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 las... See more...

Aliases for UPF3A Gene

Aliases for UPF3A Gene

  • UPF3A Regulator Of Nonsense Mediated MRNA Decay 2 3 5
  • Regulator Of Nonsense Transcripts 3A 3 4
  • Up-Frameshift Suppressor 3 Homolog A 3 4
  • Nonsense MRNA Reducing Factor 3A 3 4
  • RENT3A 3 4
  • HUpf3 3 4
  • UPF3 3 4
  • UPF3 Regulator Of Nonsense Transcripts Homolog A (Yeast) 2
  • UPF3 Regulator Of Nonsense Transcripts Homolog A 3
  • UPF3A, Regulator Of Nonsense Mediated MRNA Decay 2
  • HUPF3A 3

External Ids for UPF3A Gene

Previous GeneCards Identifiers for UPF3A Gene

  • GC13P113408
  • GC13P111235
  • GC13P114068
  • GC13P112965
  • GC13P114065
  • GC13P115047
  • GC13P095309

Summaries for UPF3A Gene

Entrez Gene Summary for UPF3A Gene

  • 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]

GeneCards Summary for UPF3A Gene

UPF3A (UPF3A Regulator Of Nonsense Mediated MRNA Decay) is a Protein Coding gene. Diseases associated with UPF3A include Retinitis Pigmentosa 51 and Pancreatic Adenosquamous Carcinoma. Among its related pathways are Gene Expression and mRNA surveillance pathway. Gene Ontology (GO) annotations related to this gene include RNA binding. An important paralog of this gene is UPF3B.

UniProtKB/Swiss-Prot Summary for UPF3A Gene

  • 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.

Gene Wiki entry for UPF3A Gene

Additional gene information for UPF3A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for UPF3A Gene

Genomics for UPF3A Gene

GeneHancer (GH) Regulatory Elements for UPF3A Gene

Promoters and enhancers for UPF3A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J114279 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 506.3 -0.1 -51 4.9 HNRNPK EP300 SIN3A NRF1 TCF12 POLR2G PHF8 ZFX ZIC2 POLR2A UPF3A HSALNG0099668 LOC105370384 lnc-UPF3A-2 lnc-RASA3-8-001 lnc-RASA3-8-002 CDC16 CHAMP1 RASA3
GH13J114286 Promoter/Enhancer 0.7 EPDnew ENCODE dbSUPER 500.7 +4.8 4803 0.3 UPF3A HSALNG0099668 CLCP2
GH13J113296 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 30.8 -983.1 -983083 4.6 RXRA EP300 ZBTB40 ZNF217 SIN3A MYC TCF12 POLR2G USF1 SP1 LAMP1 TUBGCP3 PCID2 CDC16 UPF3A GAS6-DT GAS6 CUL4A GAS6-AS1 DCUN1D2-AS
GH13J114312 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 24.9 +32.9 32945 3.4 RXRA ZBTB40 EP300 ZSCAN5C SIN3A NRF1 USF1 POLR2G SP1 NCOR1 CHAMP1 UPF3A CDC16 lnc-UPF3A-3
GH13J113772 Enhancer 1.1 FANTOM5 Ensembl ENCODE 44.9 -508.1 -508083 3.4 EP300 NONO ZNF354C AFF1 MYNN KLF9 CREB1 ZNF195 FOS ZNF112 CDC16 TMEM255B UPF3A GAS6-DT PCID2 GAS6 CHAMP1 DCUN1D2-AS GRK1 GAS6-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around UPF3A on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for UPF3A

Top Transcription factor binding sites by QIAGEN in the UPF3A gene promoter:
  • AML1a
  • AP-2gamma
  • c-Ets-1
  • COMP1
  • Evi-1
  • NF-1
  • NF-1/L
  • Nkx5-1
  • PPAR-gamma2
  • STAT5A

Genomic Locations for UPF3A Gene

Genomic Locations for UPF3A Gene
chr13:114,281,584-114,305,817
(GRCh38/hg38)
Size:
24,234 bases
Orientation:
Plus strand
chr13:115,047,059-115,071,292
(GRCh37/hg19)
Size:
24,234 bases
Orientation:
Plus strand

