RAB3D Gene (Protein Coding)

RAB3D, Member RAS Oncogene Family

GC19M011322
GIFtS:
39
See more...

Aliases for RAB3D Gene

Aliases for RAB3D Gene

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

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 Esophageal Varix and Scleral Staphyloma. Among its related pathways are Metabolism of proteins and Autophagy Pathway. 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 Summary 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 , Rfam classification and piRNA Summary for RAB3D Gene

Genomics for RAB3D Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RAB3D Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RAB3D on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RAB3D

Top Transcription factor binding sites by QIAGEN in the RAB3D gene promoter:
  • c-Ets-1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Egr-4
  • HEN1
  • STAT3

Genomic Locations for RAB3D Gene

Genomic Locations for RAB3D Gene
chr19:11,322,068-11,346,270
(GRCh38/hg38)
Size:
24,203 bases
Orientation:
Minus strand
chr19:11,432,722-11,456,946
(GRCh37/hg19)
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 Structure • Gene Density

RefSeq DNA sequence for RAB3D Gene

Proteins for RAB3D Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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 (By similarity). Interacts with CHM and CHML; phosphorylation at Thr-86 disrupts these interactions (PubMed:29125462).

    Three dimensional structures from OCA and Proteopedia for RAB3D Gene

neXtProt entry for RAB3D Gene

Protein Expression for RAB3D Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RAB3D Gene

  • Phosphorylation of Thr-86 in the switch II region by LRRK2 prevents the association of RAB regulatory proteins, including CHM and CHML.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RAB3D Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for RAB3D
  • Boster Bio Antibodies for RAB3D

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

InterPro:
Blocks:
  • Transforming protein P21 RAS signature
ProtoNet:

Suggested Antigen Peptide Sequences for RAB3D Gene

GenScript: Design optimal peptide antigens:
  • Ras-related protein Rab-3D (RAB3D_HUMAN)

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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:0000166 nucleotide binding IEA --
GO:0003924 GTPase activity 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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAB3D

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 4
extracellular 4
cytoskeleton 4
endosome 4
cytosol 4
lysosome 4
nucleus 2
golgi apparatus 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RAB3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IBA 21873635
GO:0005881 cytoplasmic microtubule IDA 21262767
GO:0005886 plasma membrane TAS --
GO:0008021 synaptic vesicle IBA 21873635
GO:0012505 endomembrane system IBA --
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 Sino Biological pathway for RAB3D Gene
1 KEGG pathway for RAB3D Gene
1 Qiagen pathway for RAB3D Gene
  • Epithelial Tight Junctions

Gene Ontology (GO) - Biological Process for RAB3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IBA --
GO:0006887 exocytosis IEA --
GO:0006904 vesicle docking involved in exocytosis IBA 21873635
GO:0009306 protein secretion IBA 21873635
GO:0015031 protein transport 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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for RAB3D Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RAB3D Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAB3D

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

No ASD Table

Relevant External Links for RAB3D Gene

GeneLoc Exon Structure for
RAB3D

Expression for RAB3D Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RAB3D Gene

mRNA expression in normal human tissues for RAB3D Gene
mRNA expression by BioGPS for RAB3D GenemRNA expression by GTEx 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, MaxQB, and MOPED for RAB3D Gene



Protein tissue co-expression partners for RAB3D Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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(4.6)
  • Blood(4.5)
  • Skin(2.9)
  • Stomach(2.7)
  • Pancreas(2.7)
  • Liver(2.6)
  • Intestine(2.5)
  • Kidney(2.2)
  • Adrenal gland(2.2)
  • Heart(2.2)
  • Spleen(2.1)
  • Eye(2)
  • