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Aliases for UPF2 Gene

Aliases for UPF2 Gene

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

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. Among its related pathways are Gene Expression and RNA transport. Gene Ontology (GO) annotations related to this gene include RNA binding and binding.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for UPF2 Gene

Genomics for UPF2 Gene

GeneHancer (GH) Regulatory Elements for UPF2 Gene

Promoters and enhancers for UPF2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10I012040 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 556.7 +0.4 439 4.1 HDGF FOXA2 PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 UPF2 DHTKD1 PROSER2-AS1 USP6NL CAMK1D LOC105376416 GC10M012019
GH10I011897 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20.5 +144.5 144508 2 HDGF FOXA2 PKNOX1 SMAD1 ARNT YY1 POLR2B ZNF766 E2F8 REST PIR36850 PROSER2 UPF2 RNU6-1095P ENSG00000228302 PROSER2-AS1 GC10P011915
GH10I012447 Enhancer 1.5 FANTOM5 Ensembl ENCODE 20.4 -405.7 -405721 2 ATF1 FEZF1 ZNF2 ZNF213 ELK1 FOS ATF7 RUNX3 SP3 JUNB UPF2 CAMK1D ENSG00000228302 ENSG00000252438 BTBD7P1 SEC61A2 GC10M012437 RNU6ATAC39P
GH10I011601 Enhancer 1.4 Ensembl ENCODE dbSUPER 19.8 +439.1 439079 4.7 PKNOX1 FOXA2 MLX ARNT ARID4B FEZF1 ZNF2 IRF4 YY1 ZNF766 UPF2 ENSG00000228302 ENSG00000271360 USP6NL GC10P011559
GH10I012193 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.8 -152.6 -152560 3.7 PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 NUDT5 CDC123 UPF2 SEC61A2 CAMK1D PIR56929
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around UPF2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the UPF2 gene promoter:

Genomic Locations for UPF2 Gene

Genomic Locations for UPF2 Gene
chr10:11,920,022-12,043,172
(GRCh38/hg38)
Size:
123,151 bases
Orientation:
Minus strand
chr10:11,962,021-12,085,169
(GRCh37/hg19)

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 StructureGene Density

RefSeq DNA sequence for UPF2 Gene

Proteins for UPF2 Gene

  • 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=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for UPF2 Gene

    Alternative splice isoforms for UPF2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for UPF2 Gene

Post-translational modifications for UPF2 Gene

Other Protein References for UPF2 Gene

No data available for DME Specific Peptides for UPF2 Gene

Domains & Families for UPF2 Gene

Gene Families for UPF2 Gene

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

Suggested Antigen Peptide Sequences for UPF2 Gene

Graphical View of Domain Structure for InterPro Entry

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

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

Function for UPF2 Gene

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:

Animal Model Products

CRISPR Products

miRNA for UPF2 Gene

miRTarBase miRNAs that target UPF2

Inhibitory RNA Products

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 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 --
GO:0035145 exon-exon junction complex 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

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 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

(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

Unigene Clusters for UPF2 Gene

UPF2 regulator of nonsense transcripts homolog (yeast):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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
ECgene alternative splicing isoforms for
UPF2

Expression for UPF2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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, PaxDb, MaxQB, and MOPED for UPF2 Gene



Protein tissue co-expression partners for UPF2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of UPF2 Gene:

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

  • Heart(4.3)
  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with UPF2: view

Primer Products

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 33 34
  • 99.74 (n)
oppossum
(Monodelphis domestica)
Mammalia UPF2 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia UPF2 33 34
  • 93.86 (n)
cow
(Bos Taurus)
Mammalia UPF2 33 34
  • 93.55 (n)
rat
(Rattus norvegicus)
Mammalia Upf2 33
  • 92.01 (n)
mouse
(Mus musculus)
Mammalia Upf2 33 16 34
  • 91.67 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 91 (a)
OneToMany
-- 34
  • 91 (a)
OneToMany
-- 34
  • 91 (a)
OneToMany
chicken
(Gallus gallus)
Aves UPF2 33 34
  • 85.05 (n)
lizard
(Anolis carolinensis)
Reptilia UPF2 34
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia upf2 33
  • 76.69 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.14937 33
zebrafish
(Danio rerio)
Actinopterygii upf2 33 34
  • 70.48 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000337 33
  • 48.48 (n)
fruit fly
(Drosophila melanogaster)
Insecta Upf2 33 34
  • 48.36 (n)
worm
(Caenorhabditis elegans)
Secernentea smg-3 34
  • 27 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NMD2 34 36 33
  • 45.79 (n)
OneToOne
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D13156g 33
  • 44.51 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR364C 33
  • 42.54 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G39260 33
  • 51.66 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
OneToMany
-- 34
  • 48 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU05267 33
  • 48.36 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes upf2 33
  • 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 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)

Paralogs for UPF2 Gene

No data available for Paralogs for UPF2 Gene

Variants for UPF2 Gene

Sequence variations from dbSNP and Humsavar for UPF2 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs1000033476 -- 11,966,528(-) G/C intron_variant
rs1000036979 -- 11,955,971(-) G/A genic_downstream_transcript_variant, intron_variant
rs1000041471 -- 11,922,462(-) G/A/T genic_downstream_transcript_variant, intron_variant
rs1000071076 -- 11,922,158(-) C/A genic_downstream_transcript_variant, intron_variant
rs1000104765 -- 11,998,595(-) G/A intron_variant

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

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

Disorders for UPF2 Gene

Additional Disease Information for UPF2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for UPF2 Gene.

No data available for MalaCards , 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 58
  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 58
  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 58
  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 58
  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 58

Products for UPF2 Gene

  • Addgene plasmids for UPF2

Sources for UPF2 Gene

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