Gene Page: UPF3A

Summary ?
GeneID65110
SymbolUPF3A
SynonymsHUPF3A|RENT3A|UPF3
DescriptionUPF3 regulator of nonsense transcripts homolog A (yeast)
ReferenceMIM:605530|HGNC:HGNC:20332|Ensembl:ENSG00000169062|HPRD:09274|Vega:OTTHUMG00000017403
Gene typeprotein-coding
Map location13q34
Pascal p-value0.027
Sherlock p-value0.321
Fetal beta1.241
DMG1 (# studies)
eGeneCaudate basal ganglia
Cortex
Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg0675619313115046767UPF3A2.04E-9-0.0091.65E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17392743chr154764240UPF3A651100.05trans
rs16955618chr1529937543UPF3A651100.08trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0000166nucleotide bindingIEA-
GO:0003723RNA bindingIEA-
GO:0005487nucleocytoplasmic transporter activityNAS11163187 
GO:0005515protein bindingIPI15231747 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000184nuclear-transcribed mRNA catabolic process, nonsense-mediated decayNAS11163187 
GO:0006810transportIEA-
GO:0051028mRNA transportIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusNAS11163187 
GO:0005737cytoplasmNAS11163187 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
DCP2FLJ33245 | NUDT20DCP2 decapping enzyme homolog (S. cerevisiae)Affinity Capture-WesternBioGRID14527413 
EXOSC10PM-Scl | PM/Scl-100 | PMSCL | PMSCL2 | RRP6 | Rrp6p | p2 | p3 | p4exosome component 10Affinity Capture-WesternBioGRID14527413 
EXOSC2RRP4 | Rrp4p | hRrp4p | p7exosome component 2Affinity Capture-WesternBioGRID14527413 
EXOSC4FLJ20591 | RRP41 | RRP41A | Rrp41p | SKI6 | Ski6p | hRrp41p | p12Aexosome component 4Affinity Capture-WesternBioGRID14527413 
GSK3B-glycogen synthase kinase 3 beta-HPRD,BioGRID15231747 
HBBCD113t-Chemoglobin, betaProtein-RNABioGRID11163187 
HNRNPA1HNRPA1 | MGC102835heterogeneous nuclear ribonucleoprotein A1-HPRD11546873 
IFITM21-8Dinterferon induced transmembrane protein 2 (1-8D)-HPRD,BioGRID15231747 
NXF1DKFZp667O0311 | MEX67 | TAPnuclear RNA export factor 1-HPRD11546873 
PARNDANpoly(A)-specific ribonuclease (deadenylation nuclease)Affinity Capture-WesternBioGRID14527413 
RBM8ABOV-1A | BOV-1B | BOV-1C | MDS014 | RBM8 | RBM8B | Y14 | ZNRP | ZRNP1RNA binding motif protein 8A-HPRD,BioGRID11546873 
SMG161E3.4 | ATX | KIAA0421 | LIPPI-3-kinase-related kinase SMG-1Affinity Capture-WesternBioGRID11544179 
THOC4ALY | BEFTHO complex 4-HPRD11546873 
UPF1FLJ43809 | FLJ46894 | HUPF1 | KIAA0221 | NORF1 | RENT1 | pNORF1UPF1 regulator of nonsense transcripts homolog (yeast)-HPRD,BioGRID11163187 
UPF2DKFZp434D222 | HUPF2 | KIAA1408 | MGC138834 | MGC138835 | RENT2 | smg-3UPF2 regulator of nonsense transcripts homolog (yeast)-HPRD,BioGRID11163187 
UPF3BHUPF3B | MRXS14 | RENT3B | UPF3XUPF3 regulator of nonsense transcripts homolog B (yeast)Affinity Capture-WesternBioGRID14527413 
XRN1DKFZp434P0721 | DKFZp686B22225 | DKFZp686F19113 | FLJ41903 | SEP15'-3' exoribonuclease 1Affinity Capture-WesternBioGRID14527413 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
REACTOME METABOLISM OF MRNA 284128All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA 330155All SZGR 2.0 genes in this pathway
REACTOME NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 17657All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN 663425All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
LAIHO COLORECTAL CANCER SERRATED DN 8647All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS DN 459276All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE DN 485334All SZGR 2.0 genes in this pathway
HAMAI APOPTOSIS VIA TRAIL UP 584356All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062725All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS UP 424268All SZGR 2.0 genes in this pathway
GALE APL WITH FLT3 MUTATED UP 5635All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI DN 172107All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973570All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER UP 298174All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS UP 7445All SZGR 2.0 genes in this pathway
SAKAI CHRONIC HEPATITIS VS LIVER CANCER UP 8363All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN 918550All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B 549316All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B 517302All SZGR 2.0 genes in this pathway