Gene Page: RIMS1

Summary ?
GeneID22999
SymbolRIMS1
SynonymsCORD7|RAB3IP2|RIM|RIM1
Descriptionregulating synaptic membrane exocytosis 1
ReferenceMIM:606629|HGNC:HGNC:17282|Ensembl:ENSG00000079841|HPRD:09435|Vega:OTTHUMG00000015009
Gene typeprotein-coding
Map location6q12-q13
Pascal p-value0.001
Fetal beta-1.584
eGeneMyers' cis & trans
SupportCANABINOID
DOPAMINE
EXOCYTOSIS
SEROTONIN
G2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWAScatGenome-wide Association StudiesThis data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGC128Genome-wide Association StudyA multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 6 

Section I. Genetics and epigenetics annotation

@CV:PGC128

SNP IDChromosomePositionAllelePFunctionGeneUp/Down Distance
rs1339227chr673155701TC6.86E-8intergenicRIMS1,KCNQ5dist=42856;dist=175870

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
RIMS1chr672926932TGNM_001168407
NM_001168408
NM_001168409
NM_001168410
NM_014989		.
.
.
p.14L>W
.		intronic
intronic
intronic
missense
intronic		SchizophreniaDNM:Fromer_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs1507047chr1650932778RIMS1229990.2trans

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
BCLAF10.970.98
ZMYM40.960.97
ZNF518B0.960.98
WAPAL0.960.97
AP001011.30.960.97
ZNF5070.960.96
RBM160.960.97
ZMYM20.960.97
WHSC1L10.960.97
KIAA05860.960.96
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
FXYD1-0.76-0.87
AF347015.31-0.76-0.87
MT-CO2-0.76-0.88
IFI27-0.74-0.87
AF347015.27-0.73-0.84
AF347015.33-0.73-0.83
HIGD1B-0.72-0.86
AF347015.8-0.72-0.86
MT-CYB-0.72-0.83
HSD17B14-0.72-0.79

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005515protein bindingIPI11438518 
GO:0005515protein bindingISS-
GO:0008270zinc ion bindingIEA-
GO:0017137Rab GTPase bindingIEA-
GO:0046872metal ion bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0045055regulated secretory pathwayNASNeurotransmitter (GO term level: 7)11438518 
GO:0048169regulation of long-term neuronal synaptic plasticityIEAneuron, Synap (GO term level: 10)-
GO:0016079synaptic vesicle exocytosisTASneuron, Synap, Neurotransmitter (GO term level: 9)11438518 
GO:0006836neurotransmitter transportIEAneuron, Neurotransmitter (GO term level: 5)-
GO:0006461protein complex assemblyIDA11438518 
GO:0007601visual perceptionIEA-
GO:0006944membrane fusionNAS11438518 
GO:0006886intracellular protein transportIEA-
GO:0050896response to stimulusIEA-
GO:0017156calcium ion-dependent exocytosisTAS11438518 
GO:0046903secretionNAS11438518 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0042734presynaptic membraneISSneuron, axon, Synap (GO term level: 5)-
GO:0042734presynaptic membraneNASneuron, axon, Synap (GO term level: 5)11438518 
GO:0045202synapseIEAneuron, Synap, Neurotransmitter, Glial (GO term level: 2)-
GO:0005886plasma membraneIEA-
GO:0030054cell junctionIEA-

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
BSNZNF231bassoon (presynaptic cytomatrix protein)Affinity Capture-WesternBioGRID14734538 
CAMK2ACAMKA | KIAA0968calcium/calmodulin-dependent protein kinase II alphaBiochemical ActivityBioGRID12871946 
ERC1Cast2 | ELKS | KIAA1081 | MGC12974 | RAB6IP2ELKS/RAB6-interacting/CAST family member 1-HPRD12391317 
ERC2CAST | CAST1 | ELKSL | KIAA0378 | MGC133063 | MGC133064 | SPBC110 | Spc110ELKS/RAB6-interacting/CAST family member 2-HPRD,BioGRID12163476 
LRRK1FLJ23119 | FLJ27465 | KIAA1790 | RIPK6 | Roco1leucine-rich repeat kinase 1Affinity Capture-MSBioGRID17353931 
RAB10-RAB10, member RAS oncogene familyAffinity Capture-WesternBioGRID12578829 
RAB26V46133RAB26, member RAS oncogene familyAffinity Capture-WesternBioGRID12578829 
RAB37FLJ30284 | FLJ32507RAB37, member RAS oncogene familyAffinity Capture-WesternBioGRID12578829 
RAB3A-RAB3A, member RAS oncogene familyAffinity Capture-Western
Reconstituted Complex		BioGRID11343654 |12578829 
RAB3B-RAB3B, member RAS oncogene familyAffinity Capture-WesternBioGRID12578829 
RAB3C-RAB3C, member RAS oncogene familyAffinity Capture-WesternBioGRID12578829 
RAB3DD2-2 | GOV | RAB16 | RAD3DRAB3D, member RAS oncogene familyAffinity Capture-WesternBioGRID12578829 
UNC13BMGC133279 | MGC133280 | MUNC13 | UNC13 | Unc13h2 | hmunc13unc-13 homolog B (C. elegans)-HPRD,BioGRID11343654 
YWHAHYWHA1tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptideAffinity Capture-Western
Reconstituted Complex
Two-hybrid		BioGRID12871946 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
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
MULLIGHAN MLL SIGNATURE 2 UP 418263All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 UP 256159All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS UP 268157All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B 549316All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE 1137655All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP 745475All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1 467251All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS UP 266142All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-12817681774m8hsa-miR-128aUCACAGUGAACCGGUCUCUUUU
hsa-miR-128bUCACAGUGAACCGGUCUCUUUC
miR-130/301112511311Ahsa-miR-130abrainCAGUGCAAUGUUAAAAGGGCAU
hsa-miR-301CAGUGCAAUAGUAUUGUCAAAGC
hsa-miR-130bbrainCAGUGCAAUGAUGAAAGGGCAU
hsa-miR-454-3pUAGUGCAAUAUUGCUUAUAGGGUUU
miR-133170217081Ahsa-miR-133aUUGGUCCCCUUCAACCAGCUGU
hsa-miR-133bUUGGUCCCCUUCAACCAGCUA
miR-13515811587m8hsa-miR-135aUAUGGCUUUUUAUUCCUAUGUGA
hsa-miR-135bUAUGGCUUUUCAUUCCUAUGUG
miR-141/200a3823891A,m8hsa-miR-141UAACACUGUCUGGUAAAGAUGG
hsa-miR-200aUAACACUGUCUGGUAACGAUGU
miR-142-5p16641670m8hsa-miR-142-5pCAUAAAGUAGAAAGCACUAC
miR-1453223291A,m8hsa-miR-145GUCCAGUUUUCCCAGGAAUCCCUU
hsa-miR-145GUCCAGUUUUCCCAGGAAUCCCUU
miR-19119411947m8hsa-miR-191brainCAACGGAAUCCCAAAAGCAGCU
miR-199109911051Ahsa-miR-199aCCCAGUGUUCAGACUACCUGUUC
hsa-miR-199bCCCAGUGUUUAGACUAUCUGUUC
miR-203.111601166m8hsa-miR-203UGAAAUGUUUAGGACCACUAG
miR-208201120171Ahsa-miR-208AUAAGACGAGCAAAAAGCUUGU
miR-218118111881A,m8hsa-miR-218brainUUGUGCUUGAUCUAACCAUGU
miR-219941011A,m8hsa-miR-219brainUGAUUGUCCAAACGCAAUUCU
miR-30-5p115611621Ahsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-325193319401A,m8hsa-miR-325CCUAGUAGGUGUCCAGUAAGUGU
miR-338856862m8hsa-miR-338brainUCCAGCAUCAGUGAUUUUGUUGA
miR-34b18031809m8hsa-miR-34bUAGGCAGUGUCAUUAGCUGAUUG
miR-3753173231Ahsa-miR-375UUUGUUCGUUCGGCUCGCGUGA
miR-495159315991Ahsa-miR-495brainAAACAAACAUGGUGCACUUCUUU
miR-496205620621Ahsa-miR-496AUUACAUGGCCAAUCUC
miR-499201120171Ahsa-miR-499UUAAGACUUGCAGUGAUGUUUAA