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Aliases for UPF2 Gene

Aliases for UPF2 Gene

  • UPF2 Regulator Of Nonsense Transcripts Homolog (Yeast) 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 3
  • Nonsense Mediated MRNA Decay Factor (C. Elegans) 2
  • Yeast Upf2p Homolog 3
  • Smg-3 Homolog 2
  • 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 Transcripts Homolog (Yeast)) is a Protein Coding gene. Among its related pathways are mRNA surveillance pathway and RNA transport. 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

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

Genomics for UPF2 Gene

Regulatory Elements for UPF2 Gene

Enhancers for UPF2 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around UPF2 on UCSC Golden Path with GeneCards custom track

Promoters for UPF2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around UPF2 on UCSC Golden Path with GeneCards custom track

Genomic Location for UPF2 Gene

Chromosome:
10
Start:
11,920,022 bp from pter
End:
12,043,172 bp from pter
Size:
123,151 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 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

Proteomics data for UPF2 Gene at MOPED

Post-translational modifications for UPF2 Gene

  • Ubiquitination at Lys 397
  • Modification sites at PhosphoSitePlus

Other Protein References for UPF2 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for UPF2 (UPF2)

No data available for DME Specific Peptides for UPF2 Gene

Domains & Families for UPF2 Gene

Suggested Antigen Peptide Sequences for UPF2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9HAU5

UniProtKB/Swiss-Prot:

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

Animal Models for UPF2 Gene

MGI Knock Outs for UPF2:

Animal Model Products

miRNA for UPF2 Gene

miRTarBase miRNAs that target UPF2

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
Jensen Localization Image for UPF2 Gene COMPARTMENTS Subcellular localization image for UPF2 gene
Compartment Confidence
cytosol 5
nucleus 5
mitochondrion 1

Gene Ontology (GO) - Cellular Components for UPF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
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:0001889 liver development 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:

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

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, 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 expression patterns with UPF2: view

Protein tissue co-expression partners for UPF2 Gene

- Elite partner

Primer Products

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
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
chimpanzee
(Pan troglodytes)
Mammalia UPF2 35
  • 99.74 (n)
  • 99.84 (a)
UPF2 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Upf2 35
  • 92.01 (n)
  • 97.24 (a)
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
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
tropical clawed frog
(Silurana tropicalis)
Amphibia upf2 35
  • 76.69 (n)
  • 86.71 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.14937 35
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)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D13156g 35
  • 44.51 (n)
  • 29.62 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NMD2 35
  • 45.79 (n)
  • 28.43 (a)
NMD2 36
  • 23 (a)
OneToOne
NMD2 38
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
rs7079388 - 12,004,547(+) CTTTG(C/T)TGGAC nc-transcript-variant, reference, missense
rs1567029 -- 11,956,130(+) tgaca(C/G)agcga intron-variant, downstream-variant-500B
rs1616880 -- 12,026,283(+) agctt(C/T)agtgc intron-variant
rs1623510 -- 12,015,009(+) AAACA(C/T)CAAAA intron-variant
rs1701474 -- 12,021,379(+) AAAAA(A/T)TTTTT intron-variant

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

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)

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
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UPF2

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 L.E. (Mol. Cell. Biol. 2001) 2 3 4 23 67
  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. (Nat. Struct. Mol. Biol. 2008) 3 23
  3. Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways. (PMID: 18256688) Ivanov P.V. … Kulozik A.E. (EMBO J. 2008) 3 23
  4. 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 Dev. 2006) 3 23
  5. CBP80 promotes interaction of Upf1 with Upf2 during nonsense-mediated mRNA decay in mammalian cells. (PMID: 16186820) Hosoda N. … Maquat L.E. (Nat. Struct. Mol. Biol. 2005) 3 23

Products for UPF2 Gene

Sources for UPF2 Gene

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