Genomic View for UPF3A Gene

Genes around UPF3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UPF3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UPF3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UPF3A Gene

Proteins for UPF3A Gene

  • Protein details for UPF3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H1J1-REN3A_HUMAN
    Recommended name:
    Regulator of nonsense transcripts 3A
    Protein Accession:
    Q9H1J1
    Secondary Accessions:
    • A2A366
    • Q5T8C3
    • Q5T8C9
    • Q7Z6N3
    • Q86YK1
    • Q9BZI8

    Protein attributes for UPF3A Gene

    Size:
    476 amino acids
    Molecular mass:
    54696 Da
    Quaternary structure:
    • Found in a post-splicing messenger ribonucleoprotein (mRNP) complex. Associates with the exon junction complex (EJC). Interacts with UPF2 and RBM8A.

    Three dimensional structures from OCA and Proteopedia for UPF3A Gene

    Alternative splice isoforms for UPF3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for UPF3A Gene

Post-translational modifications for UPF3A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for UPF3A Gene

Domains & Families for UPF3A Gene

Gene Families for UPF3A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for UPF3A Gene

Suggested Antigen Peptide Sequences for UPF3A Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ39708 fis, clone SMINT2012735, highly similar to Regulator of nonsense transcripts 3A (B3KUE7_HUMAN)
  • cDNA FLJ61452, moderately similar to Regulator of nonsense transcripts 3A (B4DXJ4_HUMAN)
  • Up-frameshift suppressor 3 homolog A (REN3A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H1J1

UniProtKB/Swiss-Prot:

REN3A_HUMAN :
  • Belongs to the RENT3 family.
Family:
  • Belongs to the RENT3 family.
genes like me logo Genes that share domains with UPF3A: view

Function for UPF3A Gene

Molecular function for UPF3A Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for UPF3A Gene

Gene Ontology (GO) - Molecular Function for UPF3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 11163187
GO:0017056 structural constituent of nuclear pore NAS 11163187
GO:0042162 telomeric DNA binding IDA 17916692
genes like me logo Genes that share ontologies with UPF3A: view
genes like me logo Genes that share phenotypes with UPF3A: view

Animal Models for UPF3A Gene

MGI Knock Outs for UPF3A:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for UPF3A Gene

Localization for UPF3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for UPF3A Gene

Nucleus. Cytoplasm. Note=Shuttling between the nucleus and the cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for UPF3A gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for UPF3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,NAS 11163187
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IBA 21873635
GO:0005737 cytoplasm NAS,IBA 11163187
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with UPF3A: view

Pathways & Interactions for UPF3A Gene

genes like me logo Genes that share pathways with UPF3A: view

Pathways by source for UPF3A Gene

Gene Ontology (GO) - Biological Process for UPF3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS --
GO:0006913 nucleocytoplasmic transport IEA --
GO:0045727 positive regulation of translation IDA,IBA 16601204
GO:0051028 mRNA transport IEA --
genes like me logo Genes that share ontologies with UPF3A: view

No data available for SIGNOR curated interactions for UPF3A Gene

Drugs & Compounds for UPF3A Gene

No Compound Related Data Available

Transcripts for UPF3A Gene

mRNA/cDNA for UPF3A Gene

11 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for UPF3A Gene

No ASD Table

Relevant External Links for UPF3A Gene

GeneLoc Exon Structure for
UPF3A

Expression for UPF3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for UPF3A Gene

Protein differential expression in normal tissues from HIPED for UPF3A Gene

This gene is overexpressed in Testis (35.8) and Pancreatic juice (23.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for UPF3A Gene



Protein tissue co-expression partners for UPF3A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for UPF3A

SOURCE GeneReport for Unigene cluster for UPF3A Gene:

Hs.533855

mRNA Expression by UniProt/SwissProt for UPF3A Gene:

Q9H1J1-REN3A_HUMAN
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.

Evidence on tissue expression from TISSUES for UPF3A Gene

  • Nervous system(4.5)
  • Eye(4.1)
genes like me logo Genes that share expression patterns with UPF3A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for UPF3A Gene

Orthologs for UPF3A Gene

This gene was present in the common ancestor of animals.

