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    RIMS3 regulating synaptic membrane exocytosis 3 [ Homo sapiens (human) ]

    Gene ID: 9783, updated on 2-Nov-2024

    Summary

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    Official Symbol
    RIMS3provided by HGNC
    Official Full Name
    regulating synaptic membrane exocytosis 3provided by HGNC
    Primary source
    HGNC:HGNC:21292
    See related
    Ensembl:ENSG00000117016 MIM:611600; AllianceGenome:HGNC:21292
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NIM3; RIM3; RIM 3
    Summary
    Predicted to enable transmembrane transporter binding activity. Predicted to be involved in several processes, including calcium ion-regulated exocytosis of neurotransmitter; modulation of chemical synaptic transmission; and regulation of synapse organization. Predicted to be located in presynaptic active zone. Predicted to be active in several cellular components, including cytoskeleton of presynaptic active zone; postsynaptic cytosol; and presynaptic membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 26.0), adrenal (RPKM 4.0) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RIMS3 in Genome Data Viewer
    Location:
    1p34.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (40620680..40692066, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (40489861..40544972, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (41086352..41131354, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378673 Neighboring gene general transcription factor IIF subunit 2 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 730 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:41093974-41095173 Neighboring gene uncharacterized LOC105378675 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:41128965-41129622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 852 Neighboring gene NFYC antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 733 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:41174578-41175204 Neighboring gene nuclear transcription factor Y subunit gamma Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:41180095-41180734 Neighboring gene microRNA 30e Neighboring gene microRNA 30c-1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. A de novo 1p34.2 microdeletion identifies the synaptic vesicle gene RIMS3 as a novel candidate for autism. Kumar RA, et al. J Med Genet, 2010 Feb. PMID 19546099, Free PMC Article
    2. Investigation of the expression of genes affecting cytomatrix active zone function in the amygdala in schizophrenia: effects of antipsychotic drugs. Weidenhofer J, et al. J Psychiatr Res, 2009 Jan. PMID 18490030
    3. Genome-Wide Detection of Copy Number Variations in Unsolved Inherited Retinal Disease. Huang XF, et al. Invest Ophthalmol Vis Sci, 2017 Jan 1. PMID 28118666
    4. The RIM/NIM family of neuronal C2 domain proteins. Interactions with Rab3 and a new class of Src homology 3 domain proteins. Wang Y, et al. J Biol Chem, 2000 Jun 30. PMID 10748113
    5. Genomic definition of RIM proteins: evolutionary amplification of a family of synaptic regulatory proteins. Wang Y, et al. Genomics, 2003 Feb. PMID 12620390

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. We identified four novel CNVs in three different genes (one duplication in USH2A gene, two duplications in CEP290 gene, and one duplication in RIMS2 gene) in total four families, at a detection rate of 8% (4/50).
      Title: Genome-Wide Detection of Copy Number Variations in Unsolved Inherited Retinal Disease.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: A de novo 1p34.2 microdeletion identifies the synaptic vesicle gene RIMS3 as a novel candidate for autism.
    3. Western blot analysis shows increased piccolo protein expression in the amygdala in schizophrenia.
      Title: Investigation of the expression of genes affecting cytomatrix active zone function in the amygdala in schizophrenia: effects of antipsychotic drugs.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0237

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables structural constituent of presynaptic active zone IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transmembrane transporter binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium-ion regulated exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of membrane potential ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of synaptic vesicle exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of synaptic vesicle exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synaptic vesicle docking IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle priming IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in presynaptic active zone TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in presynaptic active zone cytoplasmic component IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in presynaptic membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    regulating synaptic membrane exocytosis protein 3
    Names
    RIM3 gamma
    Rab-3 interacting molecule 3
    rab-3-interacting molecule 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_014747.3 → NP_055562.2  regulating synaptic membrane exocytosis protein 3

      See identical proteins and their annotated locations for NP_055562.2

      Status: VALIDATED

      Source sequence(s)
      AL031289
      Consensus CDS
      CCDS30687.1
      UniProtKB/Swiss-Prot
      D3DPV8, Q92511, Q9UJD0, X5D7U7
      Related
      ENSP00000361769.3, ENST00000372684.8
      Conserved Domains (1) summary
      cl14603
      Location:141 → 286
      C2; C2 domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      40620680..40692066 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435189.1 → XP_047291145.1  regulating synaptic membrane exocytosis protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPV8, Q92511, Q9UJD0, X5D7U7

    2. XM_047435184.1 → XP_047291140.1  regulating synaptic membrane exocytosis protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPV8, Q92511, Q9UJD0, X5D7U7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      40489861..40544972 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339778.1 → XP_054195753.1  regulating synaptic membrane exocytosis protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPV8, Q92511, Q9UJD0, X5D7U7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UJD0.1 GenPept UniProtKB/Swiss-Prot:Q9UJD0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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