Selected-GenAtlas references SOURCE GeneCards NCBI Gene Swiss-Prot Orphanet Ensembl
HGNC UniGene Nucleotide OMIM UCSC
Home Page
Symbol UPF3B contributors: mct - updated : 03-10-2017
HGNC name UPF3 regulator of nonsense transcripts homolog B (yeast)
HGNC id 20439
Corresponding disease
FGS6 FG syndrome 6
LJFS3 Lujan-Fryns syndrome 3
MRXS14 mental retardation, X-linked, syndromic 14
Location Xq24      Physical location : 118.967.988 - 118.986.991
Synonym name
  • UPF3 regulator of nonsense transcripts homolog B
  • similar to yeast Upf3, variant B
  • Synonym symbol(s) UPF3X, RENT3B, HUPF3B, MRXS14, RENT3BP1, UPF3BP2, UPF3BP3, Upf3p-X
    TYPE fragile site
    SPECIAL FEATURE head to head
    STRUCTURE 18.00 kb     11 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    MAPPING cloned Y linked N status provisional
    Physical map
    LOC389882 X LOC389882 DOCK11 Xq24 dedicator of cytokinesis 11 IL13RA1 Xq22-q26 interleukin 13 receptor, alpha 1 LOC170261 Xq24 hypothetical protein LOC170261 LOC159007 Xq24 similar to Aflatoxin B1 aldehyde reductase member 2 (AFB1-AR 1) (Aldoketoreductase 7) LOC392529 X hypothetical gene supported by NM_015198 RNF127 Xq24 ring finger protein 127 KIAA1210 Xq24 KIAA1210 protein LOC389883 X similar to Hnrpa1 protein PGRMC1 Xq22-q24 progesterone receptor membrane component 1 LOC139516 Xq24 similar to DNA segment on chromosome X and Y (unique) 155 expressed sequence; Pseudoautosomal gene XE7 (Y chromosome) MRPS17P9 Xq24 similar to DNA segment on chromosome X and Y (unique) 155 expressed sequence; Pseudoautosomal gene XE7 (Y chromosome) LOC203427 Xq24 similar to solute carrier family 25 , member 16 SLC25A5 Xq24-q26 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5 FLJ22965 Xq23 hypothetical protein FLJ22965 UBE2A Xq24-q25 ubiquitin-conjugating enzyme E2A (RAD6 homolog) NRF Xq24-q25 ubiquitin-conjugating enzyme E2A (RAD6 homolog) SEPT6 Xq24 ubiquitin-conjugating enzyme E2A (RAD6 homolog) LOC347454 Xq25 similar to hypothetical protein A630014H24 RPL39 Xq22.1-q22.2 ribosomal protein L39 LOC158796 Xq25 similar to UPF3 regulator of nonsense transcripts homolog B isoform 2 UPF3B Xq25-q26 UPF3 regulator of nonsense transcripts homolog B (yeast) ZNF183 Xq24-q25 zinc finger protein 183 (RING finger, C3HC4 type) NDUFA1 Xq24 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1, 7.5kDa AKAP28 Xq25 A-kinase anchor protein 28 NKAP Xq25 NF-kappaB activating protein OTEX Xq25 paired-like homeobox protein OTEX LOC392530 X similar to hypothetical protein FLJ22626 PEPP-2 Xq25 PEPP subfamily gene 2 LOC340576 Xq25 similar to eukaryotic translation elongation factor 1 alpha 1; CTCL tumor antigen; translation elongation factor 1 alpha 1-like 14; prostate tumor-inducing protein 1; EF1a-like protein; glucocorticoid receptor AF-1 specific elongati FLJ36576 Xq25 hypothetical protein FLJ36576 ZNF-kaiso Xq23 kaiso FLJ20716 Xq25 hypothetical protein FLJ20716 ATP1B4 Xq24 ATPase, (Na+)/K+ transporting, beta 4 polypeptide LAMP2 Xq24 lysosomal-associated membrane protein 2 RNU7P1 Xq25 RNA, U7 small nuclear pseudogene 1 RNU7P2 Xq25 RNA, U7 small nuclear pseudogene 2 CUL4B Xq23 cullin 4B MCTS1 Xq22-24 malignant T cell amplified sequence 1 C1GALT2 Xq25 core 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase 2 LOC392531 X similar to RIKEN cDNA 2900070E19 LOC389884 X similar to Proliferation-associated protein 2G4 (Cell cycle protein p38-2G4 homolog) (hG4-1) LOC255313 Xq25 hypothetical protein LOC255313 GLUD2 Xq25 glutamate dehydrogenase 2 LOC158714 Xq25 heat shock 70kDa protein 8 pseudogene
