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Aliases for RIMS3 Gene

Aliases for RIMS3 Gene

  • Regulating Synaptic Membrane Exocytosis 3 2 3 5
  • Rab-3-Interacting Molecule 3 3 4
  • RIM3 Gamma 3 4
  • RIM 3 3 4
  • Regulating Synaptic Membrane Exocytosis Protein 3 3
  • Rab-3 Interacting Molecule 3 3
  • KIAA0237 4
  • NIM3 3
  • RIM3 3
  • Nim3 4

External Ids for RIMS3 Gene

Previous GeneCards Identifiers for RIMS3 Gene

  • GC01M040549
  • GC01M040499
  • GC01M040505
  • GC01M040755
  • GC01M040858
  • GC01M041086
  • GC01M039204

Summaries for RIMS3 Gene

GeneCards Summary for RIMS3 Gene

RIMS3 (Regulating Synaptic Membrane Exocytosis 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include ion channel binding. An important paralog of this gene is RIMS1.

UniProtKB/Swiss-Prot for RIMS3 Gene

  • Regulates synaptic membrane exocytosis.

Additional gene information for RIMS3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RIMS3 Gene

Genomics for RIMS3 Gene

GeneHancer (GH) Regulatory Elements for RIMS3 Gene

Promoters and enhancers for RIMS3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J040690 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 684.1 -0.6 -617 4.4 ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 SP3 NFYC MEF2D RIMS3 NFYC-AS1 NFYC EXO5 ENSG00000259943 TRIT1 LOC105378674 ZFP69 SLFNL1 MIR30C1
GH01J040665 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 657.7 +26.4 26389 1 SIN3A ZNF2 GLIS2 ZNF143 KLF7 ATF7 SP3 GMEB1 SMARCA4 ZNF184 RIMS3 LOC105378675 GC01P040673
GH01J040708 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 24.9 -19.2 -19154 6.1 PKNOX1 SMAD1 FOXA2 ARNT ARID4B FEZF1 DMAP1 YY1 SLC30A9 POLR2B NFYC EXO5 RLF RIMS3 TRIT1 LOC105378674 NFYC-AS1 MIR30E MIR30C1 LOC105378672
GH01J040698 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 25.5 -7.5 -7459 2 HDGF ATF1 ZBTB40 BATF IRF4 ZNF121 FOS ATF7 IKZF2 RUNX3 RIMS3 LOC105378674 MIR30E MIR30C1 NFYC ZNF684 KCNQ4 EXO5 CITED4 ZFP69
GH01J040372 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.2 +316.2 316231 5.9 FEZF1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D ZNF610 GLIS1 NBN SMAP2 PPIEL EXO5 PPIE TRIT1 ENSG00000259943 NFYC-AS1 RLF LOC105378674 ENSG00000229528
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RIMS3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RIMS3 gene promoter:
  • YY1
  • NRSF form 2
  • NRSF form 1
  • GATA-1
  • E2F-3a
  • E2F-1
  • E2F-2
  • E2F-4
  • E2F-5

Genomic Locations for RIMS3 Gene

Genomic Locations for RIMS3 Gene
71,406 bases
Minus strand
44,979 bases
Minus strand

Genomic View for RIMS3 Gene

Genes around RIMS3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RIMS3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RIMS3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RIMS3 Gene

Proteins for RIMS3 Gene

  • Protein details for RIMS3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Regulating synaptic membrane exocytosis protein 3
    Protein Accession:
    Secondary Accessions:
    • D3DPV8
    • Q92511
    • X5D7U7

    Protein attributes for RIMS3 Gene

    308 amino acids
    Molecular mass:
    32796 Da
    Quaternary structure:
    • Binds PPFIA3 (By similarity). Does not bind RAB3.
    • Sequence=BAA13243.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for RIMS3 Gene


neXtProt entry for RIMS3 Gene

Post-translational modifications for RIMS3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RIMS3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RIMS3 Gene

Domains & Families for RIMS3 Gene

Gene Families for RIMS3 Gene

Protein Domains for RIMS3 Gene


Suggested Antigen Peptide Sequences for RIMS3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RIMS3: view

No data available for UniProtKB/Swiss-Prot for RIMS3 Gene

Function for RIMS3 Gene

Molecular function for RIMS3 Gene

UniProtKB/Swiss-Prot Function:
Regulates synaptic membrane exocytosis.

