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

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

Summary

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
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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_004283.4NP_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:22186
    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)