Human Gene UPF3A (ENST00000492270.1) Description and Page Index
  Description: UPF3A, regulator of nonsense mediated mRNA decay (from HGNC UPF3A)
RefSeq Summary (NM_001353651): 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]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1163655.290658.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1968540 [ECO:0000348] ##Evidence-Data-END##
Gencode Transcript: ENST00000492270.1
Gencode Gene: ENSG00000169062.15
Transcript (Including UTRs)
   Position: hg38 chr13:114,281,603-114,282,270 Size: 668 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg38 chr13:114,281,640-114,282,131 Size: 492 Coding Exon Count: 2 

Page IndexSequence and LinksCTDRNA-Seq ExpressionMicroarray ExpressionRNA Structure
Other SpeciesmRNA DescriptionsOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:114,281,603-114,282,270)mRNA (may differ from genome)Protein (105 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsHGNCLynx
MGIPubMedStanford SOURCEUniProtKBWikipedia

-  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
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -12.2037-0.330 Picture PostScript Text
3' UTR -44.70139-0.322 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.

-  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     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  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.
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.

-  Other Names for This Gene
  Alternate Gene Symbols: A0A087WZ33, AY013250, uc058ypg.1
UCSC ID: uc058ypg.1
RefSeq Accession: NM_001353651

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