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Aliases for UPF3B Gene

Aliases for UPF3B Gene

  • UPF3 Regulator Of Nonsense Transcripts Homolog B (Yeast) 2 3 5
  • Up-Frameshift Suppressor 3 Homolog On Chromosome X 3 4
  • Up-Frameshift Suppressor 3 Homolog B 3 4
  • Nonsense MRNA Reducing Factor 3B 3 4
  • Mental Retardation, X-Linked 62 2 3
  • UPF3B Pseudogene 1 2 3
  • UPF3B Pseudogene 2 2 3
  • UPF3B Pseudogene 3 2 3
  • HUPF3B 3 4
  • RENT3B 3 4
  • UPF3X 3 4
  • Regulator Of Nonsense Transcripts 3B 3
  • HUpf3p-X 4
  • Upf3p-X 3
  • UPF3BP1 3
  • UPF3BP2 3
  • UPF3BP3 3
  • MRXS14 3
  • MRX62 3

External Ids for UPF3B Gene

Previous HGNC Symbols for UPF3B Gene

  • MRX62
  • UPF3BP1
  • UPF3BP2
  • UPF3BP3

Previous GeneCards Identifiers for UPF3B Gene

  • GC0XM113785
  • GC0XM115953
  • GC0XM116943
  • GC0XM117722
  • GC0XM118749
  • GC0XM118852
  • GC0XM118967
  • GC0XM108461

Summaries for UPF3B Gene

Entrez Gene Summary for UPF3B Gene

  • 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 X. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for UPF3B Gene

UPF3B (UPF3 Regulator Of Nonsense Transcripts Homolog B (Yeast)) is a Protein Coding gene. Diseases associated with UPF3B include Non-Syndromic X-Linked Intellectual Disability and Lujan-Fryns Syndrome. Among its related pathways are Transport of Mature Transcript to Cytoplasm and mRNA Splicing - Major Pathway. GO annotations related to this gene include poly(A) RNA binding and mRNA binding. An important paralog of this gene is UPF3A.

UniProtKB/Swiss-Prot for UPF3B Gene

  • Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 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 UPF2 stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA upstream of exon-exon junctions. In vitro, stimulates translation; the function is independent of association with UPF2 and components of the EJC core.

Gene Wiki entry for UPF3B Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UPF3B Gene

Genomics for UPF3B Gene

Regulatory Elements for UPF3B Gene

Enhancers for UPF3B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XF120750 1.6 FANTOM5 Ensembl ENCODE 21.7 -900.6 -900603 5.3 HDGF PKNOX1 ATF1 ARID4B SIN3A FEZF1 ZNF48 ZNF121 GLIS2 ZNF766 NKAPP1 LINC01402 UPF3B LOC100128546 PA2G4P1
GH0XF119887 1.1 Ensembl ENCODE 25.8 -35.1 -35073 1.0 ZNF76 ARID4B SIN3A ZNF2 RAD21 ZNF121 GLIS2 KLF7 EGR2 ZNF263 UPF3B NKAPP1 LINC01402 CXorf56 GC0XP119888 GC0XP119891
GH0XF119808 0.9 ENCODE 25.3 +43.9 43858 0.9 HDAC1 PKNOX1 CBX3 ATF1 ARNT TBL1XR1 CHAMP1 GATA2 SIRT6 FOS UPF3B LOC100422368 RPL39
GH0XF119851 1 ENCODE 21.8 +0.1 80 2.2 PKNOX1 ATF1 CREB3L1 ZNF493 SIN3A BRCA1 ETS1 YY1 GLIS2 ZNF143 UPF3B RPL39 NKAPP1 LOC100422368
GH0XF119466 1.1 ENCODE 19.5 +383.8 383820 4.6 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 SP3 NFYC REST SLC25A43 UPF3B CXorf56 ENSG00000237903 RNU1-67P RHOXF1 NKAPP1 NKRF LINC01402 ZCCHC12
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around UPF3B on UCSC Golden Path with GeneCards custom track

Promoters for UPF3B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000261309 228 2400 PKNOX1 ATF1 CREB3L1 ZNF493 SIN3A BRCA1 ETS1 YY1 GLIS2 ZNF143

