upf1 UPF1 RNA helicase and ATPase [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: upf1provided by ZNC
Official Full Name: UPF1 RNA helicase and ATPaseprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-2836
See related: Ensembl:ENSDARG00000016302 AllianceGenome:ZFIN:ZDB-GENE-040426-2836
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: NORF1; rent1; zgc:55472; wu:fi40f07; wu:fj48a01
Summary: Predicted to enable RNA binding activity and RNA helicase activity. Involved in chordate embryonic development and nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Acts upstream of or within with a positive effect on positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Acts upstream of or within T cell differentiation in thymus and regulation of gene expression. Predicted to be located in P-body; nucleus; and perinuclear region of cytoplasm. Predicted to be active in cytoplasm. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 2

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (56169420..56235045)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (56045495..56111200)

Chromosome 2 - NC_007113.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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?

Pervasive changes of mRNA splicing in upf1-deficient zebrafish identify rpl10a as a regulator of T cell development.
Title: Pervasive changes of mRNA splicing in upf1-deficient zebrafish identify rpl10a as a regulator of T cell development.

Submit: New GeneRIF Correction

General gene information

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Markers

fi40f07.x1 (e-PCR)
- UniSTS:197472

fj48a01.x1 (e-PCR)
- UniSTS:188607

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within T cell differentiation in thymus	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within T cell differentiation in thymus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chordate embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chordate embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within_positive_effect positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in P-body	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: regulator of nonsense transcripts 1

Names: ATP-dependent helicase RENT1; nonsense mRNA reducing factor 1; up-frameshift suppressor 1 homolog; upf1 regulator of nonsense transcripts homolog

NP_998639.1

EC 3.6.4.-

XP_005163697.1

EC 3.6.4.-

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_213474.1 → NP_998639.1 regulator of nonsense transcripts 1

See identical proteins and their annotated locations for NP_998639.1

Status: PROVISIONAL

Source sequence(s)

BC045353

UniProtKB/TrEMBL

Q7ZVZ4

Related

ENSDARP00000013006.7, ENSDART00000021011.10

Conserved Domains (4) summary

COG1112
Location:124 → 889

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

pfam09416
Location:100 → 251

UPF1_Zn_bind; RNA helicase (UPF2 interacting domain)

pfam13087
Location:660 → 857

AAA_12; AAA domain

pfam13245
Location:457 → 514

AAA_19; Part of AAA domain

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_007113.7 Reference GRCz11 Primary Assembly

Range

56169420..56235045

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005163640.5 → XP_005163697.1 regulator of nonsense transcripts 1 isoform X1

UniProtKB/TrEMBL

A0A8M2BAV2

Conserved Domains (4) summary

COG1112
Location:124 → 888

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

pfam09416
Location:100 → 251

UPF1_Zn_bind; RNA helicase (UPF2 interacting domain)

pfam13087
Location:659 → 856

AAA_12; AAA domain

pfam13245
Location:456 → 513

AAA_19; Part of AAA domain