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Aliases for RAB3D Gene

Aliases for RAB3D Gene

  • RAB3D, Member RAS Oncogene Family 2 3 5
  • Rab3D Upregulated With Myeloid Differentiation 2 3
  • Glioblastoma Overexpressed 2 3
  • RAB16 3 4
  • GOV 3 4
  • Ras-Related Protein Rab-3D 3
  • RAD3D 3
  • D2-2 3

External Ids for RAB3D Gene

Previous HGNC Symbols for RAB3D Gene

  • GOV

Previous GeneCards Identifiers for RAB3D Gene

  • GC19M011566
  • GC19M011655
  • GC19M011280
  • GC19M011296
  • GC19M011435
  • GC19M011008

Summaries for RAB3D Gene

GeneCards Summary for RAB3D Gene

RAB3D (RAB3D, Member RAS Oncogene Family) is a Protein Coding gene. Among its related pathways are Immune System and Sertoli-Sertoli Cell Junction Dynamics. GO annotations related to this gene include GTP binding and GTPase binding. An important paralog of this gene is RAB3A.

UniProtKB/Swiss-Prot for RAB3D Gene

  • Protein transport. Probably involved in regulated exocytosis (By similarity).

Gene Wiki entry for RAB3D Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAB3D Gene

Genomics for RAB3D Gene

Regulatory Elements for RAB3D Gene

Enhancers for RAB3D 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
GH19F011369 0.2 ENCODE 12.6 -23.5 -23520 0.1 SUZ12 ZNF740 MIER1 ARID4B MAX SIN3A NCOA1 MIER2 REST KDM1A RAB3D TMEM205 CCDC159 TSPAN16 SWSAP1 PLPPR2
GH19F011373 0.5 FANTOM5 ENCODE 12.2 -30.1 -30050 6.2 HDGF PKNOX1 ARNT CREB3L1 ZFP64 SIN3A ARID4B FEZF1 DMAP1 ZNF2 TIMM29 ZNF563 ZNF627 ZNF844 TMEM205 RAB3D CCDC159 YIPF2 ZNF136 ZNF44
GH19F011379 0.2 ENCODE 12.2 -33.4 -33370 0.2 TAL1 KLF9 KDM1A CCDC159 RAB3D TMEM205 EPOR PIR61774
GH19F011380 1.1 ENCODE 12.1 -36.1 -36096 5.1 HDGF PKNOX1 CREB3L1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 KANK2 DOCK6 LOC105372273 RGL3 TMEM205 CCDC159 RAB3D CNN1 ZNF136 TIMM29
GH19F011317 0.5 Ensembl ENCODE 5.1 +24.6 24588 9.0 CREB3L1 ZFP64 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 MEF2D ZNF627 ZNF136 ZNF844 ZNF625 ENSG00000267174 ZNF44 ZNF441 ZNF491 ZNF700 ZNF763
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around RAB3D on UCSC Golden Path with GeneCards custom track

Promoters for RAB3D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000043010 -30 1401 PKNOX1 ATF1 ARID4B SIN3A DMAP1 YY1 ZNF121 GLIS2 ELK1 ZNF143

Genomic Location for RAB3D Gene

Chromosome:
19
Start:
11,322,046 bp from pter
End:
11,346,270 bp from pter
Size:
24,225 bases
Orientation:
Minus strand

Genomic View for RAB3D Gene

Genes around RAB3D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAB3D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAB3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAB3D Gene

Proteins for RAB3D Gene

  • Protein details for RAB3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95716-RAB3D_HUMAN
    Recommended name:
    Ras-related protein Rab-3D
    Protein Accession:
    O95716

    Protein attributes for RAB3D Gene

    Size:
    219 amino acids
    Molecular mass:
    24267 Da
    Quaternary structure:
    • Interacts with RIMS1, RIMS2, RPH3A, RPH3AL and RAB3IP.

    Three dimensional structures from OCA and Proteopedia for RAB3D Gene

neXtProt entry for RAB3D Gene

Post-translational modifications for RAB3D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RAB3D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RAB3D Gene

Domains & Families for RAB3D Gene

Gene Families for RAB3D Gene

Protein Domains for RAB3D Gene

Suggested Antigen Peptide Sequences for RAB3D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O95716

UniProtKB/Swiss-Prot:

RAB3D_HUMAN :
  • Belongs to the small GTPase superfamily. Rab family.
Family:
  • Belongs to the small GTPase superfamily. Rab family.
genes like me logo Genes that share domains with RAB3D: view

Function for RAB3D Gene

Molecular function for RAB3D Gene

UniProtKB/Swiss-Prot Function:
Protein transport. Probably involved in regulated exocytosis (By similarity).
UniProtKB/Swiss-Prot Induction:
Activated in myeloid differentiation.

Gene Ontology (GO) - Molecular Function for RAB3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003924 GTPase activity TAS 10023084
GO:0005525 GTP binding IEA --
GO:0030742 GTP-dependent protein binding IEA --
GO:0031489 myosin V binding IPI 24006491
genes like me logo Genes that share ontologies with RAB3D: view
genes like me logo Genes that share phenotypes with RAB3D: view

Animal Models for RAB3D Gene

MGI Knock Outs for RAB3D:

Animal Model Products

  • Taconic Biosciences Mouse Models for RAB3D

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RAB3D Gene

Localization for RAB3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAB3D Gene

Cell membrane; Lipid-anchor; Cytoplasmic side.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RAB3D Gene COMPARTMENTS Subcellular localization image for RAB3D gene
Compartment Confidence
cytoskeleton 5
extracellular 5
cytosol 4
plasma membrane 4
mitochondrion 3
golgi apparatus 1
nucleus 1
vacuole 1

