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Aliases for UPF3B Gene

Aliases for UPF3B Gene

  • UPF3 Regulator Of Nonsense Transcripts Homolog B (Yeast) 2 3
  • RENT3B 3 4 6
  • 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
  • HUpf3p-X 3 4
  • HUPF3B 3 4
  • MRXS14 3 6
  • UPF3X 3 4
  • Regulator Of Nonsense Transcripts 3B 3
  • MRX62 3

External Ids for UPF3B Gene

Previous Symbols for UPF3B Gene

  • MRX62

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 schizophrenia. Among its related pathways are Gene Expression and RNA transport. GO annotations related to this gene include nucleotide binding and nucleocytoplasmic transporter activity. 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

Genomic Location for UPF3B Gene

Start:
119,807,043 bp from pter
End:
119,853,028 bp from pter
Size:
45,986 bases
Orientation:
Minus strand

Genomic View for UPF3B Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for UPF3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UPF3B Gene

Regulatory Elements 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

Proteomics data for UPF3B Gene at MOPED

Post-translational modifications for UPF3B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for UPF3B Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for UPF3B Gene

Domains for UPF3B Gene

Protein Domains for UPF3B Gene

UniProtKB/Swiss-Prot:

REN3B_HUMAN
Family:
  • Belongs to the RENT3 family.:
    • Q9BZI7
genes like me logo Genes that share domains with UPF3B: view

No data available for Gene Families for UPF3B Gene

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:0003729 mRNA binding IDA 11546873
GO:0005487 nucleocytoplasmic transporter activity NAS 11163187
GO:0005515 protein binding IPI 11163187
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with UPF3B: view

Phenotypes for UPF3B Gene

GenomeRNAi human phenotypes for UPF3B:
genes like me logo Genes that share phenotypes with UPF3B: view

miRNA for UPF3B Gene

miRTarBase miRNAs that target UPF3B

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting 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
Jensen Localization Image for UPF3B Gene COMPARTMENTS Subcellular localization image for UPF3B gene
Compartment Confidence
nucleus 5
cytosol 4
mitochondrion 1

Gene Ontology (GO) - Cellular Components for UPF3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS 11163187
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm NAS 11163187
GO:0005829 cytosol TAS --
GO:0035145 colocalizes_with exon-exon junction complex IDA 11546873
genes like me logo Genes that share ontologies with UPF3B: view

Pathways 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:0006366 transcription from RNA polymerase II promoter TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006406 mRNA export from nucleus TAS --
genes like me logo Genes that share ontologies with UPF3B: view

Transcripts for UPF3B Gene

Unigene Clusters for UPF3B Gene

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

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 for UPF3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for UPF3B Gene

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 expressions with UPF3B: view

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 36
  • 97.96 (n)
  • 97.96 (a)
UPF3B 37
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia UPF3B 37
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia UPF3B 36
  • 93.76 (n)
  • 95.43 (a)
UPF3B 37
  • 95 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Upf3b 36
  • 86.67 (n)
  • 85.11 (a)
Upf3b 16
Upf3b 37
  • 87 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia UPF3B 37
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 69 (a)
OneToMany
-- 37
  • 65 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Upf3b 36
  • 87.45 (n)
  • 85.74 (a)
chicken
(Gallus gallus)
Aves UPF3B 36
  • 72.07 (n)
  • 71.49 (a)
UPF3B 37
  • 67 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia UPF3B 37
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.17708 36
upf3b 36
  • 62.59 (n)
  • 58.89 (a)
zebrafish
(Danio rerio)
Actinopterygii upf3b 36
  • 62.46 (n)
  • 60.62 (a)
upf3b 37
  • 56 (a)
OneToOne
zgc66390 36
fruit fly
(Drosophila melanogaster)
Insecta Upf3 37
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea smg-4 37
  • 24 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2608 37
  • 33 (a)
OneToMany
Species with no ortholog for UPF3B:
  • 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

Selected 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 MAF
rs2007262 -- 119,829,581(+) CCTCT(C/T)CCTTG intron-variant
rs2040588 -- 119,842,448(+) cgtgg(G/T)ggcgg intron-variant
rs2040589 -- 119,842,956(+) GTCAT(C/T)GAACT intron-variant
rs2239962 -- 119,834,483(+) CAAAG(C/T)GACTC utr-variant-3-prime, intron-variant
rs2239963 -- 119,835,112(+) TATGA(A/C)TATAT intron-variant

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

Variant ID Type Subtype PubMed ID
dgv2468e1 CNV Complex 17122850
dgv2469e1 CNV Complex 17122850

Relevant External Links for UPF3B Gene

HapMap Linkage Disequilibrium report
UPF3B
Human Gene Mutation Database (HGMD)
UPF3B
Locus Specific Mutation Databases (LSDB)
UPF3B

Disorders for UPF3B Gene

(1) OMIM Diseases for UPF3B Gene (300298)

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.

(1) University of Copenhagen DISEASES for UPF3B Gene

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

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 23
  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 23
  3. 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
  4. Y14 and hUpf3b form an NMD-activating complex. (PMID: 12718880) Gehring N.H. … Kulozik A.E. (Mol. Cell 2003) 3 4 23
  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 23

Products for UPF3B Gene

Sources for UPF3B Gene

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