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FLASH GENE
Symbol UPF3A contributors: mct - updated : 03-10-2017
HGNC name UPF3 regulator of nonsense transcripts homolog A (yeast)
HGNC id 20332
Location 13q34      Physical location : 115.047.077 - 115.071.281
Synonym name similar to yeast Upf3, variant A
Synonym symbol(s) UPF3, HUPF3A, RENT3A
DNA
TYPE functioning gene
STRUCTURE 24.00 kb     10 Exon(s)
10 Kb 5' upstream gene genomic sequence study
MAPPING cloned Y linked N status provisional
Physical map
ATP11A 13q34 ATPase, Class VI, type 11A LOC387950 13 LOC387950 MCF2L 13q34 MCF.2 cell line derived transforming sequence-like F7 13q34 coagulation factor VII (serum prothrombin conversion accelerator) F10 13q34 coagulation factor X PROZ 13q34 protein Z, vitamin K-dependent plasma glycoprotein FLJ11305 13q34 hypothetical protein FLJ11305 CUL4A 13q34-qter cullin 4A LAMP1 13q34 lysosomal-associated membrane protein 1 GRTP1 4q14 growth hormone regulated TBC protein 1 LOC387951 13 LOC387951 ADPRHL1 13q34 ADP-ribosylhydrolase like 1 C13orf17 13q34 chromosome 13 open reading frame 17 C13orf11 13q34 chromosome 13 open reading frame 11 TFDP1 13q34 transcription factor Dp-1 ATP4B 13q34 ATPase, H+/K+ exchanging, beta polypeptide RHOK 13q34 rhodopsin kinase LOC387952 13 hypothetical gene supported by AK126042; BC034570 GAS6 13q34 growth arrest-specific 6 MGC20579 13q34 hypothetical protein MGC20579 RASA3 13q34 RAS p21 protein activator 3 LOC390427 13 LOC390427 CDC16 13q34 CDC16 cell division cycle 16 homolog (S. cerevisiae) UPF3A 13q34 UPF3 regulator of nonsense transcripts homolog A (yeast) C13orf8 13q34 chromosome 13 open reading frame 8
RNA
TRANSCRIPTS type messenger
identificationnb exonstypebpproduct
ProteinkDaAAspecific expressionYearPubmed
- splicing 2381 54.7 476 - G.Serin
- splicing 2282 50.9 443 - G.Serin
  • lacking exon 4
  • cannot bind u1-sn RNA
  • EXPRESSION
    Type widely
    constitutive of
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Cardiovascularheart    
    Endocrineparathyroid   highly
    Lymphoid/Immunelymph node   highly
    Nervousbrain    
    Reproductivemale systemtestis  highly
    Respiratorylung    
    Urinarykidney    
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Muscularstriatumskeletal  
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • Smg4/UPF3 domain
  • one RNA recognition motif (RRM)
  • conjugated PhosphoP
    HOMOLOGY
    interspecies homolog to Drosophila BG:DS07851.3
    homolog to C.elegans C23q10.2
    ortholog to murine Upf3a
    intraspecies homolog to sequences found in the SMS repeat gene clusters SMS-REPD,SMS-REPM,SMS-REPP (see symbols) and UPF3A1,UPF3AP1,UPF3AP2
    paralog to UPF3B
    Homologene
    FAMILY
    CATEGORY RNA associated
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,nucleus
    basic FUNCTION
  • key factor in both mRNA nuclear export and mRNA surveillance for the deletion of truncated messengers and initiation of nonsense mediated mRNA decay (NMD)
  • mediating the splicing of pre-mRNA by binding to the loop I region of U1-snRNA
  • acting as a nucleocytoplasmic shuttle
  • UPF3A levels are tightly regulated by a post-transcriptional switch to maintain appropriate levels of NMD substrates in cells containing different levels of UPF3B
  • UPF3B--is critical for the nonsense-mediated RNA decay (NMD) pathway, while its autosomal counterpart--UPF3A--encodes an enigmatic protein previously shown to have trace NMD activity
  • likely UPF3A acquired repressor activity through simple impairment of a critical domain, a rapid mechanism that may have been widely used in evolution
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling
    a component component of a post-splicing multiprotein complex
    INTERACTION
    DNA
    RNA binding specifically to 20nt upstream of exon-exon junctions in mRNAs
    small molecule
    protein
  • RBM8A, THOC4 (ALY), NXF1 (TAP), UPF2
  • ability of UPF1 to impinge on premature termination, moreover, requires ATP-binding, RNA-binding and NMD cofactors UPF2 and UPF3A, UPF3B
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    ANIMAL & CELL MODELS