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Aliases for UPF3A Gene

Aliases for UPF3A Gene

  • UPF3 Regulator Of Nonsense Transcripts Homolog A (Yeast) 2 3
  • RENT3A 3 4 6
  • Up-Frameshift Suppressor 3 Homolog A 3 4
  • Nonsense MRNA Reducing Factor 3A 3 4
  • HUpf3 3 4
  • UPF3 3 4
  • 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. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for UPF3A Gene

UPF3A (UPF3 Regulator Of Nonsense Transcripts Homolog A (Yeast)) is a Protein Coding gene. Among its related pathways are Gene Expression and RNA transport. GO annotations related to this gene include RNA binding and nucleocytoplasmic transporter 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UPF3A Gene

Genomics for UPF3A Gene

Regulatory Elements for UPF3A Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for UPF3A Gene

Start:
114,281,584 bp from pter
End:
114,305,817 bp from pter
Size:
24,234 bases
Orientation:
Plus strand

Genomic View for UPF3A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for UPF3A Gene at MOPED

Post-translational modifications for UPF3A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for UPF3A Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for UPF3A Gene

Domains for UPF3A Gene

Protein Domains for UPF3A Gene

Graphical View of Domain Structure for InterPro Entry

Q9H1J1

UniProtKB/Swiss-Prot:

REN3A_HUMAN :
  • Q9H1J1
Family:
  • Belongs to the RENT3 family.
genes like me logo Genes that share domains with UPF3A: view

No data available for Gene Families for UPF3A Gene

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.

Gene Ontology (GO) - Molecular Function for UPF3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003723 RNA binding IEA --
GO:0005487 nucleocytoplasmic transporter activity NAS 11163187
GO:0005515 protein binding IPI 11163187
genes like me logo Genes that share ontologies with UPF3A: view

Animal Model Products

CRISPR Products

miRNA for UPF3A Gene

miRTarBase miRNAs that target UPF3A

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting 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
Jensen Localization Image for UPF3A Gene COMPARTMENTS Subcellular localization image for UPF3A gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 4

Gene Ontology (GO) - Cellular Components for UPF3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS 11163187
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm NAS 11163187
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with UPF3A: view

Pathways 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 NAS 11163187
GO:0010467 gene expression TAS --
GO:0016070 RNA metabolic process --
GO:0016071 mRNA metabolic process --
genes like me logo Genes that share ontologies with UPF3A: view

Transcripts for UPF3A Gene

Unigene Clusters for UPF3A Gene

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

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for UPF3A

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for UPF3A

Flow Cytometry 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 for UPF3A Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for UPF3A Gene

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.
genes like me logo Genes that share expressions with UPF3A: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues 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 LOC750926 35
  • 93.48 (n)
  • 89.81 (a)
UPF3A 36
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia UPF3A 35
  • 79.47 (n)
  • 76.6 (a)
UPF3A 36
  • 67 (a)
OneToOne
dog
(Canis familiaris)
Mammalia UPF3A 35
  • 79.44 (n)
  • 74.24 (a)
UPF3A 36
  • 73 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Upf3a 35
  • 75.95 (n)
  • 72.62 (a)
Upf3a 16
Upf3a 36
  • 69 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia UPF3A 36
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UPF3A 36
  • 67 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Upf3a 35
  • 77.13 (n)
  • 73.92 (a)
chicken
(Gallus gallus)
Aves UPF3A 35
  • 72.34 (n)
  • 67.02 (a)
UPF3A 36
  • 55 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia UPF3A 36
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia upf3a 35
  • 69.41 (n)
  • 69.15 (a)
zebrafish
(Danio rerio)
Actinopterygii upf3a 35
  • 62.12 (n)
  • 60.05 (a)
upf3a 36
  • 50 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Upf3 36
  • 23 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea smg-4 36
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2608 36
  • 28 (a)
OneToMany
Species with no ortholog for UPF3A:
  • 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

Selected 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 Sequence Context AA Info Type MAF
rs15333 -- 114,305,634(-) GCTAT(A/C)TCTAG utr-variant-3-prime, nc-transcript-variant
rs1057604 -- 114,287,272(+) CTTTC(A/C)TCAAA intron-variant
rs1135496 -- 114,287,458(+) TGGTG(G/T)TGCGT intron-variant
rs1135498 -- 114,287,463(+) GTGCG(C/T)GCCTA intron-variant
rs2464271 -- 114,298,401(-) cacca(C/T)acccg intron-variant

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

Variant ID Type Subtype PubMed ID
nsv901115 CNV Gain 21882294
esv25715 CNV Gain+Loss 19812545
nsv901116 CNV Gain 21882294
nsv826841 CNV Loss 20364138
esv1000540 CNV Insertion 20482838
esv1401261 CNV Insertion 17803354
nsv64869 CNV Insertion 16902084
nsv518491 CNV Loss 19592680

Relevant External Links for UPF3A Gene

HapMap Linkage Disequilibrium report
UPF3A

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

Disorders for UPF3A Gene

Relevant External Links for UPF3A

Genetic Association Database (GAD)
UPF3A
genes like me logo Genes that share disorders with UPF3A: view

No data available for UniProtKB/Swiss-Prot 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 L.E. (Mol. Cell. Biol. 2001) 2 3 4 23
  2. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. (PMID: 11163187) Lykke-Andersen J. … Steitz J.A. (Cell 2000) 2 3 4 23
  3. Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. (PMID: 16601204) Kunz J.B. … Gehring N.H. (RNA 2006) 3 4 23
  4. 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. (Mol. Cell 2007) 3 23
  5. The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. (PMID: 15004547) Kadlec J. … Cusack S. (Nat. Struct. Mol. Biol. 2004) 3 23

Products for UPF3A Gene

Sources for UPF3A Gene

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