UPF2 Gene (Protein Coding)

UPF2 Regulator Of Nonsense Mediated MRNA Decay

GC10M011920
GIFtS:
41
This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. 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 pr... See more...

Aliases for UPF2 Gene

Aliases for UPF2 Gene

  • UPF2 Regulator Of Nonsense Mediated MRNA Decay 2 3 5
  • RENT2 2 3 4
  • Regulator Of Nonsense Transcripts 2 3 4
  • Up-Frameshift Suppressor 2 Homolog 3 4
  • Nonsense MRNA Reducing Factor 2 3 4
  • KIAA1408 2 4
  • Smg-3 2 3
  • Smg-3 Homolog, Nonsense Mediated MRNA Decay Factor (C. Elegans) 2
  • UPF2 Regulator Of Nonsense Transcripts Homolog (Yeast) 2
  • Smg-3 Homolog, Nonsense Mediated MRNA Decay Factor 3
  • UPF2, Regulator Of Nonsense Mediated MRNA Decay 2
  • UPF2 Regulator Of Nonsense Transcripts Homolog 3
  • FRS2/UPF2/LEMD3 Fusion 3
  • Yeast Upf2p Homolog 3
  • LEMD3/UPF2 Fusion 3
  • DKFZP434D222 2
  • HUPF2 3
  • HUpf2 4
  • UPF2 5

External Ids for UPF2 Gene

Previous GeneCards Identifiers for UPF2 Gene

  • GC10M011925
  • GC10M012112
  • GC10M011966
  • GC10M012002
  • GC10M011879
  • GC10M011962

Summaries for UPF2 Gene

Entrez Gene Summary for UPF2 Gene

  • This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. 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 is located in the perinuclear area. It interacts with translation release factors and the proteins that are functional homologs of yeast Upf1p and Upf3p. Two splice variants have been found for this gene; both variants encode the same protein. [provided by RefSeq, Jul 2008]

GeneCards Summary for UPF2 Gene

UPF2 (UPF2 Regulator Of Nonsense Mediated MRNA Decay) is a Protein Coding gene. Diseases associated with UPF2 include Pancreatic Adenosquamous Carcinoma and Metaphyseal Chondrodysplasia, Schmid Type. Among its related pathways are Viral mRNA Translation and mRNA surveillance pathway. Gene Ontology (GO) annotations related to this gene include RNA binding and binding.

UniProtKB/Swiss-Prot Summary for UPF2 Gene

  • Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC). Recruited by UPF3B associated with the EJC core at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF3B stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA.

Gene Wiki entry for UPF2 Gene

Additional gene information for UPF2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for UPF2 Gene

Genomics for UPF2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for UPF2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around UPF2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for UPF2

Top Transcription factor binding sites by QIAGEN in the UPF2 gene promoter:
  • Egr-1
  • MZF-1
  • Pax-5
  • POU2F1
  • POU2F1a

Genomic Locations for UPF2 Gene

Latest Assembly
chr10:11,920,022-12,043,170
(GRCh38/hg38)
Size:
123,149 bases
Orientation:
Minus strand

Previous Assembly
chr10:11,962,021-12,085,169
(GRCh37/hg19 by Entrez Gene)
Size:
123,149 bases
Orientation:
Minus strand

chr10:11,962,021-12,085,169
(GRCh37/hg19 by Ensembl)
Size:
123,149 bases
Orientation:
Minus strand

Genomic View for UPF2 Gene

Genes around UPF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UPF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UPF2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for UPF2 Gene

Proteins for UPF2 Gene

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  • Protein details for UPF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HAU5-RENT2_HUMAN
    Recommended name:
    Regulator of nonsense transcripts 2
    Protein Accession:
    Q9HAU5
    Secondary Accessions:
    • A6NLJ5
    • D3DRS0
    • Q14BM1
    • Q5W0J4
    • Q8N8U1
    • Q9H1J2
    • Q9NWL1
    • Q9P2D9
    • Q9Y4M9

    Protein attributes for UPF2 Gene

    Size:
    1272 amino acids
    Molecular mass:
    147810 Da
    Quaternary structure:
    • Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC). Interacts with SMG1, EST1A, UPF1, UPF3A, UPF3B, EIF4A1 and EIF1.
    SequenceCaution:
    • Sequence=BAA92646.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAC04721.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for UPF2 Gene

neXtProt entry for UPF2 Gene

Protein Expression for UPF2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for UPF2 Gene

  • Ubiquitination at Lys397
  • Modification sites at PhosphoSitePlus

Other Protein References for UPF2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for UPF2 Gene

Domains & Families for UPF2 Gene

Gene Families for UPF2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for UPF2 Gene

InterPro:
Blocks:
  • Initiation factor eIF-4 gamma, middle

Suggested Antigen Peptide Sequences for UPF2 Gene

GenScript: Design optimal peptide antigens:
  • UPF2 protein (Q5BKV2_HUMAN)
  • Up-frameshift suppressor 2 homolog (RENT2_HUMAN)
genes like me logo Genes that share domains with UPF2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for UPF2 Gene

Function for UPF2 Gene

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  6. Cell Lines for research

Molecular function for UPF2 Gene

UniProtKB/Swiss-Prot Function:
Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC). Recruited by UPF3B associated with the EJC core at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF3B stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA.

Phenotypes From GWAS Catalog for UPF2 Gene

Gene Ontology (GO) - Molecular Function for UPF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 11163187
GO:0042162 telomeric DNA binding IDA 17916692
genes like me logo Genes that share ontologies with UPF2: view
genes like me logo Genes that share phenotypes with UPF2: view

Animal Models for UPF2 Gene

MGI Knock Outs for UPF2:
  • Upf2 Upf2<tm1.1Btp>

Animal Models for research

miRNA for UPF2 Gene

miRTarBase miRNAs that target UPF2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for UPF2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for UPF2 Gene

Localization for UPF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for UPF2 Gene

Cytoplasm, perinuclear region.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for UPF2 gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytoplasmic bodies (3)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for UPF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 14636577
GO:0005737 cytoplasm IDA 14636577
GO:0005829 cytosol TAS --
GO:0005844 polysome IBA 21873635
GO:0035145 exon-exon junction complex IBA,IDA 16601204
genes like me logo Genes that share ontologies with UPF2: view

Pathways & Interactions for UPF2 Gene

genes like me logo Genes that share pathways with UPF2: view

Pathways by source for UPF2 Gene

2 KEGG pathways for UPF2 Gene
1 Cell Signaling Technology pathway for UPF2 Gene

Gene Ontology (GO) - Biological Process for UPF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IBA,TAS 16488880
GO:0001889 liver development IEA --
GO:0006406 mRNA export from nucleus TAS 16488880
GO:0031100 animal organ regeneration IEA --
genes like me logo Genes that share ontologies with UPF2: view

No data available for SIGNOR curated interactions for UPF2 Gene

Drugs & Compounds for UPF2 Gene

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(1) Drugs for UPF2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for UPF2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with UPF2: view

Transcripts for UPF2 Gene

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mRNA/cDNA for UPF2 Gene

2 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for UPF2

Alternative Splicing Database (ASD) splice patterns (SP) for UPF2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^
SP1:
SP2: - - - - - - - - - - - - - - - -
SP3: -

ExUns: 25
SP1:
SP2:
SP3:

Relevant External Links for UPF2 Gene

GeneLoc Exon Structure for
UPF2

Expression for UPF2 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for UPF2 Gene

mRNA expression in normal human tissues for UPF2 Gene
mRNA expression by BioGPS for UPF2 GenemRNA expression by GTEx for UPF2 Gene

Protein differential expression in normal tissues from HIPED for UPF2 Gene

This gene is overexpressed in Lymph node (7.1), Peripheral blood mononuclear cells (7.1), and CD8 Tcells (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for UPF2 Gene



Protein tissue co-expression partners for UPF2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for UPF2

SOURCE GeneReport for Unigene cluster for UPF2 Gene:

Hs.370689

mRNA Expression by UniProt/SwissProt for UPF2 Gene:

Q9HAU5-RENT2_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for UPF2 Gene

  • Nervous system(4.5)
  • Heart(4.4)
  • Blood(2.6)
  • Muscle(2.3)
  • Kidney(2.3)
  • Liver(2.2)
  • Spleen(2.1)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with UPF2: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for UPF2 Gene

