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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
  • NIM3 3 4
  • Regulating Synaptic Membrane Exocytosis Protein 3 3
  • Rab-3 Interacting Molecule 3 3
  • KIAA0237 4
  • RIM3 3

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. 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

Regulatory Elements for RIMS3 Gene

Enhancers for RIMS3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H040690 1.4 ENCODE dbSUPER 34.1 -0.6 -618 4.4 ZFP64 DMAP1 YY1 SLC30A9 SP3 NFYC MEF2D ZNF610 GLIS1 NBN ENSG00000259943 RIMS3 EXO5 NFYC-AS1 RLF LOC105378674 ZFP69 SLFNL1 TRIT1 MIR30C1
GH01H040698 1.7 FANTOM5 Ensembl ENCODE dbSUPER 25.5 -7.5 -7459 2 HDGF ATF1 ZBTB40 BATF ZNF121 FOS ATF7 RUNX3 CREM IKZF2 RIMS3 LOC105378674 MIR30E MIR30C1 NFYC ZNF684 KCNQ4 EXO5 CITED4 ZFP69
GH01H040703 1.2 Ensembl ENCODE dbSUPER 21.2 -11.7 -11717 1.2 HDGF PKNOX1 JUN ZNF384 FOSL1 PATZ1 FOS IKZF2 SMARCE1 ZNF362 RIMS3 LOC105378674 MIR30E MIR30C1 LOC105378672 KCNQ4 NFYC-AS1 GC01P040752
GH01H040735 1.3 Ensembl ENCODE dbSUPER 17.9 -44.1 -44102 1.3 ZBTB21 TAL1 JUN MAX CEBPG TCF12 ZNF316 ZNF366 SCRT2 ZNF600 RIMS3 LOC105378674 MIR30C1 NFYC KCNQ4 GC01P040752 NFYC-AS1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RIMS3 on UCSC Golden Path with GeneCards custom track

Promoters for RIMS3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000005237 84 2001 ZFP64 DMAP1 YY1 SLC30A9 SP3 NFYC MEF2D ZNF610 GLIS1 NBN

Genomic Locations for RIMS3 Gene

Genomic Locations for RIMS3 Gene
71,406 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: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:

Animal Model Products

Inhibitory RNA Products

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:0045202 synapse IEA --
GO:0048786 presynaptic active zone TAS 15217342
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:0006836 neurotransmitter transport IEA --
GO:0006887 exocytosis IEA --
GO:0017156 calcium ion regulated exocytosis ISS --
GO:0042391 regulation of membrane potential ISS --
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

Unigene Clusters for RIMS3 Gene

Regulating synaptic membrane exocytosis 3:
Representative Sequences:

Inhibitory RNA Products

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, PaxDb, 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 33 34
  • 99.89 (n)
(Canis familiaris)
Mammalia RIMS3 33 34
  • 92.75 (n)
(Bos Taurus)
Mammalia RIMS3 33 34
  • 91.77 (n)
(Rattus norvegicus)
Mammalia Rims3 33
  • 90.88 (n)
(Mus musculus)
Mammalia Rims3 33 16 34
  • 90.34 (n)
(Monodelphis domestica)
Mammalia RIMS3 34
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia RIMS3 34
  • 85 (a)
(Gallus gallus)
Aves RIMS3 33 34
  • 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 33 34
  • 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)

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 Sequence Context AA Info Type
rs1000000440 -- 40,625,031(+) CTCTC(A/G)CCTTT utr-variant-3-prime
rs1000072262 -- 40,621,336(+) AGATG(A/C)CCCTT utr-variant-3-prime
rs1000099129 -- 40,669,173(+) AGGGA(A/G)CTAAC intron-variant
rs1000152269 -- 40,649,921(+) GTGTA(A/G)GAAGG intron-variant
rs1000165796 -- 40,627,590(+) GGTTC(C/T)GCAGT intron-variant

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

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

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)

Relevant External Links for RIMS3 Gene

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

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

Disorders for RIMS3 Gene

Relevant External Links for RIMS3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 60
  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 60
  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 45 60
  4. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 60
  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 60

Products for RIMS3 Gene

Sources for RIMS3 Gene

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