Phenotypes From GWAS Catalog for RIMS3 Gene

Gene Ontology (GO) - Molecular Function for RIMS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0017137 Rab GTPase binding IBA --
GO:0044325 ion channel binding ISS --
genes like me logo Genes that share ontologies with RIMS3: view
genes like me logo Genes that share phenotypes with RIMS3: view

Animal Models for RIMS3 Gene

MGI Knock Outs for RIMS3:
  • Rims3 Rims3<tm1b(KOMP)Wtsi>
  • Rims3 Rims3<tm1a(KOMP)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RIMS3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RIMS3 Gene

Localization for RIMS3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RIMS3 Gene

Cell junction, synapse.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RIMS3 gene
Compartment Confidence
nucleus 3
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RIMS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030054 cell junction IEA --
GO:0042734 presynaptic membrane IBA --
GO:0045202 synapse IBA,IEA --
GO:0048786 presynaptic active zone TAS 15217342
GO:0048788 cytoskeleton of presynaptic active zone IBA --
genes like me logo Genes that share ontologies with RIMS3: view

Pathways & Interactions for RIMS3 Gene

SuperPathways for RIMS3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RIMS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006887 exocytosis IEA --
GO:0017156 calcium ion regulated exocytosis ISS --
GO:0042391 regulation of membrane potential ISS --
GO:0048167 regulation of synaptic plasticity IBA --
GO:0048791 calcium ion-regulated exocytosis of neurotransmitter IBA --
genes like me logo Genes that share ontologies with RIMS3: view

No data available for Pathways by source and SIGNOR curated interactions for RIMS3 Gene

Drugs & Compounds for RIMS3 Gene

No Compound Related Data Available

Transcripts for RIMS3 Gene

mRNA/cDNA for RIMS3 Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(102) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RIMS3 Gene

Regulating synaptic membrane exocytosis 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RIMS3

Alternative Splicing Database (ASD) splice patterns (SP) for RIMS3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP2: -

Relevant External Links for RIMS3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RIMS3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RIMS3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RIMS3 Gene

This gene is overexpressed in Brain - Cortex (x10.0), Brain - Frontal Cortex (BA9) (x8.8), and Brain - Anterior cingulate cortex (BA24) (x6.1).

Protein differential expression in normal tissues from HIPED for RIMS3 Gene

This gene is overexpressed in Breast (35.1), Brain (23.8), and Frontal cortex (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RIMS3 Gene

Protein tissue co-expression partners for RIMS3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RIMS3 Gene:


SOURCE GeneReport for Unigene cluster for RIMS3 Gene:


Evidence on tissue expression from TISSUES for RIMS3 Gene

  • Nervous system(4.9)
  • Bone marrow(4)
genes like me logo Genes that share expression patterns with RIMS3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RIMS3 Gene

Orthologs for RIMS3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RIMS3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RIMS3 34 33
  • 99.89 (n)
(Canis familiaris)
Mammalia RIMS3 34 33
  • 92.75 (n)
(Bos Taurus)
Mammalia RIMS3 34 33
  • 91.77 (n)
(Rattus norvegicus)
Mammalia Rims3 33
  • 90.88 (n)
(Mus musculus)
Mammalia Rims3 16 34 33
  • 90.34 (n)
(Monodelphis domestica)
Mammalia RIMS3 34
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia RIMS3 34
  • 85 (a)
(Gallus gallus)
Aves RIMS3 34 33
  • 79.61 (n)
(Anolis carolinensis)
Reptilia RIMS3 34
  • 79 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rims3 33
  • 75.55 (n)
(Danio rerio)
Actinopterygii rims3 34 33
  • 74.02 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rim 34
  • 4 (a)
(Caenorhabditis elegans)
Secernentea unc-10 34
  • 7 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1713 34
  • 9 (a)
Species where no ortholog for RIMS3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RIMS3 Gene

Gene Tree for RIMS3 (if available)
Gene Tree for RIMS3 (if available)
Evolutionary constrained regions (ECRs) for RIMS3: view image

Paralogs for RIMS3 Gene

Paralogs for RIMS3 Gene

(3) SIMAP similar genes for RIMS3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RIMS3: view

Variants for RIMS3 Gene

Sequence variations from dbSNP and Humsavar for RIMS3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000000440 -- 40,625,031(-) G/A 3_prime_UTR_variant
rs1000072262 -- 40,621,336(-) A/C 3_prime_UTR_variant
rs1000099129 -- 40,669,173(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000152269 -- 40,649,921(-) G/A intron_variant
rs1000165796 -- 40,627,590(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RIMS3 Gene

Variant ID Type Subtype PubMed ID
esv2747397 CNV deletion 23290073
esv3561171 CNV deletion 23714750
nsv1113106 CNV deletion 24896259
nsv1150990 CNV deletion 26484159
nsv473417 CNV novel sequence insertion 20440878
nsv546064 CNV gain 21841781
nsv599 CNV deletion 18451855

Variation tolerance for RIMS3 Gene

Residual Variation Intolerance Score: 38.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.62; 45.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RIMS3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RIMS3 Gene

Disorders for RIMS3 Gene

Additional Disease Information for RIMS3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RIMS3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RIMS3 Gene

Publications for RIMS3 Gene

  1. Genomic definition of RIM proteins: evolutionary amplification of a family of synaptic regulatory proteins. (PMID: 12620390) Wang Y … Südhof TC (Genomics 2003) 2 3 4 58
  2. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. (PMID: 24722188) Corominas R … Iakoucheva LM (Nature communications 2014) 3 4 58
  3. A de novo 1p34.2 microdeletion identifies the synaptic vesicle gene RIMS3 as a novel candidate for autism. (PMID: 19546099) Kumar RA … Dobyns WB (Journal of medical genetics 2010) 3 44 58
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for RIMS3 Gene

Sources for RIMS3 Gene

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