UPF3A UPF3A regulator of nonsense mediated mRNA decay [Homo sapiens (human)] - Gene

Summary

Official Symbol: UPF3Aprovided by HGNC
Official Full Name: UPF3A regulator of nonsense mediated mRNA decayprovided by HGNC
Primary source: HGNC:HGNC:20332
See related: Ensembl:ENSG00000169062 MIM:605530; AllianceGenome:HGNC:20332
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: UPF3; HUPF3A; RENT3A
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 13. Several splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
Expression: Ubiquitous expression in testis (RPKM 21.9), thyroid (RPKM 13.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q34

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (114281601..114305817)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (113490661..113514877)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (115047076..115071292)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

Genetic compensation response could exist in colorectal cancer: UPF3A upregulates the oncogenic homologue gene SRSF3 expression corresponding to SRSF6 to promote colorectal cancer metastasis.
Title: Genetic compensation response could exist in colorectal cancer: UPF3A upregulates the oncogenic homologue gene SRSF3 expression corresponding to SRSF6 to promote colorectal cancer metastasis.
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.
(Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A.
Title: (Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A.
Study observed that CHERP and its binding partner SR140 are significantly upregulated in human clinical colorectal cancer tissues (CRC) and clarified how CHERP/SR140 exert an oncogenic role in CRC development partially through regulating expression of UPF3A variants.
Title: U2-related proteins CHERP and SR140 contribute to colorectal tumorigenesis via alternative splicing regulation.
Results suggest that UPF3A levels are tightly regulated by a post-transcriptional switch to maintain appropriate levels of NMD substrates in cells containing different levels of UPF3B.
Title: A UPF3-mediated regulatory switch that maintains RNA surveillance.
The Upf complex communicates with the exon-junction complex and triggers nonsense-mediated decay in the cytoplasm.
Title: Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm.
hUpf3a is much less active than hUpf3b to induce NMD and to stimulate translation
Title: Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation.
The complex between the interacting domains of human UPF2 and UPF3b at a 1.95 A resolution.
Title: The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-64094 (e-PCR)
- UniSTS:68889

SHGC-52734 (e-PCR)
- UniSTS:72502

GDB:595856 (e-PCR)
- UniSTS:158036

SHGC-67307 (e-PCR)
- UniSTS:89991

SHGC-132824 (e-PCR)
- UniSTS:173968

G27732 (e-PCR)
- UniSTS:76459

RH17923 (e-PCR)
- UniSTS:89809

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
NOT involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IDA Inferred from Direct Assay 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 translation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
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
part_of exon-exon junction complex	TAS Traceable Author Statement more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in neuron projection	IEA Inferred from Electronic Annotation more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay 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 3A

Names: UPF3 regulator of nonsense transcripts homolog A; hUpf3; nonsense mRNA reducing factor 3A; up-frameshift suppressor 3 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.

Genomic

NG_029528.1 RefSeqGene

Range

5018..29234

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001353644.2 → NP_001340573.1 regulator of nonsense transcripts 3A isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3), as well as variants 4-7, encodes isoform c.

Source sequence(s)

AL160396

UniProtKB/TrEMBL

B3KUE7

Conserved Domains (1) summary

cl28310
Location:89 → 257

Rho; Transcription termination factor Rho [Transcription]
NM_001353645.1 → NP_001340574.1 regulator of nonsense transcripts 3A isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (4), as well as variants 3 and 5-7, encodes isoform c.

Source sequence(s)

AL160396

UniProtKB/TrEMBL

B3KUE7

Conserved Domains (1) summary

cl28310
Location:89 → 257

Rho; Transcription termination factor Rho [Transcription]
NM_001353646.1 → NP_001340575.1 regulator of nonsense transcripts 3A isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (5), as well as variants 3, 4, 6, and 7, encodes isoform c.

Source sequence(s)

AL160396

UniProtKB/TrEMBL

B3KUE7

Conserved Domains (1) summary

cl28310
Location:89 → 257

Rho; Transcription termination factor Rho [Transcription]
NM_001353647.1 → NP_001340576.1 regulator of nonsense transcripts 3A isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (6), as well as variants 3-5 and 7, encodes isoform c.

Source sequence(s)

AL160396

UniProtKB/TrEMBL

B3KUE7

Conserved Domains (1) summary

cl28310
Location:89 → 257

Rho; Transcription termination factor Rho [Transcription]
NM_001353648.2 → NP_001340577.1 regulator of nonsense transcripts 3A isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (7), as well as variants 3-6, encodes isoform c.

Source sequence(s)

AL160396

UniProtKB/TrEMBL

B3KUE7

Conserved Domains (1) summary

cl28310
Location:89 → 257

Rho; Transcription termination factor Rho [Transcription]
NM_001353649.1 → NP_001340578.1 regulator of nonsense transcripts 3A isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (8), as well as variant 9, encodes isoform d.

Source sequence(s)

AL160396

Conserved Domains (1) summary

cl28310
Location:85 → 253

Rho; Transcription termination factor Rho [Transcription]
NM_001353650.1 → NP_001340579.1 regulator of nonsense transcripts 3A isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (9), as well as variant 8, encodes isoform d.

