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Aliases for UPF2 Gene

Aliases for UPF2 Gene

  • UPF2 Regulator Of Nonsense Transcripts Homolog (Yeast) 2 3
  • RENT2 3 4 6
  • Up-Frameshift Suppressor 2 Homolog 3 4
  • Nonsense MRNA Reducing Factor 2 3 4
  • HUPF2 3 4
  • Smg-3 Homolog, Nonsense Mediated MRNA Decay Factor 3
  • Nonsense Mediated MRNA Decay Factor (C. Elegans) 2
  • Regulator Of Nonsense Transcripts 2 3
  • Yeast Upf2p Homolog 3
  • Smg-3 Homolog 2
  • KIAA1408 4
  • Smg-3 3

External Ids for UPF2 Gene

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 Transcripts Homolog (Yeast)) is a Protein Coding gene. Among its related pathways are Translational Control and Gene Expression. GO annotations related to this gene include RNA 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UPF2 Gene

Genomics for UPF2 Gene

Genomic Location for UPF2 Gene

Start:
11,920,022 bp from pter
End:
12,043,170 bp from pter
Size:
123,149 bases
Orientation:
Minus strand

Genomic View for UPF2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for UPF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UPF2 Gene

Regulatory Elements 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

Proteomics data for UPF2 Gene at MOPED

Post-translational modifications for UPF2 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys397

Other Protein References for UPF2 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for UPF2 Gene

Domains for UPF2 Gene

Suggested Antigen Peptide Sequences for UPF2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9HAU5

UniProtKB/Swiss-Prot:

RENT2_HUMAN
Domain:
  • Contains 3 MIF4G domains.:
    • Q9HAU5
genes like me logo Genes that share domains with UPF2: view

No data available for Gene Families 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.

Gene Ontology (GO) - Molecular Function for UPF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0005488 binding --
GO:0005515 protein binding IPI 11163187
genes like me logo Genes that share ontologies with UPF2: view

Phenotypes for UPF2 Gene

MGI mutant phenotypes for UPF2:
inferred from 2 alleles
GenomeRNAi human phenotypes for UPF2:
genes like me logo Genes that share phenotypes with UPF2: view

Animal Models for UPF2 Gene

MGI Knock Outs for UPF2:

miRNA for UPF2 Gene

miRTarBase miRNAs that target UPF2

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting 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
Jensen Localization Image for UPF2 Gene COMPARTMENTS Subcellular localization image for UPF2 gene
Compartment Confidence
nucleus 5
cytosol 4
mitochondrion 1

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:0035145 exon-exon junction complex IDA 16601204
GO:0048471 perinuclear region of cytoplasm IEA --
genes like me logo Genes that share ontologies with UPF2: view

Pathways for UPF2 Gene

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

Pathways by source for UPF2 Gene

1 Cell Signaling Technology pathway 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:0010467 gene expression TAS --
GO:0016070 RNA metabolic process --
genes like me logo Genes that share ontologies with UPF2: view

Compounds for UPF2 Gene

(4) Novoseek inferred chemical compound relationships for UPF2 Gene

Compound -log(P) Hits PubMed IDs
nitrobenzylthioinosine 79.1 2
uridine 56 4
nucleoside 52.2 5
purine 32 1
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:

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 for UPF2 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for UPF2 Gene

SOURCE GeneReport for Unigene cluster for UPF2 Gene Hs.370689

mRNA Expression by UniProt/SwissProt for UPF2 Gene

Q9HAU5-RENT2_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expressions with UPF2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues 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 35
  • 99.74 (n)
  • 99.84 (a)
UPF2 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia UPF2 35
  • 93.55 (n)
  • 97.72 (a)
UPF2 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia UPF2 35
  • 93.86 (n)
  • 97.8 (a)
UPF2 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Upf2 35
  • 91.67 (n)
  • 97.16 (a)
Upf2 16
Upf2 36
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia UPF2 36
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 91 (a)
OneToMany
-- 36
  • 91 (a)
OneToMany
-- 36
  • 91 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Upf2 35
  • 92.01 (n)
  • 97.24 (a)
chicken
(Gallus gallus)
Aves UPF2 35
  • 85.05 (n)
  • 93.38 (a)
UPF2 36
  • 92 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia UPF2 36
  • 92 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.14937 35
tropical clawed frog
(Silurana tropicalis)
Amphibia upf2 35
  • 76.69 (n)
  • 86.71 (a)
zebrafish
(Danio rerio)
Actinopterygii upf2 35
  • 70.48 (n)
  • 81.22 (a)
upf2 36
  • 79 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000337 35
  • 48.48 (n)
  • 44.98 (a)
fruit fly
(Drosophila melanogaster)
Insecta Upf2 35
  • 48.36 (n)
  • 42.01 (a)
Upf2 36
  • 36 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea smg-3 36
  • 27 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR364C 35
  • 42.54 (n)
  • 29.15 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NMD2 35
  • 45.79 (n)
  • 28.43 (a)
NMD2 36
  • 23 (a)
OneToOne
NMD2 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D13156g 35
  • 44.51 (n)
  • 29.62 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G39260 35
  • 51.66 (n)
  • 42.69 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU05267 35
  • 48.36 (n)
  • 40.2 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes upf2 35
  • 44.8 (n)
  • 33.08 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 52 (a)
OneToMany
-- 36
  • 48 (a)
OneToMany
Species with no ortholog for UPF2:
  • 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 Sequence Context AA Info Type MAF
rs1009033 -- 11,953,744(+) ACCCT(C/T)AAATC intron-variant
rs1024101 -- 12,032,756(+) aaaGA(C/T)TCTCT intron-variant
rs1043043 -- 11,920,060(-) GAAAT(C/T)TGACC utr-variant-3-prime
rs1110247 -- 11,945,048(-) TATTG(G/T)TCATG intron-variant
rs1141092 -- 12,035,163(-) tcaaa(A/G)aaaaa synonymous-codon, reference

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

Variant ID Type Subtype PubMed ID
nsv894876 CNV Loss 21882294
nsv894879 CNV Gain 21882294
nsv831785 CNV Gain 17160897
nsv523183 CNV Gain 19592680
dgv37n21 CNV Gain 19592680

Relevant External Links for UPF2 Gene

HapMap Linkage Disequilibrium report
UPF2
Human Gene Mutation Database (HGMD)
UPF2

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

Disorders for UPF2 Gene

Relevant External Links for UPF2

Genetic Association Database (GAD)
UPF2
Human Genome Epidemiology (HuGE) Navigator
UPF2
genes like me logo Genes that share disorders with UPF2: view

No data available for UniProtKB/Swiss-Prot 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 L.E. (Mol. Cell. Biol. 2001) 2 3 4 23
  2. Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1. (PMID: 12554878) Chiu S.-Y. … Maquat L.E. (RNA 2003) 3 4 23
  3. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. (PMID: 11163187) Lykke-Andersen J. … Steitz J.A. (Cell 2000) 3 4 23
  4. The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. (PMID: 15004547) Kadlec J. … Cusack S. (Nat. Struct. Mol. Biol. 2004) 3 4 23
  5. 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. (Nat. Struct. Mol. Biol. 2008) 3 4 23

Products for UPF2 Gene

  • Addgene plasmids for UPF2

Sources for UPF2 Gene

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