Gene Ontology (GO) - Cellular Components for RAB3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005881 cytoplasmic microtubule IDA 21262767
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0030133 transport vesicle IEA --
genes like me logo Genes that share ontologies with RAB3D: view

Pathways & Interactions for RAB3D Gene

genes like me logo Genes that share pathways with RAB3D: view

Pathways by source for RAB3D Gene

1 Qiagen pathway for RAB3D Gene

Gene Ontology (GO) - Biological Process for RAB3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006887 exocytosis IEA --
GO:0007264 small GTPase mediated signal transduction IEA --
GO:0015031 protein transport IEA --
GO:0017157 regulation of exocytosis IEA --
genes like me logo Genes that share ontologies with RAB3D: view

No data available for SIGNOR curated interactions for RAB3D Gene

Transcripts for RAB3D Gene

mRNA/cDNA for RAB3D Gene

Unigene Clusters for RAB3D Gene

RAB3D, member RAS oncogene family:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for RAB3D Gene

No ASD Table

Relevant External Links for RAB3D Gene

GeneLoc Exon Structure for
RAB3D
ECgene alternative splicing isoforms for
RAB3D

Expression for RAB3D Gene

mRNA expression in normal human tissues for RAB3D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RAB3D Gene

This gene is overexpressed in Whole Blood (x11.2).

Protein differential expression in normal tissues from HIPED for RAB3D Gene

This gene is overexpressed in Frontal cortex (14.2), Oral epithelium (7.8), Brain (7.3), and Peripheral blood mononuclear cells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RAB3D Gene



Protein tissue co-expression partners for RAB3D Gene

NURSA nuclear receptor signaling pathways regulating expression of RAB3D Gene:

RAB3D

SOURCE GeneReport for Unigene cluster for RAB3D Gene:

Hs.744916

mRNA Expression by UniProt/SwissProt for RAB3D Gene:

O95716-RAB3D_HUMAN
Tissue specificity: Highly expressed in granulocytes of peripheral blood. Constitutively expressed at low levels in all hematopoietic cell lines investigated.
genes like me logo Genes that share expression patterns with RAB3D: view

Primer Products

Orthologs for RAB3D Gene

This gene was present in the common ancestor of animals.

Orthologs for RAB3D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RAB3D 34 35
  • 99.09 (n)
cow
(Bos Taurus)
Mammalia RAB3D 34 35
  • 90.56 (n)
dog
(Canis familiaris)
Mammalia RAB3D 34 35
  • 88.89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RAB3D 35
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rab3d 34
  • 87.37 (n)
mouse
(Mus musculus)
Mammalia Rab3d 34 16 35
  • 87.21 (n)
oppossum
(Monodelphis domestica)
Mammalia RAB3D 35
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RAB3D 35
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rab3d 34
  • 75.77 (n)
Str.4787 34
zebrafish
(Danio rerio)
Actinopterygii rab3db 35
  • 76 (a)
OneToMany
rab3da 34 35
  • 72.6 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4063 34
fruit fly
(Drosophila melanogaster)
Insecta Rab3 36 35
  • 74 (a)
worm
(Caenorhabditis elegans)
Secernentea rab-3 36 35
  • 73 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 74 (a)
OneToMany
Species where no ortholog for RAB3D 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)
  • chicken (Gallus gallus)
  • 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)
  • 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 RAB3D Gene

ENSEMBL:
Gene Tree for RAB3D (if available)
TreeFam:
Gene Tree for RAB3D (if available)

Paralogs for RAB3D Gene

Variants for RAB3D Gene

Sequence variations from dbSNP and Humsavar for RAB3D Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs10401767 -- 11,327,428(+) agttt(C/T)gctct intron-variant, downstream-variant-500B
rs10422156 -- 11,327,346(+) GGGCA(A/G)ATCTG intron-variant, downstream-variant-500B
rs10422167 -- 11,327,366(+) TATCC(A/G)CGCGT intron-variant, downstream-variant-500B
rs1044000 -- 11,322,205(-) TGATT(C/T)TGAAA intron-variant, utr-variant-3-prime
rs1061327 -- 11,323,971(-) GCAGT(C/T)TGAAG intron-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for RAB3D Gene

Variant ID Type Subtype PubMed ID
esv3643670 CNV loss 21293372
nsv519802 CNV loss 19592680
nsv578615 CNV loss 21841781
nsv833752 CNV loss 17160897

Variation tolerance for RAB3D Gene

Residual Variation Intolerance Score: 68% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.77; 58.00% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RAB3D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB3D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAB3D Gene

Disorders for RAB3D Gene

Relevant External Links for RAB3D

Genetic Association Database (GAD)
RAB3D
Human Genome Epidemiology (HuGE) Navigator
RAB3D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RAB3D

No disorders were found for RAB3D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RAB3D Gene

Publications for RAB3D Gene

  1. Molecular cloning of cDNA encoding human Rab3D whose expression is upregulated with myeloid differentiation. (PMID: 10023084) Nishio H. … Yamaguchi Y. (Biochim. Biophys. Acta 1999) 2 3 4 22 64
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64
  3. Rab3D and annexin A2 play a role in regulated secretion of vWF, but not tPA, from endothelial cells. (PMID: 15257287) Knop M. … Gerke V. (EMBO J. 2004) 3 22 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Assignment of the GOV (Glioblastoma overexpressed) gene to human chromosome band 19p13.2 by fluorescence in situ hybridization. (PMID: 10072586) Chen X.N. … Sehgal A. (Cytogenet. Cell Genet. 1998) 2 3 64

Products for RAB3D Gene

Sources for RAB3D Gene

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