Upf2 UPF2 regulator of nonsense transcripts homolog (yeast) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Upf2provided by MGI
Official Full Name: UPF2 regulator of nonsense transcripts homolog (yeast)provided by MGI
Primary source: MGI:MGI:2449307
See related: Ensembl:ENSMUSG00000043241 AllianceGenome:MGI:2449307
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Predicted to enable telomeric DNA binding activity. Acts upstream of or within animal organ regeneration and liver development. Predicted to be located in several cellular components, including cytoplasmic ribonucleoprotein granule; cytosol; and perinuclear region of cytoplasm. Predicted to be part of exon-exon junction complex. Predicted to be active in cytoplasm. Is expressed in several structures, including liver; lung; pancreas; spleen; and testis. Orthologous to human UPF2 (UPF2 regulator of nonsense mediated mRNA decay). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in CNS E11.5 (RPKM 6.1), bladder adult (RPKM 4.3) and 23 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 A1; 2 3.62 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (5956218..6061514)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (5951447..6056703)

Chromosome 2 - NC_000068.8 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Progression of the pluripotent epiblast depends upon the NMD factor UPF2.
Title: Progression of the pluripotent epiblast depends upon the NMD factor UPF2.
Immunotherapy for breast cancer using EpCAM aptamer tumor-targeted gene knockdown.
Title: Immunotherapy for breast cancer using EpCAM aptamer tumor-targeted gene knockdown.
UPF2 leads to degradation of dendritically targeted mRNAs to regulate synaptic plasticity and cognitive function.
Title: UPF2 leads to degradation of dendritically targeted mRNAs to regulate synaptic plasticity and cognitive function.
our findings indicate that impaired UPF2-dependent nonsense-mediated decay leads to neurodevelopmental dysfunction
Title: Inhibition of Upf2-Dependent Nonsense-Mediated Decay Leads to Behavioral and Neurophysiological Abnormalities by Activating the Immune Response.
we report that UPF2-mediated nonsense-mediated mRNA decay (NMD) plays an essential role in male germ cells by eliminating ubiquitous genes-derived, longer 3'UTR transcripts, and that this role is independent of its canonical role in degrading "premature termination codon" (PTC)-containing transcripts in somatic cell lineages
Title: UPF2-Dependent Nonsense-Mediated mRNA Decay Pathway Is Essential for Spermatogenesis by Selectively Eliminating Longer 3'UTR Transcripts.
Upon removal of TDRD6, the association of several mRNAs with UPF1 and UPF2 is disturbed, and the long 3' UTR-stimulated but not the downstream exon-exon junction triggered pathway of NMD is impaired.This function depends on TDRD6-promoted assembly of mRNA and decay enzymes in Chromatoid bodies .
Title: Chromatoid Body Protein TDRD6 Supports Long 3' UTR Triggered Nonsense Mediated mRNA Decay.
UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome.
Title: UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome.
Study find that loss of Upf2 during fetal liver development is incompatible with postnatal life due to failure of terminal differentiation. Moreover, deletion of Upf2 in the adult liver results in hepatosteatosis and disruption of liver homeostasis.
Title: UPF2 is a critical regulator of liver development, function and regeneration.
Hematopoietic-specific deletion of Upf2, a core NMD factor, led to the rapid, complete, and lasting cell-autonomous extinction of all hematopoietic stem and progenitor populations.
Title: NMD is essential for hematopoietic stem and progenitor cells and for eliminating by-products of programmed DNA rearrangements.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables telomeric DNA binding	IEA Inferred from Electronic Annotation more info
enables telomeric DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within animal organ regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within liver development	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
involved_in 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to unfolded protein	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic ribonucleoprotein granule	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic ribonucleoprotein granule	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	TAS Traceable Author Statement more info
part_of exon-exon junction complex	IBA Inferred from Biological aspect of Ancestor more info
part_of exon-exon junction complex	IEA Inferred from Electronic Annotation more info
part_of exon-exon junction complex	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: regulator of nonsense transcripts 2

Names: nonsense mRNA reducing factor 2; up-frameshift suppressor 2 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)

NM_001081132.1 → NP_001074601.1 regulator of nonsense transcripts 2

See identical proteins and their annotated locations for NP_001074601.1

Status: PROVISIONAL

Source sequence(s)

AL928735, AL928924, CR388026

Consensus CDS

CCDS38041.1

UniProtKB/Swiss-Prot

A2AT37

Related

ENSMUSP00000058375.7, ENSMUST00000060092.13

Conserved Domains (4) summary

smart00543
Location:569 → 756

MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)

pfam02854
Location:774 → 984

MIF4G; MIF4G domain

pfam04050
Location:1091 → 1215

Upf2; Up-frameshift suppressor 2

cl19727
Location:357 → 420

DUF1451; Zinc-ribbon containing domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

5956218..6061514

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006497486.2 → XP_006497549.1 regulator of nonsense transcripts 2 isoform X2

See identical proteins and their annotated locations for XP_006497549.1

Conserved Domains (3) summary

smart00543
Location:771 → 984

MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)

pfam04050
Location:1086 → 1214

Upf2; Up-frameshift suppressor 2

cl19727
Location:357 → 420

DUF1451; Zinc-ribbon containing domain
XM_006497487.2 → XP_006497550.1 regulator of nonsense transcripts 2 isoform X3

Conserved Domains (3) summary

smart00543
Location:771 → 984

MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)

pfam04050
Location:1086 → 1215

Upf2; Up-frameshift suppressor 2

cl19727
Location:357 → 420

DUF1451; Zinc-ribbon containing domain
XM_006497488.5 → XP_006497551.1 regulator of nonsense transcripts 2 isoform X4

Conserved Domains (2) summary

smart00543
Location:167 → 362

MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)

cl19727
Location:357 → 420

DUF1451; Zinc-ribbon containing domain
XM_006497485.5 → XP_006497548.1 regulator of nonsense transcripts 2 isoform X1

See identical proteins and their annotated locations for XP_006497548.1

UniProtKB/Swiss-Prot

A2AT37

Conserved Domains (4) summary

smart00543
Location:569 → 756

MIF4G; Middle domain of eukaryotic initiation factor 4G (eIF4G)

pfam02854
Location:774 → 984

MIF4G; MIF4G domain

pfam04050
Location:1091 → 1215

Upf2; Up-frameshift suppressor 2

cl19727
Location:357 → 420

DUF1451; Zinc-ribbon containing domain