Gene Page:RAB3A

Summary?
GeneID 5864
Symbol RAB3A
Synonyms -
Description RAB3A, member RAS oncogene family
Reference MIM:179490|HGNC:HGNC:9777|Ensembl:ENSG00000105649|HPRD:01535|Vega:OTTHUMG00000137378
Gene type protein-coding
Map location 19p13.2
Pascal p-value 0.488
Sherlock p-value 0.894
Fetal beta -1.555
DMG 2 (# studies)
Support INTRACELLULAR 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 set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Nishioka_2013 Genome-wide DNA methylation analysis The 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_2014 Genome-wide DNA methylation analysis This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 3
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature High-throughput literature-search Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 7

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg21529164 19 18313289 RAB3A 3.28E-5 0.607 0.019 DMG:Wockner_2014
cg22617898 19 18313388 RAB3A 4.194E-4 0.584 0.045 DMG:Wockner_2014
cg26001336 19 18315002 RAB3A -0.023 0.58 DMG: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
Gene Pearson's Correlation Spearman's Correlation
CXorf39 0.53 0.58
DNAJC6 0.52 0.60
UBE3C 0.51 0.59
USH2A 0.50 0.37
MEF2A 0.50 0.60
PLEKHB2 0.50 0.57
ARID5B 0.49 0.60
SOD2 0.49 0.56
AC010896.1 0.49 0.55
DDHD2 0.49 0.56
Top 10 negatively co-expressed genes
Gene Pearson'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 function 去的术语 Evidence Neuro keywords PubMed ID
GO:0000166 nucleotide binding IEA -
: 0003924 GTPase activity IMP 10859313
GO:0005515 protein binding 新闻学会 10859313
GO:0005515 protein binding ISS -
GO:0005525 GTP binding IEA -
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0007409 axonogenesis IEA neuron, axon, neurite (GO term level: 12) -
GO:0016188 synaptic vesicle maturation IEA Synap (GO term level: 8) -
GO:0031630 regulation of synaptic vesicle fusion to presynaptic membrane IEA Synap, Neurotransmitter (GO term level: 11) -
GO:0007274 neuromuscular synaptic transmission IEA neuron, Synap (GO term level: 7) -
GO:0016079 synaptic vesicle exocytosis IEA neuron, Synap, Neurotransmitter (GO term level: 9) -
GO:0048790 maintenance of presynaptic active zone structure IEA neuron, Synap, Neurotransmitter (GO term level: 9) -
: 0003016 respiratory system process IEA -
GO:0009791 post-embryonic development IEA -
GO:0007005 mitochondrion organization IEA -
GO:0007264 small GTPase mediated signal transduction IEA -
GO:0015031 protein transport IEA -
GO:0050975 sensory perception of touch IEA -
GO:0051602 response to electrical stimulus IEA -
GO:0030324 lung development IEA -
GO:0017157 regulation of exocytosis IEA -
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0008021 synaptic vesicle TAS Synap, Neurotransmitter (GO term level: 12) 9194562
GO:0005737 cytoplasm IDA 18029348
GO:0005886 plasma membrane IEA -

Section IV. Protein-protein interaction annotation

Interactors Aliases B Official full name B Experimental Source PubMed ID
BSN ZNF231 bassoon (presynaptic cytomatrix protein) Affinity Capture-Western BioGRID 14734538
CASK CAGH39 |发生| FLJ22219 | FLJ31914 | LIN2 | MICPCH | TNRC8 calcium/calmodulin-dependent serine protein kinase (MAGUK family) - HPRD 11377421
CHM DXS540 | FLJ38564 | GGTA | HSD-32 | MGC102710 | REP-1 | TCD choroideremia (Rab escort protein 1) - HPRD,BioGRID 12535645
CHML FLJ10071 | FLJ13361 | REP2 choroideremia-like (Rab escort protein 2) - HPRD,BioGRID 12535645
DMXL2 FLJ26672 | KIAA0856 | RC3 Dmx-like 2 - HPRD 11809763
RAB3IL1 GRAB RAB3A interacting protein (rabin3)-like 1 - HPRD 11516400
RAB3IP FLJ14660 | FLJ22548 | MGC71495 | RABIN3 RAB3A interacting protein (rabin3) - HPRD 7532276
RABAC1 PRA1 | PRAF1 | YIP3 Rab acceptor 1 (prenylated) - HPRD,BioGRID 9341137
RABGGTB GGTB Rab geranylgeranyltransferase, beta subunit - HPRD,BioGRID 8706741
RABIF MSS4 | RASGFR3 | RASGRF3 RAB interacting factor - HPRD,BioGRID 9013620
RIMS1 CORD7 | KIAA0340 | MGC167823 | MGC176677 | RAB3IP2 | RIM | RIM1 regulating synaptic membrane exocytosis 1 Affinity Capture-Western
Reconstituted Complex		 BioGRID 11343654|12578829
RIMS2 DKFZp781A0653 | KIAA0751 | OBOE | RAB3IP3 | RIM2 regulating synaptic membrane exocytosis 2 - HPRD,BioGRID 12578829
RPH3A KIAA0985 rabphilin 3A homolog (mouse) - HPRD 10025402|12937130
RPH3A KIAA0985 rabphilin 3A homolog (mouse) Affinity Capture-Western
Co-crystal Structure
Reconstituted Complex		 BioGRID 8636125|10025402
|12578829
RPH3AL NOC2 rabphilin 3类似(没有C2域) - HPRD,BioGRID 11134008|12578829
SYTL4 DKFZp451P0116 | FLJ40960 | SLP4 synaptotagmin-like 4 - HPRD,BioGRID 11773082
SYTL5 slp5 synaptotagmin-like 5 - HPRD,BioGRID 12051743


Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
BIOCARTA RAB PATHWAY 12 8 All SZGR 2.0 genes in this pathway
REACTOME GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 15 13 All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES 186 155 All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279 221 All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RELEASE CYCLE 34 30 All SZGR 2.0 genes in this pathway
REACTOME DOPAMINE NEUROTRANSMITTER RELEASE CYCLE 11 11 All SZGR 2.0 genes in this pathway
REACTOME ACETYLCHOLINE NEUROTRANSMITTER RELEASE CYCLE 10 9 All SZGR 2.0 genes in this pathway
REACTOME NOREPINEPHRINE NEUROTRANSMITTER RELEASE CYCLE 10 10 All SZGR 2.0 genes in this pathway
REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 17 16 All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN UP 184 125 All SZGR 2.0 genes in this pathway
WATTEL AUTONOMOUS THYROID ADENOMA UP 73 47 All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM4 261 153 All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS 957 597 All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775 494 All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES 648 385 All SZGR 2.0 genes in this pathway
LEE TARGETS OF PTCH1 AND SUFU DN 83 69 All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS POSTNATAL 63 50 All SZGR 2.0 genes in this pathway
LU AGING BRAIN DN 153 120 All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237 837 All SZGR 2.0 genes in this pathway
YIH RESPONSE TO ARSENITE C4 18 12 All SZGR 2.0 genes in this pathway
WANG LSD1 TARGETS DN 39 30 All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305 895 All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103 714 All SZGR 2.0 genes in this pathway
NIELSEN GIST 98 66 All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE M G1 148 95 All SZGR 2.0 genes in this pathway
ACOSTA PROLIFERATION INDEPENDENT MYC TARGETS UP 84 51 All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A 898 516 All SZGR 2.0 genes in this pathway
ROESSLER LIVER CANCER METASTASIS UP 107 72 All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725 838 All SZGR 2.0 genes in this pathway