Source sequence(s)

AL160396

Conserved Domains (1) summary

cl28310
Location:85 → 253

Rho; Transcription termination factor Rho [Transcription]
NM_001353651.2 → NP_001340580.1 regulator of nonsense transcripts 3A isoform e

Status: REVIEWED

Source sequence(s)

AL160396

Conserved Domains (1) summary

cd12727
Location:66 → 149

RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
NM_001353652.2 → NP_001340581.1 regulator of nonsense transcripts 3A isoform f

Status: REVIEWED

Source sequence(s)

AL160396

Conserved Domains (1) summary

cd12727
Location:66 → 152

RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
NM_023011.4 → NP_075387.1 regulator of nonsense transcripts 3A isoform hUpf3p

See identical proteins and their annotated locations for NP_075387.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (Upf3p).

Source sequence(s)

AY013250, BC008694, BQ008047

Consensus CDS

CCDS9543.1

UniProtKB/Swiss-Prot

A2A366, Q5T8C3, Q5T8C9, Q7Z6N3, Q86YK1, Q9BZI8, Q9H1J1

Related

ENSP00000364448.3, ENST00000375299.8

Conserved Domains (1) summary

pfam03467
Location:65 → 225

Smg4_UPF3; Smg-4/UPF3 family
NM_080687.3 → NP_542418.1 regulator of nonsense transcripts 3A isoform hUpf3pdelta

See identical proteins and their annotated locations for NP_542418.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to transcript variant 1. The resulting isoform (hUpf3pdelta) lacks an internal segment, compared to isoform hUpf3p.

Source sequence(s)

AY013250, BC023569, BQ008047

Consensus CDS

CCDS9544.1

UniProtKB/Swiss-Prot

Q9H1J1

Related

ENSP00000329592.5, ENST00000351487.5

Conserved Domains (2) summary

cd12727
Location:66 → 149

RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)

cl28310
Location:257 → 440

Rho; Transcription termination factor Rho [Transcription]

RNA

NR_148482.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396, BC047735
NR_148483.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148484.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148485.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148486.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148487.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148488.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148489.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148490.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148491.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148492.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148493.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396

Related

ENST00000475218.2
NR_148494.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148495.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396
NR_148496.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL160396

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000013.11 Reference GRCh38.p14 Primary Assembly

Range

114281601..114305817

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011534844.2 → XP_011533146.1 regulator of nonsense transcripts 3A isoform X1

Conserved Domains (1) summary

cd12727
Location:66 → 150

RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
XM_047430546.1 → XP_047286502.1 regulator of nonsense transcripts 3A isoform X4
XM_047430549.1 → XP_047286505.1 regulator of nonsense transcripts 3A isoform X8
XM_011534846.2 → XP_011533148.1 regulator of nonsense transcripts 3A isoform X3

Conserved Domains (1) summary

pfam03467
Location:65 → 225

Smg4_UPF3; Smg-4/UPF3 family
XM_024449402.2 → XP_024305170.1 regulator of nonsense transcripts 3A isoform X7

Conserved Domains (1) summary

cd12727
Location:66 → 152

RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
XM_024449403.2 → XP_024305171.1 regulator of nonsense transcripts 3A isoform X9

Conserved Domains (1) summary

cd12727
Location:66 → 152

RRM_like_Smg4_UPF3A; RNA recognition motif-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A)
XM_047430547.1 → XP_047286503.1 regulator of nonsense transcripts 3A isoform X5
XM_011534845.3 → XP_011533147.1 regulator of nonsense transcripts 3A isoform X2

See identical proteins and their annotated locations for XP_011533147.1

Conserved Domains (1) summary

cl17169
Location:10 → 95

RRM_SF; RNA recognition motif (RRM) superfamily
XM_047430548.1 → XP_047286504.1 regulator of nonsense transcripts 3A isoform X6

UniProtKB/TrEMBL

B3KUE7
XM_024449401.2 → XP_024305169.1 regulator of nonsense transcripts 3A isoform X6

UniProtKB/TrEMBL

B3KUE7

Conserved Domains (1) summary

cl28310
Location:89 → 257

Rho; Transcription termination factor Rho [Transcription]

Alternate T2T-CHM13v2.0

Genomic

NC_060937.1 Alternate T2T-CHM13v2.0

Range

113490661..113514877

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054374866.1 → XP_054230841.1 regulator of nonsense transcripts 3A isoform X1
XM_054374869.1 → XP_054230844.1 regulator of nonsense transcripts 3A isoform X4
XM_054374873.1 → XP_054230848.1 regulator of nonsense transcripts 3A isoform X8
XM_054374868.1 → XP_054230843.1 regulator of nonsense transcripts 3A isoform X3
XM_054374872.1 → XP_054230847.1 regulator of nonsense transcripts 3A isoform X7
XM_054374874.1 → XP_054230849.1 regulator of nonsense transcripts 3A isoform X10
XM_054374875.1 → XP_054230850.1 regulator of nonsense transcripts 3A isoform X9
XM_054374870.1 → XP_054230845.1 regulator of nonsense transcripts 3A isoform X5
XM_054374867.1 → XP_054230842.1 regulator of nonsense transcripts 3A isoform X2
XM_054374871.1 → XP_054230846.1 regulator of nonsense transcripts 3A isoform X6

UniProtKB/TrEMBL

B3KUE7
XM_054374876.1 → XP_054230851.1 regulator of nonsense transcripts 3A isoform X6

UniProtKB/TrEMBL

B3KUE7