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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. Diseases associated with RAB3D include Thiopurines, Poor Metabolism Of, 1. Among its related pathways are Metabolism of proteins and Innate Immune System. Gene Ontology (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

Additional gene information for RAB3D Gene

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

Genomics for RAB3D Gene

GeneHancer (GH) Regulatory Elements for RAB3D Gene

Promoters and enhancers for RAB3D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I011343 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.5 524 5 CLOCK FEZF1 DMAP1 YY1 ZNF213 ZNF143 ZNF548 SP3 NFYC MEF2D PIR44072 RAB3D PIR37751 TMEM205 CCDC159 ILF3 ZNF136 KRI1 ZNF627 ZNF844
GH19I011337 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 550.4 +7.4 7420 2.9 FOXA2 KLF17 SIN3A ZBTB7B RAD21 GTF3C2 ZNF335 ZNF121 GLIS2 EGR1 RAB3D ENSG00000267174 RGL3 DOCK6 GC19P011341
GH19I011373 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.2 -30.1 -30050 6.2 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ENSG00000267277 SWSAP1 PIR61774 ILF3 KRI1 ZNF627 ZNF136 ZNF442 ZNF844 ZNF44
GH19I011379 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.2 -36.1 -36096 5.1 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 EPOR KRI1 ILF3 TIMM29 ZNF44 ZNF136 ZNF433 ZNF878 ZNF20 ZNF563
GH19I011369 Enhancer 0.6 ENCODE 12.7 -23.5 -23520 0.1 HDAC1 AFF1 ARID4B MAX NCOA1 SIN3A MIER2 REST ZBTB40 ZNF143 RAB3D TMEM205 CCDC159 TSPAN16 SWSAP1 ENSG00000267277 PLPPR2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RAB3D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RAB3D gene promoter:

Genomic Locations for RAB3D Gene

Genomic Locations for RAB3D Gene
chr19:11,322,046-11,346,270
(GRCh38/hg38)
Size:
24,225 bases
Orientation:
Minus strand
chr19:11,432,722-11,456,946
(GRCh37/hg19)

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

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

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.

Phenotypes From GWAS Catalog for RAB3D Gene

Gene Ontology (GO) - Molecular Function for RAB3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003924 GTPase activity IEA,TAS --
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

Clone 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RAB3D gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 5
cytosol 4
lysosome 4
mitochondrion 3
golgi apparatus 2
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

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 TAS --
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

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:0015031 protein transport IEA --
GO:0017157 regulation of exocytosis IEA --
GO:0018125 peptidyl-cysteine methylation IEA --
genes like me logo Genes that share ontologies with RAB3D: view

No data available for SIGNOR curated interactions for RAB3D Gene

Drugs & Compounds for RAB3D Gene

No Compound Related Data Available

Transcripts for RAB3D Gene

mRNA/cDNA for RAB3D Gene

Unigene Clusters for RAB3D Gene

RAB3D, member RAS oncogene family:
Representative Sequences:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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.

Evidence on tissue expression from TISSUES for RAB3D Gene

  • Nervous system(4.5)
  • Blood(4.4)
  • Pancreas(2.4)
  • Stomach(2.4)
  • Intestine(2.2)
genes like me logo Genes that share expression patterns with RAB3D: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RAB3D Gene

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 33 34
  • 99.09 (n)
cow
(Bos Taurus)
Mammalia RAB3D 33 34
  • 90.56 (n)
dog
(Canis familiaris)
Mammalia RAB3D 33 34
  • 88.89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RAB3D 34
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rab3d 33
  • 87.37 (n)
mouse
(Mus musculus)
Mammalia Rab3d 33 16 34
  • 87.21 (n)
oppossum
(Monodelphis domestica)
Mammalia RAB3D 34
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RAB3D 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rab3d 33
  • 75.77 (n)
Str.4787 33
zebrafish
(Danio rerio)
Actinopterygii rab3db 34
  • 76 (a)
OneToMany
rab3da 33 34
  • 72.6 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4063 33
fruit fly
(Drosophila melanogaster)
Insecta Rab3 35 34
  • 74 (a)
worm
(Caenorhabditis elegans)
Secernentea rab-3 35 34
  • 73 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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

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

Variants for RAB3D Gene

Sequence variations from dbSNP and Humsavar for RAB3D Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000143239 -- 11,338,023(-) C/T intron_variant
rs1000192517 -- 11,324,606(-) C/T 3_prime_UTR_variant
rs1000492575 -- 11,337,739(-) T/C intron_variant
rs1000655333 -- 11,328,553(-) AGAAGAA/AGAA intron_variant
rs1000878478 -- 11,324,403(-) C/T 3_prime_UTR_variant

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)

Additional Variant Information for RAB3D Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for RAB3D Gene

MalaCards: The human disease database

(1) MalaCards diseases for RAB3D Gene - From: DISEASES

Disorder Aliases PubMed IDs
thiopurines, poor metabolism of, 1
  • thpm1
- elite association - COSMIC cancer census association via MalaCards
Search RAB3D in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RAB3D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with RAB3D: view

No data available for 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 (Biochimica et biophysica acta 1999) 2 3 4 22 58
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Rab3D and annexin A2 play a role in regulated secretion of vWF, but not tPA, from endothelial cells. (PMID: 15257287) Knop M … Gerke V (The EMBO journal 2004) 3 22 58
  5. Assignment of the GOV (Glioblastoma overexpressed) gene to human chromosome band 19p13.2 by fluorescence in situ hybridization. (PMID: 10072586) Chen XN … Sehgal A (Cytogenetics and cell genetics 1998) 2 3 58

Products for RAB3D Gene

Sources for RAB3D Gene

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