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    - splicing 2381 57.8 483 - G.Serin
    having exon 8 (eleven exons)
    - splicing 2342 56.2 470 - G.Serin
    lacking exon 8 (ten exons)
    Type ubiquitous
       expressed in (based on citations)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Nervousbrain     Homo sapiens
    Reproductivemale systemprostate   
    Respiratoryrespiratory tractlarynx  highly
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Blood / Hematopoieticbone marrow   
    Connectivebone  highly
    Muscularstriatumskeletal highly
    SystemCellPubmedSpeciesStageRna symbol
    Nervousneuron Homo sapiens
    cell lineage
    cell lines
    at STAGE
  • one RNA recognition motif (RRM)
  • Smg4/UPF3 domain
    interspecies ortholog to yeast S.cerevisiae Upf3p
    homolog to Drosophila DS07851.3
    ortholog to C.elegans C23G10.2/SMG.4
    intraspecies paralog to UPF3A
    FAMILY nonsense-mediated mRNA decay complex
    CATEGORY RNA associated
    SUBCELLULAR LOCALIZATION     intracellular
  • in neural stem cells, UPF3B protein was detected in the cytoplasm and in the nucleus, and enriched in the nucleolus
  • basic FUNCTION
  • involved in both mRNA nuclear export and mRNA surveillance for the detection of truncated messengers and initiation of nonsense mediated mRNA decay NMD
  • important component of the nonsense-mediated mRNA decay surveillance machinery
  • 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
  • is a core member of the nonsense-mediated mRNA decay (NMD) pathway that functions to rapidly degrade transcripts with premature termination codons (PTCs)
  • is involved in the nonsense-mediated mRNA decay pathway (NMD) that controls mRNA stability and functions in the prevention of the synthesis of truncated proteins
  • UPF3B and UPF1 are down-regulated during differentiation of neural stem cells into neurons
  • 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
  • interacts with the release factors, delays translation termination and dissociates post-termination ribosomal complexes that are devoid of the nascent peptide
  • is likely involved in the crosstalk between the NMD machinery and the premature termination codons (PTCs)-bound ribosome, a central mechanistic step of RNA surveillance
    a component component of a post-splicing multiprotein complex
    RNA binding specifically to 20nt upstream of exon-exon junctions in mRNAs
    small molecule
  • RBM8A, THOC4 (ALY), NXF1 (TAP), UPF2
  • DCP2
  • in the UPF trimeric complex, UPF2 and UPF3B cooperatively stimulate both ATPase and RNA helicase activities of UPF1
  • SATB2 binds to the UPF3B promoter, and SATB2 expression significantly activates gene transcription using the UPF3B promoter
  • ability of UPF1 to impinge on premature termination, moreover, requires ATP-binding, RNA-binding and NMD cofactors UPF2 and UPF3A, UPF3B
  • UPF1 and ribosomes are new interaction partners of UPF3B
  • cell & other
    activated by SATB2, that activates UPF3B expression through binding to its promoter
    corresponding disease(s) LJFS3 , FGS6 , MRXS14
    Variant & Polymorphism
    Candidate gene
    Therapy target