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    RAB3D RAB3D, member RAS oncogene family [ Homo sapiens (human) ]

    Gene ID: 9545, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RAB3Dprovided by HGNC
    Official Full Name
    RAB3D, member RAS oncogene familyprovided by HGNC
    Primary source
    HGNC:HGNC:9779
    See related
    Ensembl:ENSG00000105514 MIM:604350; AllianceGenome:HGNC:9779
    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
    GOV; D2-2; RAB16; RAD3D
    Summary
    Enables myosin V binding activity. Involved in bone resorption and positive regulation of regulated secretory pathway. Located in cytoplasmic microtubule and secretory vesicle. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in skin (RPKM 24.5), esophagus (RPKM 14.0) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAB3D in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (11322068..11339657, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (11449052..11466642, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (11432744..11450333, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene dedicator of cytokinesis 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11354157-11354967 Neighboring gene angiopoietin like 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11363424-11364392 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11364393-11365361 Neighboring gene Sharpr-MPRA regulatory region 11176 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:11367378-11367534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10106 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:11408869-11409370 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:11409371-11409870 Neighboring gene tetraspanin 16 Neighboring gene uncharacterized HSPC102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11456465-11457295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11461146-11461646 Neighboring gene transmembrane protein 205 Neighboring gene coiled-coil domain containing 159

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. High expression of Rab3D predicts poor prognosis and associates with tumor progression in colorectal cancer. Luo Y, et al. Int J Biochem Cell Biol, 2016 Jun. PMID 27046094
    2. Isolation and characterization of a novel gene from human glioblastoma multiforme tumor tissue. Sehgal A, et al. Int J Cancer, 1997 May 16. PMID 9178809
    3. Molecular cloning of cDNA encoding human Rab3D whose expression is upregulated with myeloid differentiation. Nishio H, et al. Biochim Biophys Acta, 1999 Feb 16. PMID 10023084
    4. Assignment of the GOV (Glioblastoma overexpressed) gene to human chromosome band 19p13.2 by fluorescence in situ hybridization. Chen XN, et al. Cytogenet Cell Genet, 1998. PMID 10072586
    5. Silencing of Rab3D suppresses the proliferation and invasion of esophageal squamous cell carcinoma cells. Zhang J, et al. Biomed Pharmacother, 2017 Jul. PMID 28472755

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CircECE1 promotes osteosarcoma progression through regulating RAB3D by sponging miR-588.
      Title: CircECE1 promotes osteosarcoma progression through regulating RAB3D by sponging miR-588.
    2. [miR-125b-5p inhibits proliferation and migration of osteosarcoma cells by negatively regulating RAB3D expression].
      Title: [miR-125b-5p inhibits proliferation and migration of osteosarcoma cells by negatively regulating RAB3D expression].
    3. Hsa_circ_0006732 regulates colorectal cancer cell proliferation, invasion and EMT by miR-127-5p/RAB3D axis.
      Title: Hsa_circ_0006732 regulates colorectal cancer cell proliferation, invasion and EMT by miR-127-5p/RAB3D axis.
    4. Hsa_circ_0103232 promotes melanoma cells proliferation and invasion via targeting miR-661/RAB3D.
      Title: Hsa_circ_0103232 promotes melanoma cells proliferation and invasion via targeting miR-661/RAB3D.
    5. Rab3 proteins and cancer: Exit strategies.
      Title: Rab3 proteins and cancer: Exit strategies.
    6. GDP/GTP exchange factor MADD drives activation and recruitment of secretory Rab GTPases to Weibel-Palade bodies.
      Title: GDP/GTP exchange factor MADD drives activation and recruitment of secretory Rab GTPases to Weibel-Palade bodies.
    7. Long non-coding RNA FGD5-AS1 enhances osteosarcoma cell proliferation and migration by targeting miR-506-3p/RAB3D axis.
      Title: Long non-coding RNA FGD5-AS1 enhances osteosarcoma cell proliferation and migration by targeting miR-506-3p/RAB3D axis.
    8. targeting the Rab3D may be a potential therapeutic target for treatment of esophageal squamous cell carcinoma.
      Title: Silencing of Rab3D suppresses the proliferation and invasion of esophageal squamous cell carcinoma cells.
    9. increased Rab3D expression is associated with invasiveness of CRC cells
      Title: High expression of Rab3D predicts poor prognosis and associates with tumor progression in colorectal cancer.
    10. High expression of small GTPase Rab3D promotes cancer progression and metastasis.
      Title: High expression of small GTPase Rab3D promotes cancer progression and metastasis.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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
    Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTP-dependent protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables myosin V binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables myosin V binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in bone resorption IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of regulated secretory pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in azurophil granule membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in cytoplasmic microtubule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in secretory vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in synaptic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in zymogen granule IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ras-related protein Rab-3D
    Names
    Rab3D upregulated with myeloid differentiation
    epididymis secretory sperm binding protein
    glioblastoma overexpressed

    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_004283.4 → NP_004274.1  ras-related protein Rab-3D

      See identical proteins and their annotated locations for NP_004274.1

      Status: VALIDATED

      Source sequence(s)
      AC011472, AF019226, BC016471, BQ011121, DA241826
      Consensus CDS
      CCDS12257.1
      UniProtKB/Swiss-Prot
      O95716
      UniProtKB/TrEMBL
      A0A024R7G2, B2R8W8
      Related
      ENSP00000222120.2, ENST00000222120.8
      Conserved Domains (1) summary
      cd01865
      Location:22 → 186
      Rab3; Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      11322068..11339657 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      11449052..11466642 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95716.1 GenPept UniProtKB/Swiss-Prot:O95716

    Gene LinkOut

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

    Chemical Information
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