Genomic Location for UPF3B Gene

Chromosome:
X
Start:
119,805,311 bp from pter
End:
119,853,028 bp from pter
Size:
47,718 bases
Orientation:
Minus strand

Genomic View for UPF3B Gene

Genes around UPF3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UPF3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UPF3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UPF3B Gene

Proteins for UPF3B Gene

  • Protein details for UPF3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BZI7-REN3B_HUMAN
    Recommended name:
    Regulator of nonsense transcripts 3B
    Protein Accession:
    Q9BZI7
    Secondary Accessions:
    • D3DWI3
    • D3DWI4
    • Q0VAK8
    • Q9H1J0

    Protein attributes for UPF3B Gene

    Size:
    483 amino acids
    Molecular mass:
    57762 Da
    Quaternary structure:
    • Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC); the EJC core components EIF4A3 and the MAGOH-RBM8A dimer form a composite binding site for UPF3B which overlaps with the EJC binding site for WIBG. Interacts with EST1A, UPF2 and RBM8A.

    Three dimensional structures from OCA and Proteopedia for UPF3B Gene

    Alternative splice isoforms for UPF3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for UPF3B Gene

Post-translational modifications for UPF3B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for UPF3B Gene

Domains & Families for UPF3B Gene

Gene Families for UPF3B Gene

Protein Domains for UPF3B Gene

Suggested Antigen Peptide Sequences for UPF3B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BZI7

UniProtKB/Swiss-Prot:

REN3B_HUMAN :
  • Belongs to the RENT3 family.
Family:
  • Belongs to the RENT3 family.
genes like me logo Genes that share domains with UPF3B: view

Function for UPF3B Gene

Molecular function for UPF3B 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) and serving as link between the EJC core and NMD machinery. Recruits UPF2 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 UPF2 stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA upstream of exon-exon junctions. In vitro, stimulates translation; the function is independent of association with UPF2 and components of the EJC core.

Gene Ontology (GO) - Molecular Function for UPF3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003723 RNA binding IEA --
GO:0003729 mRNA binding IDA 11546873
GO:0005487 nucleocytoplasmic transporter activity NAS 11163187
GO:0005515 protein binding IPI 11163187
genes like me logo Genes that share ontologies with UPF3B: view
genes like me logo Genes that share phenotypes with UPF3B: view

Human Phenotype Ontology for UPF3B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for UPF3B Gene

miRTarBase miRNAs that target UPF3B

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for UPF3B Gene

Localization for UPF3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for UPF3B Gene

Nucleus. Cytoplasm. Note=Shuttling between the nucleus and the cytoplasm.

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 UPF3B gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 4
mitochondrion 1

Gene Ontology (GO) - Cellular Components for UPF3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS,IDA 11163187
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm NAS,IDA 11163187
GO:0005815 microtubule organizing center IDA --
genes like me logo Genes that share ontologies with UPF3B: view

Pathways & Interactions for UPF3B Gene

genes like me logo Genes that share pathways with UPF3B: view

Gene Ontology (GO) - Biological Process for UPF3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS --
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006405 RNA export from nucleus TAS --
GO:0006406 mRNA export from nucleus TAS --
genes like me logo Genes that share ontologies with UPF3B: view

No data available for SIGNOR curated interactions for UPF3B Gene

Transcripts for UPF3B Gene

Unigene Clusters for UPF3B Gene

UPF3 regulator of nonsense transcripts homolog B (yeast):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for UPF3B Gene

No ASD Table

Relevant External Links for UPF3B Gene

GeneLoc Exon Structure for
UPF3B
ECgene alternative splicing isoforms for
UPF3B

Expression for UPF3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for UPF3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for UPF3B Gene

This gene is overexpressed in Lung (23.7), Peripheral blood mononuclear cells (7.7), and Testis (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for UPF3B Gene



Protein tissue co-expression partners for UPF3B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of UPF3B Gene:

UPF3B

SOURCE GeneReport for Unigene cluster for UPF3B Gene:

Hs.103832

mRNA Expression by UniProt/SwissProt for UPF3B Gene:

Q9BZI7-REN3B_HUMAN
Tissue specificity: Expressed in testis, uterus, prostate, heart, muscle, brain, spinal cord and placenta.
genes like me logo Genes that share expression patterns with UPF3B: view

Primer Products

No data available for mRNA differential expression in normal tissues for UPF3B Gene

Orthologs for UPF3B Gene

This gene was present in the common ancestor of animals.

