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    RIN3 Ras and Rab interactor 3 [ Homo sapiens (human) ]

    Gene ID: 79890, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RIN3provided by HGNC
    Official Full Name
    Ras and Rab interactor 3provided by HGNC
    Primary source
    HGNC:HGNC:18751
    See related
    Ensembl:ENSG00000100599 MIM:610223; AllianceGenome:HGNC:18751
    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
    Summary
    Summary: This protein encoded by this gene is a member of the RIN family of Ras interaction-interference proteins, which are binding partners to the RAB5 small GTPases. The protein functions as a guanine nucleotide exchange for RAB5B and RAB31. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
    Expression
    Broad expression in bone marrow (RPKM 13.0), spleen (RPKM 13.0) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RIN3 in Genome Data Viewer
    Location:
    14q32.12
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (92513781..92688994)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (86743365..86920782)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (92980125..93155339)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92790043-92790622 Neighboring gene solute carrier family 24 member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92832163-92832664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92916101-92916601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:92937002-92937866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92966603-92967104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92967105-92967604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6034 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:92980671-92981174 Neighboring gene uncharacterized LOC124903365 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:92990985-92991808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92994044-92994801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92994802-92995558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92997484-92997984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:92997985-92998485 Neighboring gene MPRA-validated peak2237 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8933 Neighboring gene NANOG hESC enhancer GRCh37_chr14:93039726-93040227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8938 Neighboring gene Sharpr-MPRA regulatory region 14383 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:93090702-93091901 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93122369-93122870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93128149-93128650 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:93131812-93131989 Neighboring gene uncharacterized LOC124903364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93152626-93153253 Neighboring gene Sharpr-MPRA regulatory region 13986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6038 Neighboring gene Sharpr-MPRA regulatory region 11533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93175352-93175977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93175978-93176602 Neighboring gene Sharpr-MPRA regulatory region 3328 Neighboring gene legumain Neighboring gene MPRA-validated peak2238 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6039 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:93260331-93260478 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93260501-93261045 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93261046-93261589 Neighboring gene golgin A5

    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
    • 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. Tyr-phosphorylation signals translocate RIN3, the small GTPase Rab5-GEF, to early endocytic vesicles. Yoshikawa M, et al. Biochem Biophys Res Commun, 2008 Jul 18. PMID 18486601
    2. Genetic Variation in RIN3 in the Belgian Population Supports Its Involvement in the Pathogenesis of Paget's Disease of Bone and Modifies the Age of Onset. De Ridder R, et al. Calcif Tissue Int, 2019 Jun. PMID 30726512
    3. Targeted sequencing of the Paget's disease associated 14q32 locus identifies several missense coding variants in RIN3 that predispose to Paget's disease of bone. Vallet M, et al. Hum Mol Genet, 2015 Jun 1. PMID 25701875, Free PMC Article
    4. The neuronal-specific isoform of BIN1 regulates β-secretase cleavage of APP and Aβ generation in a RIN3-dependent manner. Bhattacharyya R, et al. Sci Rep, 2022 Mar 3. PMID 35241726, Free PMC Article
    5. Differential Recognition Preferences of the Three Src Homology 3 (SH3) Domains from the Adaptor CD2-associated Protein (CD2AP) and Direct Association with Ras and Rab Interactor 3 (RIN3). Rouka E, et al. J Biol Chem, 2015 Oct 16. PMID 26296892, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The neuronal-specific isoform of BIN1 regulates beta-secretase cleavage of APP and Abeta generation in a RIN3-dependent manner.
      Title: The neuronal-specific isoform of BIN1 regulates β-secretase cleavage of APP and Aβ generation in a RIN3-dependent manner.
    2. Genetic Variation in RIN3 in the Belgian Population Supports Its Involvement in the Pathogenesis of Paget's Disease of Bone and Modifies the Age of Onset.
      Title: Genetic Variation in RIN3 in the Belgian Population Supports Its Involvement in the Pathogenesis of Paget's Disease of Bone and Modifies the Age of Onset.
    3. RIN3 may be involved in endolysosomal transport-a process known to be important to development of early onset AD.
      Title: Early-Onset Alzheimer Disease and Candidate Risk Genes Involved in Endolysosomal Transport.
    4. RIN3 may contribute to Paget's disease of bone susceptibility by affecting osteoclast function.
      Title: Targeted sequencing of the Paget's disease associated 14q32 locus identifies several missense coding variants in RIN3 that predispose to Paget's disease of bone.
    5. discovered novel interaction candidates for CD2AP and characterized subtle yet significant differences in the recognition preferences of its three SH3 domains for c-CBL, ALIX, and RIN3
      Title: Differential Recognition Preferences of the Three Src Homology 3 (SH3) Domains from the Adaptor CD2-associated Protein (CD2AP) and Direct Association with Ras and Rab Interactor 3 (RIN3).
    6. The study reports a novel association between a variant within RIN3 and lower limb-bone mineral density and note its previous association with risk of Paget's disease.
      Title: Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
    7. RIN3 is a negative regulator of mast cell responses to SCF
      Title: RIN3 is a negative regulator of mast cell responses to SCF.
    8. RIN3 specifically acts as a GEF for Rab31.
      Title: Characterization of RIN3 as a guanine nucleotide exchange factor for the Rab5 subfamily GTPase Rab31.
    9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    10. Tyrosine-phosphorylation signals are involved in the RIN3 activation and translocation to early endocytic vesicles.
      Title: Tyr-phosphorylation signals translocate RIN3, the small GTPase Rab5-GEF, to early endocytic vesicles.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    EBI GWAS Catalog

