Description: Homo sapiens UPF3 regulator of nonsense transcripts homolog B (yeast) (UPF3B), transcript variant 1, mRNA. RefSeq Summary (NM_080632): 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]. Transcript (Including UTRs) Position: hg19 chrX:118,967,989-118,986,991 Size: 19,003 Total Exon Count: 11 Strand: - Coding Region Position: hg19 chrX:118,968,841-118,986,891 Size: 18,051 Coding Exon Count: 11
ID:REN3B_HUMAN DESCRIPTION: RecName: Full=Regulator of nonsense transcripts 3B; AltName: Full=Nonsense mRNA reducing factor 3B; AltName: Full=Up-frameshift suppressor 3 homolog B; Short=hUpf3B; AltName: Full=Up-frameshift suppressor 3 homolog on chromosome X; Short=hUpf3p-X; 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 indepenedent of association with UPF2 and components of the EJC core. SUBUNIT: 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. INTERACTION: P38919:EIF4A3; NbExp=4; IntAct=EBI-372780, EBI-299104; Q9Y5S9:RBM8A; NbExp=8; IntAct=EBI-372780, EBI-447231; Q92900:UPF1; NbExp=8; IntAct=EBI-372780, EBI-373471; Q9HAU5:UPF2; NbExp=6; IntAct=EBI-372780, EBI-372073; SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Shuttling between the nucleus and the cytoplasm. TISSUE SPECIFICITY: Expressed in testis, uterus, prostate, heart, muscle, brain, spinal cord and placenta. DISEASE: Defects in UPF3B are the cause of mental retardation syndromic X-linked type 14 (MRXS14) [MIM:300676]. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptative 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. SIMILARITY: Belongs to the RENT3 family.
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on Q9BZI7
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
AY013251 - Homo sapiens hUPF3B mRNA, complete cds. AF318576 - Homo sapiens UPF3X (UPF3X) mRNA, complete cds. AK093728 - Homo sapiens cDNA FLJ36409 fis, clone THYMU2010448, highly similar to Regulator of nonsense transcripts 3B. AX748280 - Sequence 1805 from Patent EP1308459. JD154059 - Sequence 135083 from Patent EP1572962. JD144981 - Sequence 126005 from Patent EP1572962. JD257856 - Sequence 238880 from Patent EP1572962. JD280998 - Sequence 262022 from Patent EP1572962. JD403487 - Sequence 384511 from Patent EP1572962. JD264098 - Sequence 245122 from Patent EP1572962. BC121017 - Homo sapiens UPF3 regulator of nonsense transcripts homolog B (yeast), mRNA (cDNA clone MGC:149647 IMAGE:40117102), complete cds. BC121018 - Homo sapiens UPF3 regulator of nonsense transcripts homolog B (yeast), mRNA (cDNA clone IMAGE:40117107), complete cds. JD315148 - Sequence 296172 from Patent EP1572962. JD315720 - Sequence 296744 from Patent EP1572962. JD141005 - Sequence 122029 from Patent EP1572962. JD348912 - Sequence 329936 from Patent EP1572962. BC008494 - Homo sapiens UPF3 regulator of nonsense transcripts homolog B (yeast), mRNA (cDNA clone IMAGE:4273603), with apparent retained intron.
Biochemical and Signaling Pathways
Reactome (by CSHL, EBI, and GO)
Protein Q9BZI7 (Reactome details) participates in the following event(s):
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage R-HSA-156661 Formation of Exon Junction Complex R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally R-HSA-72185 mRNA polyadenylation R-HSA-72180 Cleavage of mRNA at the 3'-end R-HSA-75096 Docking of the TAP:EJC Complex with the NPC R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B) R-HSA-75098 mRNP complex dissociates from cytosolic face of NPC R-HSA-927832 UPF1 binds an mRNP with a termination codon preceding an Exon Junction Complex R-HSA-927889 SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex) R-HSA-72163 mRNA Splicing - Major Pathway R-HSA-72172 mRNA Splicing R-HSA-72187 mRNA 3'-end processing R-HSA-109688 Cleavage of Growing Transcript in the Termination Region R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA R-HSA-9010553 Regulation of expression of SLITs and ROBOs R-HSA-73856 RNA Polymerase II Transcription Termination R-HSA-72202 Transport of Mature Transcript to Cytoplasm R-HSA-8953854 Metabolism of RNA R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) R-HSA-376176 Signaling by ROBO receptors R-HSA-73857 RNA Polymerase II Transcription R-HSA-927802 Nonsense-Mediated Decay (NMD) R-HSA-422475 Axon guidance R-HSA-74160 Gene expression (Transcription) R-HSA-1266738 Developmental Biology
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