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FLASH GENE

Symbol

UPF3B

contributors: mct - updated : 03-10-2017

HGNC name	UPF3 regulator of nonsense transcripts homolog B (yeast)
HGNC id	20439

FLASH GENE DNA RNA EXPRESSION PROTEIN DISORDER ANIMAL & CELL MODELS

DNA

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

RNA

TRANSCRIPTS	type	messenger

identification nb exons type bp product Protein kDa AA specific expression Year Pubmed UPF3B-V1 or hUpf3-X - splicing 2381 57.8 483 - G.Serin having exon 8 (eleven exons) UPF3B-V2 - splicing 2342 56.2 470 - G.Serin lacking exon 8 (ten exons)

EXPRESSION

Type	ubiquitous

expressed in	(based on citations)
organ(s)	System Organ level 1 Organ level 2 Organ level 3 Organ level 4 Level Pubmed Species Stage Rna symbol Digestive liver         Nervous brain         Homo sapiens Reproductive male system prostate       Respiratory respiratory tract larynx     highly Urinary kidney

tissue

System Tissue Tissue level 1 Tissue level 2 Level Pubmed Species Stage Rna symbol Blood / Hematopoietic bone marrow       Connective bone     highly Muscular striatum skeletal   highly

cells

System Cell Pubmed Species Stage Rna symbol Nervous neuron Homo sapiens

cell lineage

cell lines

fluid/secretion

at STAGE

PROTEIN

PHYSICAL PROPERTIES

STRUCTURE

motifs/domains	one RNA recognition motif (RRM)
	Smg4/UPF3 domain

HOMOLOGY

interspecies	ortholog to yeast S.cerevisiae Upf3p
	homolog to Drosophila DS07851.3
	ortholog to C.elegans C23G10.2/SMG.4

intraspecies

paralog to UPF3A

Homologene

FAMILY

nonsense-mediated mRNA decay complex

CATEGORY

RNA associated

SUBCELLULAR LOCALIZATION	intracellular
	intracellular,cytoplasm
	intracellular,nucleus,nucleolus
text	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)
	MYCN, PIGV and UPF3B regulate likely synapse development
	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

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
	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

REGULATION

activated by

SATB2, that activates UPF3B expression through binding to its promoter

ASSOCIATED DISORDERS

corresponding disease(s)

LJFS3 , FGS6 , MRXS14

Susceptibility

Variant & Polymorphism

Candidate gene

Marker

Therapy target

ANIMAL & CELL MODELS