UPF3B UPF3B regulator of nonsense mediated mRNA decay [Homo sapiens (human)] - Gene

Summary

Official Symbol: UPF3Bprovided by HGNC
Official Full Name: UPF3B regulator of nonsense mediated mRNA decayprovided by HGNC
Primary source: HGNC:HGNC:20439
See related: Ensembl:ENSG00000125351 MIM:300298; AllianceGenome:HGNC:20439
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MRX62; MRX82; UPF3X; HUPF3B; MRXS14; RENT3B; UPF3BP1; UPF3BP2; UPF3BP3; Upf3p-X
Summary: This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome X. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in lymph node (RPKM 5.0), brain (RPKM 4.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xq24

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (119805311..119852963, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (118180438..118228084, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (118967985..118986926, complement)

Chromosome X - NC_000023.11 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nonsense mediated decay factor UPF3B is associated with cMyBP-C haploinsufficiency in hypertrophic cardiomyopathy patients.
Title: Nonsense mediated decay factor UPF3B is associated with cMyBP-C haploinsufficiency in hypertrophic cardiomyopathy patients.
Up-Frameshift Suppressor 3 as a prognostic biomarker and correlated with immune infiltrates: A pan-cancer analysis.
Title: Up-Frameshift Suppressor 3 as a prognostic biomarker and correlated with immune infiltrates: A pan-cancer analysis.
Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation.
Title: Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation.
Mammalian UPF3A and UPF3B can activate nonsense-mediated mRNA decay independently of their exon junction complex binding.
Title: Mammalian UPF3A and UPF3B can activate nonsense-mediated mRNA decay independently of their exon junction complex binding.
Human UPF3A and UPF3B enable fault-tolerant activation of nonsense-mediated mRNA decay.
Title: Human UPF3A and UPF3B enable fault-tolerant activation of nonsense-mediated mRNA decay.
A synonymous UPF3B variant causing a speech disorder implicates NMD as a regulator of neurodevelopmental disorder gene networks.
Title: A synonymous UPF3B variant causing a speech disorder implicates NMD as a regulator of neurodevelopmental disorder gene networks.
RNAseq studies reveal that depletion of ICE1 globally enhances accumulation and stability of NMD-target mRNAs. Further, our data suggest that ICE1 uses a putative MIF4G domain to interact with exon junction complex (EJC) proteins and promotes the association of the NMD protein UPF3B with the EJC.
Title: ICE1 promotes the link between splicing and nonsense-mediated mRNA decay.
The authors discovered that UPF3B (i) interacts with the release factors, (ii) delays translation termination and (iii) dissociates post-termination ribosomal complexes that are devoid of the nascent peptide.
Title: Dual function of UPF3B in early and late translation termination.
UPF3B gene mutation is associated with Lujan-Fryns syndrome.
Title: Tentative clinical diagnosis of Lujan-Fryns syndrome--A conglomeration of different genetic entities?
the neurodevelopmental phenotype of UPF3B missense mutation is caused by impairment of nonsense-mediated mRNA decay pathway function altering neuronal differentiation.
Title: Full UPF3B function is critical for neuronal differentiation of neural stem cells.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Syndromic X-linked intellectual disability 14 MedGen: C1970822 OMIM: 300676 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2021-02-09) ClinGen Genome Curation PagePubMed Triplosensitivity No evidence available (Last evaluated 2021-02-09) ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of UPF3 regulator of nonsense transcripts homolog B (UPF3B) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify UPF3 regulator of nonsense transcripts homolog B (UPF3B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify UPF3 regulator of nonsense transcripts homolog B (UPF3B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify UPF3 regulator of nonsense transcripts homolog B (UPF3B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify UPF3 regulator of nonsense transcripts homolog B (UPF3B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH47685 (e-PCR)
- UniSTS:78883

D8S2279 (e-PCR)
- UniSTS:473907

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in brain development	IEA Inferred from Electronic Annotation more info
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in neuron projection development	IEA Inferred from Electronic Annotation more info
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	IDA Inferred from Direct Assay more info	PubMed
involved_in 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	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of mRNA cis splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of translation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of translation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in centriolar satellite	IDA Inferred from Direct Assay more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	NAS Non-traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
part_of exon-exon junction complex	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: regulator of nonsense transcripts 3B

Names: UPF3 regulator of nonsense transcripts homolog B; UPF3B pseudogene 1; UPF3B pseudogene 2; UPF3B pseudogene 3; nonfunctional UPF3B regulator of nonsense mediated mRNA decay; nonsense mRNA reducing factor 3B; up-frameshift suppressor 3 homolog B; up-frameshift suppressor 3 homolog on chromosome X

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.

Genomic

NG_009241.2 RefSeqGene

Range

5000..23941

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_023010.4 → NP_075386.1 regulator of nonsense transcripts 3B isoform 2

See identical proteins and their annotated locations for NP_075386.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate coding segment, compared to variant 1, and encodes the shorter protein (isoform 2).

Source sequence(s)

AC002477, AY013251, BC121017

Consensus CDS

CCDS14587.1

UniProtKB/TrEMBL

B3KSJ3

Related

ENSP00000245418.2, ENST00000345865.6

Conserved Domains (1) summary

cd12728
Location:50 → 137

RRM_like_Smg4_UPF3B; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B)
NM_080632.3 → NP_542199.1 regulator of nonsense transcripts 3B isoform 1

See identical proteins and their annotated locations for NP_542199.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer protein (isoform 1), also known as hUpf3-X.

Source sequence(s)

AA657616, AF318576, BC121017

Consensus CDS

CCDS14588.1

UniProtKB/Swiss-Prot

D3DWI3, D3DWI4, Q0VAK8, Q9BZI7, Q9H1J0

UniProtKB/TrEMBL

B3KSJ3

Related

ENSP00000276201.3, ENST00000276201.7

Conserved Domains (1) summary

cd12728
Location:50 → 137

RRM_like_Smg4_UPF3B; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B)