    Description
    Genome-Wide Association Identifies Regulatory Loci Associated with Distinct Local Histogram Emphysema Patterns.
    EBI GWAS Catalog
    Genome-wide association identifies three new susceptibility loci for Paget's disease of bone.
    EBI GWAS Catalog
    Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
    EBI GWAS Catalog
    IREB2 and GALC are Associated with Pulmonary Artery Enlargement in Chronic Obstructive Pulmonary Disease.
    EBI GWAS Catalog
    Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease.
    EBI GWAS Catalog
    Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
    EBI GWAS Catalog
    Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11700, FLJ22439, DKFZp762H1613

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables small GTPase binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables small GTPase binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytosis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of negative regulation of mast cell chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of receptor internalization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of vesicle size IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endocytic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ras and Rab interactor 3
    Names
    RAB5 interacting protein 3
    ras interaction/interference protein 3

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001319987.2 → NP_001306916.1  ras and Rab interactor 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AB081753, AK026092, AK128338, BC032614
      UniProtKB/TrEMBL
      Q6ZRC2
      Related
      ENST00000418924.6
      Conserved Domains (4) summary
      TIGR03483
      Location:240 → 339
      FtsZ_alphas_C; cell division protein FtsZ, alphaProteobacterial C-terminal extension
      pfam02204
      Location:665 → 767
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      cl00155
      Location:807 → 886
      UBQ; Ubiquitin-like proteins
      cl15255
      Location:9 → 78
      SH2; Src homology 2 (SH2) domain

    2. NM_024832.5 → NP_079108.3  ras and Rab interactor 3 isoform 1

      See identical proteins and their annotated locations for NP_079108.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB081753, AK026092, BC025248, BC070062, BX248258, DR003779
      Consensus CDS
      CCDS32144.1
      UniProtKB/Swiss-Prot
      Q76LB3, Q8NF30, Q8TB24, Q8TEE8, Q8WYP4, Q9H6A5, Q9HAG1
      UniProtKB/TrEMBL
      A0A087WWY9
      Related
      ENSP00000216487.7, ENST00000216487.12
      Conserved Domains (4) summary
      cd10395
      Location:52 → 153
      SH2_RIN3; Src homology 2 (SH2) domain found in Ras and Rab interactor 3 (RIN3)-like proteins
      TIGR03483
      Location:315 → 414
      FtsZ_alphas_C; cell division protein FtsZ, alphaProteobacterial C-terminal extension
      pfam02204
      Location:740 → 842
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
      cl00155
      Location:882 → 961
      UBQ; Ubiquitin-like proteins

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      92513781..92688994
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      86743365..86920782
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_024892.1: Suppressed sequence

      Description
      NM_024892.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TB24.4 GenPept UniProtKB/Swiss-Prot:Q8TB24

    Gene LinkOut

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

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