Gene Page:RIMS3

Summary?
GeneID 9783
Symbol RIMS3
Synonyms NIM3|RIM3
Description regulating synaptic membrane exocytosis 3
Reference MIM:611600|HGNC:HGNC:21292|Ensembl:ENSG00000117016|HPRD:17976|Vega:OTTHUMG00000007453
Gene type protein-coding
Map location 1p34.2
Pascal p-value 0.02
Sherlock p-value 0.97
Fetal beta -2.045
DMG 1 (# studies)
Support EXOCYTOSIS

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
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). 1
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,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg07244188 1 41114200 RIMS3 2.046E-4 0.53 0.035 DMG:Wockner_2014


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
KIAA0100 0.91 0.90
NPLOC4 0.90 0.88
CLCN6 0.90 0.89
TRAPPC10 0.90 0.90
CYFIP2 0.90 0.92
LONP2 0.90 0.87
FBXW11 0.89 0.87
RAB5B 0.89 0.87
NARS 0.89 0.85
CNNM2 0.89 0.88
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.21 -0.71 -0.58
GNG11 -0.64 -0.56
IL32 -0.63 -0.54
VAMP5 -0.63 -0.53
C1orf54 -0.63 -0.60
FXYD1 -0.63 -0.53
AP002478.3 -0.63 -0.57
MT-CO2 -0.62 -0.52
HIGD1B -0.62 -0.55
AC098691.2 -0.61 -0.52

Section III. Gene Ontology annotation

Molecular function GO term Evidence Neuro keywords PubMed ID
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds IEA -
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0006836 neurotransmitter transport IEA neuron, Neurotransmitter (GO term level: 5) -
GO:0005975 carbohydrate metabolic process IEA -
GO:0006887 exocytosis IEA -
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0045202 synapse IEA neuron, Synap, Neurotransmitter, Glial (GO term level: 2) -
GO:0030054 cell junction IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
GARY CD5 TARGETS UP 473 314 All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY DN 367 220 All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN 800 473 All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 DN 464 276 All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION UP 142 93 All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR 293 193 All SZGR 2.0 genes in this pathway
BASSO CD40 SIGNALING DN 68 44 All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN 287 208 All SZGR 2.0 genes in this pathway
WANG LSD1 TARGETS DN 39 30 All SZGR 2.0 genes in this pathway
RAY TUMORIGENESIS BY ERBB2 CDC25A DN 159 105 All SZGR 2.0 genes in this pathway
LEE INTRATHYMIC T PROGENITOR 21 14 All SZGR 2.0 genes in this pathway
SHEDDEN肺癌好生存A4 196 124 All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP 756 494 All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP 682 440 All SZGR 2.0 genes in this pathway
ROLEF GLIS3 TARGETS 37 29 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-103/107 103 109 1A hsa-miR-103brain AGCAGCAUUGUACAGGGCUAUGA
hsa-miR-107brain AGCAGCAUUGUACAGGGCUAUCA
miR-128 3797 3803 m8 hsa-miR-128a UCACAGUGAACCGGUCUCUUUU
hsa-miR-128b UCACAGUGAACCGGUCUCUUUC
miR-137 5618 5624 m8 hsa-miR-137 UAUUGCUUAAGAAUACGCGUAG
hsa-miR-137 UAUUGCUUAAGAAUACGCGUAG
miR-138 1185 1191 m8 hsa-miR-138brain AGCUGGUGUUGUGAAUC
miR-182 5745 5751 m8 hsa-miR-182 UUUGGCAAUGGUAGAACUCACA
miR-214 101 107 m8 hsa-miR-214brain ACAGCAGGCACAGACAGGCAG
miR-218 3594 3600 1A hsa-miR-218brain UUGUGCUUGAUCUAACCAUGU
hsa-miR-218brain UUGUGCUUGAUCUAACCAUGU
miR-221/222 613 620 1A,m8 hsa-miR-221brain AGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brain AGCUACAUCUGGCUACUGGGUCUC
hsa-miR-221brain AGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brain AGCUACAUCUGGCUACUGGGUCUC
hsa-miR-221brain AGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brain AGCUACAUCUGGCUACUGGGUCUC
hsa-miR-221brain AGCUACAUUGUCUGCUGGGUUUC
hsa-miR-222brain AGCUACAUCUGGCUACUGGGUCUC
miR-31 5743 5750 1A,m8 hsa-miR-31 AGGCAAGAUGCUGGCAUAGCUG
miR-324-3p 140 146 m8 hsa-miR-324-3p CCACUGCCCCAGGUGCUGCUGG
miR-34/449 3511 3517 1A hsa-miR-34abrain UGGCAGUGUCUUAGCUGGUUGUU
hsa-miR-34c AGGCAGUGUAGUUAGCUGAUUGC
hsa-miR-449 UGGCAGUGUAUUGUUAGCUGGU
hsa-miR-449b AGGCAGUGUAUUGUUAGCUGGC
miR-493-5p 5788 5794 m8 hsa-miR-493-5p UUGUACAUGGUAGGCUUUCAUU
miR-9 4295 4301 1A hsa-miR-9SZ UCUUUGGUUAUCUAGCUGUAUGA
hsa-miR-9SZ UCUUUGGUUAUCUAGCUGUAUGA