Orthologs for UPF3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia UPF3B 34 35
  • 97.96 (n)
cow
(Bos Taurus)
Mammalia UPF3B 35
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia UPF3B 34 35
  • 93.76 (n)
rat
(Rattus norvegicus)
Mammalia Upf3b 34
  • 87.45 (n)
mouse
(Mus musculus)
Mammalia Upf3b 34 16 35
  • 86.67 (n)
oppossum
(Monodelphis domestica)
Mammalia UPF3B 35
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 69 (a)
OneToMany
-- 35
  • 65 (a)
OneToMany
chicken
(Gallus gallus)
Aves UPF3B 34 35
  • 72.07 (n)
lizard
(Anolis carolinensis)
Reptilia UPF3B 35
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia upf3b 34
  • 62.59 (n)
Str.17708 34
zebrafish
(Danio rerio)
Actinopterygii upf3b 34 35
  • 62.46 (n)
zgc66390 34
fruit fly
(Drosophila melanogaster)
Insecta Upf3 35
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea smg-4 35
  • 24 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2608 35
  • 33 (a)
OneToMany
Species where no ortholog for UPF3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for UPF3B Gene

ENSEMBL:
Gene Tree for UPF3B (if available)
TreeFam:
Gene Tree for UPF3B (if available)

Paralogs for UPF3B Gene

Paralogs for UPF3B Gene

(1) SIMAP similar genes for UPF3B Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for UPF3B Gene

genes like me logo Genes that share paralogs with UPF3B: view

Variants for UPF3B Gene

Sequence variations from dbSNP and Humsavar for UPF3B Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs122468182 Mental retardation, X-linked, syndromic, 14 (MRXS14) [MIM:300676], Pathogenic 119,843,293(-) CAGAA(G/T)ATAGA reference, missense
rs122468181 Pathogenic 119,837,771(-) GAGAT(A/C/T)GAATA reference, synonymous-codon, stop-gained
rs794727881 Pathogenic 119,841,206(-) AGAAA(-/GAAA)AAGAC reference, frameshift-variant
rs143538947 Uncertain significance 119,837,938(+) GCCTA(C/T)GGCGC reference, missense
rs483352765 Uncertain significance 119,841,111(-) TTCCA(C/G)AAAGG reference, missense

Structural Variations from Database of Genomic Variants (DGV) for UPF3B Gene

Variant ID Type Subtype PubMed ID
esv2758888 CNV gain 17122850

Variation tolerance for UPF3B Gene

Residual Variation Intolerance Score: 31.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.16; 23.51% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for UPF3B Gene

Human Gene Mutation Database (HGMD)
UPF3B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
UPF3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UPF3B Gene

Disorders for UPF3B Gene

MalaCards: The human disease database

(4) MalaCards diseases for UPF3B Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
non-syndromic x-linked intellectual disability
  • mrx
lujan-fryns syndrome
  • x-linked mental retardation with marfanoid habitus
fryns syndrome
  • diaphragmatic hernia, abnormal face, and distal limb anomalies
childhood-onset schizophrenia
  • childhood schizophrenia
- elite association - COSMIC cancer census association via MalaCards
Search UPF3B in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

REN3B_HUMAN
  • Mental retardation, X-linked, syndromic, 14 (MRXS14) [MIM:300676]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXS14 patients manifest mental retardation associated with other variable signs such as autistic features, slender build, poor musculature, long, thin face, high-arched palate, high nasal bridge, and pectus deformities. {ECO:0000269 PubMed:17704778}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for UPF3B

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UPF3B
genes like me logo Genes that share disorders with UPF3B: view

No data available for Genatlas for UPF3B Gene

Publications for UPF3B 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 22 64
  2. 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) 2 3 4 22 64
  3. 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 22 64
  4. Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. (PMID: 16601204) Kunz J.B. … Gehring N.H. (RNA 2006) 3 4 22 64
  5. 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 22 64

Products for UPF3B Gene

Sources for UPF3B Gene

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