) promptly triggers a genetic compensation response (GCR)that involves Upf3a and components of the COMPASS complex; findings provide a potential mechanistic basis for the GCR, and may help lead to the development of therapeutic strategies that treat missense mutations associated with genetic disorders
Title: PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables telomeric DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within mRNA transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of translation	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: regulator of nonsense transcripts 3A

Names: UPF3 regulator of nonsense transcripts homolog A

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_001202448.1 → NP_001189377.1 regulator of nonsense transcripts 3A

Status: VALIDATED

Source sequence(s)

BX601644

UniProtKB/Swiss-Prot

B0S733

Related

ENSDARP00000114416.1, ENSDART00000139608.3

Conserved Domains (1) summary

pfam03467
Location:43 → 200

Smg4_UPF3; Smg-4/UPF3 family

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_007120.7 Reference GRCz11 Primary Assembly

Range

34902137..34915395 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005167850.4 → XP_005167907.1 regulator of nonsense transcripts 3A isoform X1

UniProtKB/TrEMBL

A0A8M2BFY4

Conserved Domains (1) summary

pfam03467
Location:43 → 200

Smg4_UPF3; Smg-4/UPF3 family
XM_068223438.1 → XP_068079539.1 regulator of nonsense transcripts 3A isoform X2

UniProtKB/Swiss-Prot

B0S733, Q4VBI8

Related

ENSDARP00000091501.5, ENSDART00000100728.5