Orthologs for UPF2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for UPF2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia UPF2 29 30
  • 99.74 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia UPF2 30
  • 95 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia UPF2 29 30
  • 93.86 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia UPF2 29 30
  • 93.55 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Upf2 29
  • 92.01 (n)
Mouse
(Mus musculus)
 Mammalia Upf2 29 16 30
  • 91.67 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 30
  • 91 (a)
 OneToMany
-- 30
  • 91 (a)
 OneToMany
-- 30
  • 91 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves UPF2 29 30
  • 85.05 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia UPF2 30
  • 92 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia upf2 29
  • 76.69 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.14937 29
Zebrafish
(Danio rerio)
 Actinopterygii upf2 29 30
  • 70.48 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP000337 29
  • 48.48 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta Upf2 29 30
  • 48.36 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea smg-3 30
  • 27 (a)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes NMD2 29 30 32 32
  • 45.79 (n)
 OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0D13156g 29
  • 44.51 (n)
A. gosspyii yeast
(Eremothecium gossypii)
 Saccharomycetes AGOS_AGR364C 29
  • 42.54 (n)
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT2G39260 29
  • 51.66 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 30
  • 52 (a)
 OneToMany
-- 30
  • 48 (a)
 OneToMany
Bread mold
(Neurospora crassa)
 Ascomycetes NCU05267 29
  • 48.36 (n)
Fission Yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes upf2 29
  • 44.8 (n)
Species where no ortholog for UPF2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for UPF2 Gene

ENSEMBL:
Gene Tree for UPF2 (if available)
TreeFam:
Gene Tree for UPF2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for UPF2: view image
Alliance of Genome Resources:
Additional Orthologs for UPF2

Paralogs for UPF2 Gene

No data available for Paralogs for UPF2 Gene

Variants for UPF2 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for UPF2 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
996716 Association: Autism spectrum disorder 12,035,333(-) C/A
NM_015542.4(UPF2):c.91G>T (p.Val31Leu) 		MISSENSE
rs118004016 Likely Benign: not provided 12,001,769(-) C/G
NM_015542.4(UPF2):c.1561G>C (p.Glu521Gln) 		MISSENSE
rs1215786588 Likely Benign: not provided 11,929,857(-) T/A
NM_015542.4(UPF2):c.3809+8A>T 		INTRON
rs1260428708 Likely Benign: not provided 11,929,858(-) G/A
NM_015542.4(UPF2):c.3809+7C>T 		INTRON
rs142327199 Benign: not provided 11,959,276(-) G/A
NM_015542.4(UPF2):c.2265C>T (p.Cys755=) 		SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for UPF2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for UPF2 Gene

Variant ID Type Subtype PubMed ID
dgv37n21 CNV gain 19592680
dgv955n54 CNV loss 21841781
nsv1035894 CNV gain 25217958
nsv1119784 CNV deletion 24896259
nsv473140 CNV novel sequence insertion 20440878
nsv523183 CNV gain 19592680
nsv831785 CNV gain 17160897

Variation tolerance for UPF2 Gene

Residual Variation Intolerance Score: 1.64% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.62; 56.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for UPF2 Gene

Human Gene Mutation Database (HGMD)
UPF2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
UPF2
Leiden Open Variation Database (LOVD)
UPF2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UPF2 Gene

Disorders for UPF2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for UPF2 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search UPF2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for UPF2

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with UPF2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for UPF2 Gene

Publications for UPF2 Gene

  1. Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4). (PMID: 11113196) Serin G … Maquat LE (Molecular and cellular biology 2001) 2 3 4 22
  2. NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity. (PMID: 18066079) Chamieh H … Le Hir H (Nature structural & molecular biology 2008) 3 4 22
  3. Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. (PMID: 16452507) Kashima I … Ohno S (Genes & development 2006) 3 4 22
  4. Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. (PMID: 16209946) Gehring NH … Kulozik AE (Molecular cell 2005) 3 4 22
  5. The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. (PMID: 15004547) Kadlec J … Cusack S (Nature structural & molecular biology 2004) 3 4 22

ExternalLinks

View latest publications for UPF2 gene in Mastermind

Products for UPF2 Gene

  • Addgene plasmids for UPF2

Sources for UPF2 Gene