Free for academic non-profit institutions. Other users need a Commercial license

Aliases for UPF3A Gene

Aliases for UPF3A Gene

  • UPF3A, Regulator Of Nonsense Mediated MRNA Decay 2 3 5
  • 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
  • Regulator Of Nonsense Transcripts 3A 3
  • 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. Among its related pathways are Gene Expression and RNA transport. Gene Ontology (GO) annotations related to this gene include RNA binding and nuclear pore activity. An important paralog of this gene is UPF3B.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies 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
GH13I114279 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 556.4 -0.4 -371 4.3 HDGF CLOCK SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 UPF3A GC13P114279 LOC105370384 CDC16 CHAMP1 RASA3
GH13I114126 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 18.3 -151.9 -151872 7 HDGF SMAD1 ARNT SIN3A ZNF2 IRF4 POLR2B ZNF213 FOS REST RASA3 CDC16 PCID2 CHAMP1 GAS6 UPF3A GAS6-AS1 DCUN1D2-AS LINC00565 PIR55533
GH13I113296 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 22.5 -983.9 -983890 2.6 CLOCK MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 LAMP1 CDC16 PCID2 TUBGCP3 UPF3A GAS6-AS2 GAS6 CUL4A GAS6-AS1 DCUN1D2-AS
GH13I114104 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 32.2 -172.6 -172568 9.3 RING1 CTCF MEIS2 PKNOX1 ZNF529 MAX ZIC2 RAD21 POLR2A SCRT2 PIR43235 RASA3-IT1 CDC16 UPF3A RASA3 PIR39138 PIR55533
GH13I114312 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 16.6 +32.9 32945 3.4 HDGF PKNOX1 CLOCK MLX ZFP64 SIN3A ZNF2 IRF4 E2F8 ZNF207 CHAMP1 UPF3A CDC16 GAS6-AS1 LINC01054
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around UPF3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the UPF3A gene promoter:

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)

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

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:0005487 nuclear pore activity NAS 11163187
GO:0005515 protein binding IPI 11163187
GO:0042162 telomeric DNA binding IDA 17916692
genes like me logo Genes that share ontologies with UPF3A: view

Phenotypes for UPF3A Gene

GenomeRNAi human phenotypes for UPF3A:
genes like me logo Genes that share phenotypes with UPF3A: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , 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

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for UPF3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus NAS,IDA 11163187
GO:0005737 cytoplasm NAS 11163187
GO:0005829 cytosol TAS --
GO:0035145 colocalizes_with exon-exon junction complex TAS 11546873
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:0006810 transport IEA --
GO:0006913 nucleocytoplasmic transport IEA --
GO:0045727 positive regulation of translation IDA 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

Unigene Clusters for UPF3A Gene

UPF3 regulator of nonsense transcripts homolog A (yeast):
Representative Sequences:

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
ECgene alternative splicing isoforms for
UPF3A

Expression for UPF3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for UPF3A Gene



Protein tissue co-expression partners for UPF3A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of UPF3A Gene:

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 34
  • 98 (a)
OneToOne
LOC750926 33
  • 93.48 (n)
cow
(Bos Taurus)
Mammalia UPF3A 33 34
  • 79.47 (n)
dog
(Canis familiaris)
Mammalia UPF3A 33 34
  • 79.44 (n)
rat
(Rattus norvegicus)
Mammalia Upf3a 33
  • 77.13 (n)
mouse
(Mus musculus)
Mammalia Upf3a 33 16 34
  • 75.95 (n)
oppossum
(Monodelphis domestica)
Mammalia UPF3A 34
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UPF3A 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves UPF3A 33 34
  • 72.34 (n)
lizard
(Anolis carolinensis)
Reptilia UPF3A 34
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia upf3a 33
  • 69.41 (n)
zebrafish
(Danio rerio)
Actinopterygii upf3a 33 34
  • 62.12 (n)
fruit fly
(Drosophila melanogaster)
Insecta Upf3 34
  • 23 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea smg-4 34
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2608 34
  • 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)

Paralogs for UPF3A Gene

Paralogs for UPF3A Gene

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

Pseudogenes.org Pseudogenes for UPF3A Gene

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

Variants for UPF3A Gene

Sequence variations from dbSNP and Humsavar for UPF3A Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs1000041544 -- 114,289,705(+) T/G genic_downstream_transcript_variant, intron_variant
rs1000120348 -- 114,291,350(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000186409 -- 114,292,519(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000249106 -- 114,284,972(+) C/G intron_variant
rs1000606194 -- 114,305,116(+) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant

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

Additional Disease Information for UPF3A

No disorders were found for UPF3A Gene.

No data available for MalaCards , 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 22 58
  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 22 58
  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 22 58
  4. A UPF3-mediated regulatory switch that maintains RNA surveillance. (PMID: 19503078) Chan WK … Wilkinson MF (Nature structural & molecular biology 2009) 3 22 58
  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 22 58

Products for UPF3A Gene

Sources for UPF3A Gene

Content
Loading form....