Human Gene UPF2 (ENST00000357604.10) from GENCODE V44
  Description: Homo sapiens UPF2 regulator of nonsense mediated mRNA decay (UPF2), transcript variant 2, mRNA. (from RefSeq NM_015542)
RefSeq Summary (NM_015542): This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. 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 is located in the perinuclear area. It interacts with translation release factors and the proteins that are functional homologs of yeast Upf1p and Upf3p. Two splice variants have been found for this gene; both variants encode the same protein. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000357604.10
Gencode Gene: ENSG00000151461.20
Transcript (Including UTRs)
   Position: hg38 chr10:11,920,022-12,042,809 Size: 122,788 Total Exon Count: 22 Strand: -
Coding Region
   Position: hg38 chr10:11,921,298-12,035,423 Size: 114,126 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:11,920,022-12,042,809)mRNA (may differ from genome)Protein (1272 aa)
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-  Comments and Description Text from UniProtKB
  ID: RENT2_HUMAN
DESCRIPTION: RecName: Full=Regulator of nonsense transcripts 2; AltName: Full=Nonsense mRNA reducing factor 2; AltName: Full=Up-frameshift suppressor 2 homolog; Short=hUpf2;
FUNCTION: Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC). Recruited by UPF3B associated with the EJC core 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. In cooperation with UPF3B stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA.
SUBUNIT: Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC). Interacts with SMG1, EST1A, UPF1, UPF3A, UPF3B, EIF4A1 and EIF1.
INTERACTION: Q96Q15:SMG1; NbExp=6; IntAct=EBI-372073, EBI-1049832; Q92900:UPF1; NbExp=8; IntAct=EBI-372073, EBI-373471; Q9BZI7:UPF3B; NbExp=6; IntAct=EBI-372073, EBI-372780;
SUBCELLULAR LOCATION: Cytoplasm, perinuclear region.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Contains 3 MIF4G domains.
SEQUENCE CAUTION: Sequence=BAA92646.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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: 16.31 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 423.50 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
5' UTR -27.7073-0.379 Picture PostScript Text
3' UTR -328.501276-0.257 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
IPR016024 - ARM-type_fold
IPR016021 - MIF4-like_typ_1/2/3
IPR003890 - MIF4G-like_typ-3
IPR007193 - Up-fram_suppressor-2

Pfam Domains:
PF02854 - MIF4G domain
PF04050 - Up-frameshift suppressor 2

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1UW4 - X-ray MuPIT 2WJV - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9HAU5
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-  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    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0042162 telomeric DNA binding

Biological Process:
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0001889 liver development
GO:0006406 mRNA export from nucleus
GO:0031100 animal organ regeneration

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005844 polysome
GO:0035145 exon-exon junction complex
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK074375 - Homo sapiens cDNA FLJ23795 fis, clone HEP22107.
AL080198 - Homo sapiens mRNA; cDNA DKFZp434D222 (from clone DKFZp434D222).
AF301013 - Homo sapiens regulator of nonsense transcripts 2 (RENT2) mRNA, complete cds.
AK000764 - Homo sapiens cDNA FLJ20757 fis, clone HEP01520.
AB037829 - Homo sapiens KIAA1408 mRNA for KIAA1408 protein.
AF318574 - Homo sapiens UPF2 (UPF2) mRNA, complete cds.
AK096191 - Homo sapiens cDNA FLJ38872 fis, clone MESAN2013674, highly similar to Homo sapiens regulator of nonsense transcripts 2 (RENT2) mRNA.
BC114964 - Homo sapiens UPF2 regulator of nonsense transcripts homolog (yeast), mRNA (cDNA clone MGC:138835 IMAGE:40082739), complete cds.
BC115737 - Homo sapiens UPF2 regulator of nonsense transcripts homolog (yeast), mRNA (cDNA clone MGC:138834 IMAGE:40082728), complete cds.
AK295209 - Homo sapiens cDNA FLJ56346 complete cds, highly similar to Regulator of nonsense transcripts 2.
AY013249 - Homo sapiens hUPF2 mRNA, complete cds.
BX647325 - Homo sapiens mRNA; cDNA DKFZp779F0615 (from clone DKFZp779F0615).
AK124930 - Homo sapiens cDNA FLJ42940 fis, clone BRSSN2018925.
JD301833 - Sequence 282857 from Patent EP1572962.
JD449880 - Sequence 430904 from Patent EP1572962.
JD520877 - Sequence 501901 from Patent EP1572962.
JD299011 - Sequence 280035 from Patent EP1572962.
JD037553 - Sequence 18577 from Patent EP1572962.
JD173837 - Sequence 154861 from Patent EP1572962.
JD565751 - Sequence 546775 from Patent EP1572962.
JD378877 - Sequence 359901 from Patent EP1572962.
JD233243 - Sequence 214267 from Patent EP1572962.
JD364067 - Sequence 345091 from Patent EP1572962.
JD050756 - Sequence 31780 from Patent EP1572962.
JD491630 - Sequence 472654 from Patent EP1572962.
JD488839 - Sequence 469863 from Patent EP1572962.
JD127625 - Sequence 108649 from Patent EP1572962.
JD141242 - Sequence 122266 from Patent EP1572962.
JD133021 - Sequence 114045 from Patent EP1572962.
JD178925 - Sequence 159949 from Patent EP1572962.
JD373241 - Sequence 354265 from Patent EP1572962.
JD276935 - Sequence 257959 from Patent EP1572962.
JD401461 - Sequence 382485 from Patent EP1572962.
JD064912 - Sequence 45936 from Patent EP1572962.
AB463336 - Synthetic construct DNA, clone: pF1KA1408, Homo sapiens UPF2 gene for UPF2 regulator of nonsense transcripts homolog, without stop codon, in Flexi system.
AK310925 - Homo sapiens cDNA, FLJ17967.
KY966261 - Homo sapiens cell line 95T1000 FRS2/UPF2/LEMD3 fusion mRNA, partial sequence.
KY966272 - Homo sapiens cell line 95T1000 LEMD3/UPF2 fusion mRNA, partial sequence.
BC090919 - Homo sapiens UPF2 regulator of nonsense transcripts homolog (yeast), mRNA (cDNA clone IMAGE:30371337), partial cds.
BC054011 - Homo sapiens cDNA clone IMAGE:6604251, partial cds.

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

Protein Q9HAU5 (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

-  Other Names for This Gene
  Alternate Gene Symbols: A6NLJ5, D3DRS0, ENST00000357604.1, ENST00000357604.2, ENST00000357604.3, ENST00000357604.4, ENST00000357604.5, ENST00000357604.6, ENST00000357604.7, ENST00000357604.8, ENST00000357604.9, KIAA1408, NM_015542, Q14BM1, Q5W0J4, Q8N8U1, Q9H1J2, Q9HAU5, Q9NWL1, Q9P2D9, Q9Y4M9, RENT2, RENT2_HUMAN, uc001ilb.1, uc001ilb.2, uc001ilb.3, uc001ilb.4, uc001ilb.5
UCSC ID: ENST00000357604.10
RefSeq Accession: NM_015542
Protein: Q9HAU5 (aka RENT2_HUMAN)
CCDS: CCDS7086.1

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