Gene Page: RAB3A

Summary ?
GeneID5864
SymbolRAB3A
Synonyms-
DescriptionRAB3A, member RAS oncogene family
ReferenceMIM:179490|HGNC:HGNC:9777|Ensembl:ENSG00000105649|HPRD:01535|Vega:OTTHUMG00000137378
Gene typeprotein-coding
Map location19p13.2
Pascal p-value0.488
Sherlock p-value0.894
Fetal beta-1.555
DMG2 (# studies)
SupportINTRACELLULAR TRAFFICKING
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_clathrin
G2Cdb.human_mGluR5
G2Cdb.human_PocklingtonH1
G2Cdb.human_Synaptosome
G2Cdb.humanNRC
G2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Nishioka_2013Genome-wide DNA methylation analysisThe authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. 3
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 3
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,schizophrenic,schizophrenics,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 7 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg215291641918313289RAB3A3.28E-50.6070.019DMG:Wockner_2014
cg226178981918313388RAB3A4.194E-40.5840.045DMG:Wockner_2014
cg260013361918315002RAB3A-0.0230.58DMG:Nishioka_2013


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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
CXorf390.530.58
DNAJC60.520.60
UBE3C0.510.59
USH2A0.500.37
MEF2A0.500.60
PLEKHB20.500.57
ARID5B0.490.60
SOD20.490.56
AC010896.10.490.55
DDHD20.490.56
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C1orf61-0.32-0.41
IL32-0.30-0.35
RAB34-0.29-0.31
GNG5-0.29-0.32
AC098691.2-0.28-0.29
RPS27L-0.27-0.31
METRN-0.27-0.29
IRF7-0.27-0.27
RFXANK-0.27-0.23
AL022328.1-0.27-0.26

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0000166nucleotide bindingIEA-
GO:0003924GTPase activityIMP10859313 
GO:0005515protein bindingIPI10859313 
GO:0005515protein bindingISS-
GO:0005525GTP bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007409axonogenesisIEAneuron, axon, neurite (GO term level: 12)-
GO:0016188synaptic vesicle maturationIEASynap (GO term level: 8)-
GO:0031630regulation of synaptic vesicle fusion to presynaptic membraneIEASynap, Neurotransmitter (GO term level: 11)-
GO:0007274neuromuscular synaptic transmissionIEAneuron, Synap (GO term level: 7)-
GO:0016079synaptic vesicle exocytosisIEAneuron, Synap, Neurotransmitter (GO term level: 9)-
GO:0048790maintenance of presynaptic active zone structureIEAneuron, Synap, Neurotransmitter (GO term level: 9)-
GO:0003016respiratory system processIEA-
GO:0009791post-embryonic developmentIEA-
GO:0007005mitochondrion organizationIEA-
GO:0007264small GTPase mediated signal transductionIEA-
GO:0015031protein transportIEA-
GO:0050975sensory perception of touchIEA-
GO:0051602response to electrical stimulusIEA-
GO:0030324lung developmentIEA-
GO:0017157regulation of exocytosisIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0008021synaptic vesicleTASSynap, Neurotransmitter (GO term level: 12)9194562 
GO:0005737cytoplasmIDA18029348 
GO:0005886plasma membraneIEA-

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
BSNZNF231bassoon (presynaptic cytomatrix protein)Affinity Capture-WesternBioGRID14734538 
CASKCAGH39 | CMG | FLJ22219 | FLJ31914 | LIN2 | MICPCH | TNRC8calcium/calmodulin-dependent serine protein kinase (MAGUK family)-HPRD11377421 
CHMDXS540 | FLJ38564 | GGTA | HSD-32 | MGC102710 | REP-1 | TCDchoroideremia (Rab escort protein 1)-HPRD,BioGRID12535645 
CHMLFLJ10071 | FLJ13361 | REP2choroideremia-like (Rab escort protein 2)-HPRD,BioGRID12535645 
DMXL2FLJ26672 | KIAA0856 | RC3Dmx-like 2-HPRD11809763 
RAB3IL1GRABRAB3A interacting protein (rabin3)-like 1-HPRD11516400 
RAB3IPFLJ14660 | FLJ22548 | MGC71495 | RABIN3RAB3A interacting protein (rabin3)-HPRD7532276 
RABAC1PRA1 | PRAF1 | YIP3Rab acceptor 1 (prenylated)-HPRD,BioGRID9341137 
RABGGTBGGTBRab geranylgeranyltransferase, beta subunit-HPRD,BioGRID8706741 
RABIFMSS4 | RASGFR3 | RASGRF3RAB interacting factor-HPRD,BioGRID9013620 
RIMS1CORD7 | KIAA0340 | MGC167823 | MGC176677 | RAB3IP2 | RIM | RIM1regulating synaptic membrane exocytosis 1Affinity Capture-Western
Reconstituted Complex		BioGRID11343654 |12578829 
RIMS2DKFZp781A0653 | KIAA0751 | OBOE | RAB3IP3 | RIM2regulating synaptic membrane exocytosis 2-HPRD,BioGRID12578829 
RPH3AKIAA0985rabphilin 3A homolog (mouse)-HPRD10025402 |12937130 
RPH3AKIAA0985rabphilin 3A homolog (mouse)Affinity Capture-Western
Co-crystal Structure
Reconstituted Complex		BioGRID8636125 |10025402 
|12578829 
RPH3ALNOC2rabphilin 3A-like (without C2 domains)-HPRD,BioGRID11134008|12578829 
SYTL4DKFZp451P0116 | FLJ40960 | SLP4synaptotagmin-like 4-HPRD,BioGRID11773082 
SYTL5slp5synaptotagmin-like 5-HPRD,BioGRID12051743 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
BIOCARTA RAB PATHWAY 128All SZGR 2.0 genes in this pathway
REACTOME GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 1513All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES 186155All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279221All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RELEASE CYCLE 3430All SZGR 2.0 genes in this pathway
REACTOME DOPAMINE NEUROTRANSMITTER RELEASE CYCLE 1111All SZGR 2.0 genes in this pathway
REACTOME ACETYLCHOLINE NEUROTRANSMITTER RELEASE CYCLE 109All SZGR 2.0 genes in this pathway
REACTOME NOREPINEPHRINE NEUROTRANSMITTER RELEASE CYCLE 1010All SZGR 2.0 genes in this pathway
REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 1716All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN UP 184125All SZGR 2.0 genes in this pathway
WATTEL AUTONOMOUS THYROID ADENOMA UP 7347All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM4 261153All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS 957597All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES 648385All SZGR 2.0 genes in this pathway
LEE TARGETS OF PTCH1 AND SUFU DN 8369All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS POSTNATAL 6350All SZGR 2.0 genes in this pathway
LU AGING BRAIN DN 153120All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
YIH RESPONSE TO ARSENITE C4 1812All SZGR 2.0 genes in this pathway
WANG LSD1 TARGETS DN 3930All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
NIELSEN GIST 9866All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE M G1 14895All SZGR 2.0 genes in this pathway
ACOSTA PROLIFERATION INDEPENDENT MYC TARGETS UP 8451All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A 898516All SZGR 2.0 genes in this pathway
ROESSLER LIVER CANCER METASTASIS UP 10772All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway