Gene Page:RIMS1

Summary?
GeneID 22999
Symbol RIMS1
Synonyms CORD7|RAB3IP2|RIM|RIM1
Description regulating synaptic membrane exocytosis 1
Reference MIM:606629|HGNC:HGNC:17282|Ensembl:ENSG00000079841|HPRD:09435|Vega:OTTHUMG00000015009
Gene type protein-coding
Map location 6q12-q13
Pascal p-value 0.001
Fetal beta -1.584
eGene Myers' cis & trans
Support CANABINOID
DOPAMINE
EXOCYTOSIS
SEROTONIN
G2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:GWAScat Genome-wide Association Studies This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdb Genome-wide Association Studies GWASdb records for schizophrenia
CV:PGC128 Genome-wide Association Study A 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:PGCnp Genome-wide Association Study GWAS
DNM:Fromer_2014 Whole Exome Sequencing analysis This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 6

Section I. Genetics and epigenetics annotation

@CV:PGC128

SNP ID Chromosome Position Allele P Function Gene Up/Down Distance
rs1339227 chr6 73155701 TC 6.86E-8 intergenic RIMS1,KCNQ5 dist=42856;dist=175870

@DNM table

Gene Chromosome Position Ref Alt Transcript AA change Mutation type Sift CG46 Trait Study
RIMS1 chr6 72926932 T G NM_001168407
NM_001168408
NM_001168409
NM_001168410
NM_014989		 .
.
.
p.14L>W
.		 intronic
intronic
intronic
missense
intronic		 Schizophrenia DNM:Fromer_2014

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs1507047 chr16 50932778 RIMS1 22999 0.2 trans

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
BCLAF1 0.97 0.98
ZMYM4 0.96 0.97
ZNF518B 0.96 0.98
WAPAL 0.96 0.97
AP001011.3 0.96 0.97
ZNF507 0.96 0.96
RBM16 0.96 0.97
ZMYM2 0.96 0.97
WHSC1L1 0.96 0.97
KIAA0586 0.96 0.96
Top 10 negatively co-expressed genes
Gene Pearson'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 function 去的术语 Evidence Neuro keywords PubMed ID
GO:0005515 protein binding 新闻学会 11438518
GO:0005515 protein binding ISS -
GO:0008270 zinc ion binding IEA -
GO:0017137 Rab GTPase binding IEA -
GO:0046872 metal ion binding IEA -
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0045055 regulated secretory pathway NAS Neurotransmitter (GO term level: 7) 11438518
GO:0048169 regulation of long-term neuronal synaptic plasticity IEA neuron, Synap (GO term level: 10) -
去:0016079 synaptic vesicle exocytosis TAS neuron, Synap, Neurotransmitter (GO term level: 9) 11438518
GO:0006836 neurotransmitter transport IEA neuron, Neurotransmitter (GO term level: 5) -
GO:0006461 protein complex assembly IDA 11438518
GO:0007601 visual perception IEA -
GO:0006944 membrane fusion NAS 11438518
GO:0006886 intracellular protein transport IEA -
GO:0050896 response to stimulus IEA -
GO:0017156 calcium ion-dependent exocytosis TAS 11438518
GO:0046903 secretion NAS 11438518
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0042734 presynaptic membrane ISS neuron, axon, Synap (GO term level: 5) -
GO:0042734 presynaptic membrane NAS neuron, axon, Synap (GO term level: 5) 11438518
GO:0045202 synapse IEA neuron, Synap, Neurotransmitter, Glial (GO term level: 2) -
GO:0005886 plasma membrane IEA -
GO:0030054 cell junction 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
CAMK2A CAMKA | KIAA0968 calcium/calmodulin-dependent protein kinase II alpha Biochemical Activity BioGRID 12871946
ERC1 Cast2 | ELKS | KIAA1081 | MGC12974 | RAB6IP2 麋鹿RAB6-interacting /家庭我mber 1 - HPRD 12391317
ERC2 CAST | CAST1 | ELKSL | KIAA0378 | MGC133063 | MGC133064 | SPBC110 | Spc110 麋鹿RAB6-interacting /家庭我mber 2 - HPRD,BioGRID 12163476
LRRK1 FLJ23119 | FLJ27465 | KIAA1790 | RIPK6 | Roco1 leucine-rich repeat kinase 1 Affinity Capture-MS BioGRID 17353931
RAB10 - RAB10, member RAS oncogene family Affinity Capture-Western BioGRID 12578829
RAB26 V46133 RAB26, member RAS oncogene family Affinity Capture-Western BioGRID 12578829
RAB37 FLJ30284 | FLJ32507 RAB37, member RAS oncogene family Affinity Capture-Western BioGRID 12578829
RAB3A - RAB3A, member RAS oncogene family Affinity Capture-Western
Reconstituted Complex		 BioGRID 11343654|12578829
RAB3B - RAB3B, member RAS oncogene family Affinity Capture-Western BioGRID 12578829
RAB3C - RAB3C, member RAS oncogene family Affinity Capture-Western BioGRID 12578829
RAB3D D2-2 | GOV | RAB16 | RAD3D RAB3D, member RAS oncogene family Affinity Capture-Western BioGRID 12578829
UNC13B MGC133279 | MGC133280 | MUNC13 | UNC13 | Unc13h2 | hmunc13 unc-13 homolog B (C. elegans) - HPRD,BioGRID 11343654
YWHAH YWHA1 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide Affinity Capture-Western
Reconstituted Complex
Two-hybrid		 BioGRID 12871946


Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
REACTOME谷氨酸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
MULLIGHAN MLL SIGNATURE 2 UP 418 263 All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 1652 1023 All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442 892 All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779 480 All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 UP 256 159 All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS UP 268 157 All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305 895 All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491 319 All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B 549 316 All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE 1137 655 All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP 745 475 All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1 467 251 All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS UP 266 142 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

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-128 1768 1774 m8 hsa-miR-128a UCACAGUGAACCGGUCUCUUUU
hsa-miR-128b UCACAGUGAACCGGUCUCUUUC
miR-130/301 1125 1131 1A hsa-miR-130abrain CAGUGCAAUGUUAAAAGGGCAU
hsa-miR-301 CAGUGCAAUAGUAUUGUCAAAGC
hsa-miR-130bbrain CAGUGCAAUGAUGAAAGGGCAU
hsa-miR-454-3p UAGUGCAAUAUUGCUUAUAGGGUUU
miR-133 1702 1708 1A hsa-miR-133a UUGGUCCCCUUCAACCAGCUGU
hsa-miR-133b UUGGUCCCCUUCAACCAGCUA
miR-135 1581 1587 m8 hsa-miR-135a UAUGGCUUUUUAUUCCUAUGUGA
hsa-miR-135b UAUGGCUUUUCAUUCCUAUGUG
miR-141/200a 382 389 1A,m8 hsa-miR-141 UAACACUGUCUGGUAAAGAUGG
hsa-miR-200a UAACACUGUCUGGUAACGAUGU
miR-142-5p 1664 1670 m8 hsa-miR-142-5p CAUAAAGUAGAAAGCACUAC
miR-145 322 329 1A,m8 hsa-miR-145 GUCCAGUUUUCCCAGGAAUCCCUU
hsa-miR-145 GUCCAGUUUUCCCAGGAAUCCCUU
miR-191 1941 1947 m8 hsa-miR-191brain CAACGGAAUCCCAAAAGCAGCU
miR-199 1099 1105 1A hsa-miR-199a CCCAGUGUUCAGACUACCUGUUC
hsa-miR-199b CCCAGUGUUUAGACUAUCUGUUC
miR-203.1 1160 1166 m8 hsa-miR-203 UGAAAUGUUUAGGACCACUAG
miR-208 2011 2017 1A hsa-miR-208 AUAAGACGAGCAAAAAGCUUGU
miR-218 1181 1188 1A,m8 hsa-miR-218brain UUGUGCUUGAUCUAACCAUGU
miR-219 94 101 1A,m8 hsa-miR-219brain UGAUUGUCCAAACGCAAUUCU
miR-30-5p 1156 1162 1A hsa-miR-30a-5p UGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrain UGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZ UGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZ UGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5p UGUAAACAUCCUUGACUGGA
miR-325 1933 1940 1A,m8 hsa-miR-325 CCUAGUAGGUGUCCAGUAAGUGU
miR-338 856 862 m8 hsa-miR-338brain UCCAGCAUCAGUGAUUUUGUUGA
miR-34b 1803 1809 m8 hsa-miR-34b UAGGCAGUGUCAUUAGCUGAUUG
miR-375 317 323 1A hsa-miR-375 UUUGUUCGUUCGGCUCGCGUGA
miR-495 1593 1599 1A hsa-miR-495brain AAACAAACAUGGUGCACUUCUUU
miR-496 2056 2062 1A hsa-miR-496 AUUACAUGGCCAAUCUC
miR-499 2011 2017 1A hsa-miR-499 UUAAGACUUGCAGUGAUGUUUAA