Orthologs for UPF3A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia UPF3A 31
  • 98 (a)
OneToOne
LOC750926 30
  • 93.48 (n)
cow
(Bos Taurus)
Mammalia UPF3A 31 30
  • 79.47 (n)
OneToOne
dog
(Canis familiaris)
Mammalia UPF3A 31 30
  • 79.44 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Upf3a 30
  • 77.13 (n)
mouse
(Mus musculus)
Mammalia Upf3a 17 31 30
  • 75.95 (n)
oppossum
(Monodelphis domestica)
Mammalia UPF3A 31
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UPF3A 31
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves UPF3A 31 30
  • 72.34 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia UPF3A 31
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia upf3a 30
  • 69.41 (n)
zebrafish
(Danio rerio)
Actinopterygii upf3a 31 30
  • 62.12 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Upf3 31
  • 23 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea smg-4 31
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2608 31
  • 28 (a)
OneToMany
Species where no ortholog for UPF3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for UPF3A Gene

ENSEMBL:
Gene Tree for UPF3A (if available)
TreeFam:
Gene Tree for UPF3A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for UPF3A: view image

Paralogs for UPF3A Gene

Paralogs for UPF3A Gene

(1) SIMAP similar genes for UPF3A Gene using alignment to 2 proteins:

  • REN3A_HUMAN
  • B3KUE7_HUMAN

Pseudogenes.org Pseudogenes for UPF3A Gene

genes like me logo Genes that share paralogs with UPF3A: view

Variants for UPF3A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for UPF3A Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
rs3752105 - p.Arg64Lys

Additional dbSNP identifiers (rs#s) for UPF3A Gene

Structural Variations from Database of Genomic Variants (DGV) for UPF3A Gene

Variant ID Type Subtype PubMed ID
dgv1745n100 CNV gain 25217958
dgv1746n100 CNV gain 25217958
dgv1747n100 CNV gain 25217958
dgv1748n100 CNV gain 25217958
dgv589e212 CNV loss 25503493
dgv590e212 CNV loss 25503493
esv1000540 CNV insertion 20482838
esv1401261 CNV insertion 17803354
esv25715 CNV gain+loss 19812545
esv3410207 CNV duplication 20981092
esv3418334 CNV duplication 20981092
esv3582871 CNV gain 25503493
esv3633642 CNV gain 21293372
esv3633643 CNV gain 21293372
esv3633644 CNV gain 21293372
esv3633645 CNV loss 21293372
nsv1043111 CNV gain 25217958
nsv518491 CNV loss 19592680
nsv563533 CNV loss 21841781
nsv563534 CNV gain 21841781
nsv64869 CNV insertion 16902084
nsv826841 CNV loss 20364138

Variation tolerance for UPF3A Gene

Residual Variation Intolerance Score: 68.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.51; 82.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for UPF3A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
UPF3A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UPF3A Gene

Disorders for UPF3A Gene

MalaCards: The human disease database

(5) MalaCards diseases for UPF3A Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search UPF3A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for UPF3A

genes like me logo Genes that share disorders with UPF3A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for UPF3A Gene

Publications for UPF3A Gene

  1. Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4). (PMID: 11113196) Serin G … Maquat LE (Molecular and cellular biology 2001) 2 3 4 23 54
  2. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. (PMID: 11163187) Lykke-Andersen J … Steitz JA (Cell 2000) 2 3 4 23 54
  3. Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. (PMID: 16601204) Kunz JB … Gehring NH (RNA (New York, N.Y.) 2006) 3 4 23 54
  4. A UPF3-mediated regulatory switch that maintains RNA surveillance. (PMID: 19503078) Chan WK … Wilkinson MF (Nature structural & molecular biology 2009) 3 23 54
  5. Communication with the exon-junction complex and activation of nonsense-mediated decay by human Upf proteins occur in the cytoplasm. (PMID: 17803942) Singh G … Lykke-Andersen J (Molecular cell 2007) 3 23 54

Products for UPF3A Gene

Sources for UPF3A Gene