Human Gene UPF3A (ENST00000351487.5) Description and Page Index
  Description: Homo sapiens UPF3A regulator of nonsense mediated mRNA decay (UPF3A), transcript variant 19, non-coding RNA. (from RefSeq NR_148489)
RefSeq Summary (NM_080687): 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 13. Several splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017].
Gencode Transcript: ENST00000351487.5
Gencode Gene: ENSG00000169062.15
Transcript (Including UTRs)
   Position: hg38 chr13:114,281,628-114,305,808 Size: 24,181 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr13:114,281,640-114,304,917 Size: 23,278 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr13:114,281,628-114,305,808)mRNA (may differ from genome)Protein (443 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Regulator of nonsense transcripts 3A; AltName: Full=Nonsense mRNA reducing factor 3A; AltName: Full=Up-frameshift suppressor 3 homolog A; Short=hUpf3;
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. However, UPF3A is shown to be only marginally active in NMD as compared to UPF3B. Binds spliced mRNA upstream of exon-exon junctions. In vitro, weakly stimulates translation.
SUBUNIT: Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC). Interacts with UPF2 and RBM8A.
INTERACTION: Q9Y5S9:RBM8A; NbExp=4; IntAct=EBI-521530, EBI-447231; Q92900:UPF1; NbExp=4; IntAct=EBI-521530, EBI-373471;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Shuttling between the nucleus and the cytoplasm.
TISSUE SPECIFICITY: Isoform 1 is strongly expressed in testis, uterus, muscle, fetal brain and spinal cord. Isoform 2 is strongly expressed in fetal brain and spinal cord.
SIMILARITY: Belongs to the RENT3 family.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 48.42 RPKM in Brain - Cerebellum
Total median expression: 913.26 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -223.40891-0.251 Picture PostScript Text

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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005120 - Nonsense_mediated_decay_UPF3
IPR012677 - Nucleotide-bd_a/b_plait

Pfam Domains:
PF03467 - Smg-4/UPF3 family

Protein Data Bank (PDB) 3-D Structure
MuPIT help


ModBase Predicted Comparative 3D Structure on Q9H1J1
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0017056 structural constituent of nuclear pore
GO:0042162 telomeric DNA binding

Biological Process:
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0006913 nucleocytoplasmic transport
GO:0045727 positive regulation of translation
GO:0051028 mRNA transport

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle
GO:0035145 exon-exon junction complex

-  Descriptions from all associated GenBank mRNAs
  AY013250 - Homo sapiens hUPF3A mRNA, complete cds.
LF384336 - JP 2014500723-A/191839: Polycomb-Associated Non-Coding RNAs.
MA619913 - JP 2018138019-A/191839: Polycomb-Associated Non-Coding RNAs.
BC023569 - Homo sapiens UPF3 regulator of nonsense transcripts homolog A (yeast), mRNA (cDNA clone MGC:20683 IMAGE:4127465), complete cds.
BC047735 - Homo sapiens UPF3 regulator of nonsense transcripts homolog A (yeast), mRNA (cDNA clone IMAGE:6046156), with apparent retained intron.
KJ894603 - Synthetic construct Homo sapiens clone ccsbBroadEn_03997 UPF3A gene, encodes complete protein.
AK302003 - Homo sapiens cDNA FLJ61452 complete cds, moderately similar to Regulator of nonsense transcripts 3A.
AF318575 - Homo sapiens UPF3 (UPF3) mRNA, complete cds.
AK097027 - Homo sapiens cDNA FLJ39708 fis, clone SMINT2012735, highly similar to Regulator of nonsense transcripts 3A.
BC008694 - Homo sapiens UPF3 regulator of nonsense transcripts homolog A (yeast), mRNA (cDNA clone IMAGE:3866772), complete cds.
AK001069 - Homo sapiens cDNA FLJ10207 fis, clone HEMBA1005475.
AK294545 - Homo sapiens cDNA FLJ57970 complete cds, highly similar to Regulator of nonsense transcripts 3A.
LF371315 - JP 2014500723-A/178818: Polycomb-Associated Non-Coding RNAs.
MA606892 - JP 2018138019-A/178818: Polycomb-Associated Non-Coding RNAs.
AK092586 - Homo sapiens cDNA FLJ35267 fis, clone PROST2005272.
AX747614 - Sequence 1139 from Patent EP1308459.
JD474447 - Sequence 455471 from Patent EP1572962.
JD487069 - Sequence 468093 from Patent EP1572962.
JD251621 - Sequence 232645 from Patent EP1572962.
JD202804 - Sequence 183828 from Patent EP1572962.
JD088893 - Sequence 69917 from Patent EP1572962.
JD301357 - Sequence 282381 from Patent EP1572962.
JD232110 - Sequence 213134 from Patent EP1572962.
JD260321 - Sequence 241345 from Patent EP1572962.
JD495014 - Sequence 476038 from Patent EP1572962.
JD323714 - Sequence 304738 from Patent EP1572962.
JD144221 - Sequence 125245 from Patent EP1572962.
JD457875 - Sequence 438899 from Patent EP1572962.
JD207483 - Sequence 188507 from Patent EP1572962.
JD343383 - Sequence 324407 from Patent EP1572962.
JD143952 - Sequence 124976 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H1J1 (Reactome details) participates in the following event(s):

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-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-376176 Signaling by ROBO receptors
R-HSA-927802 Nonsense-Mediated Decay (NMD)
R-HSA-422475 Axon guidance
R-HSA-8953854 Metabolism of RNA
R-HSA-1266738 Developmental Biology
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-927802 Nonsense-Mediated Decay (NMD)
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A2A366, NR_148489, Q5T8C3, Q5T8C9, Q7Z6N3, Q86YK1, Q9BZI8, Q9H1J1, REN3A_HUMAN, RENT3A, uc001vuq.1, uc001vuq.2, uc001vuq.3, uc001vuq.4, UPF3
UCSC ID: uc001vuq.4
RefSeq Accession: NM_080687
Protein: Q9H1J1 (aka REN3A_HUMAN)
CCDS: CCDS9544.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.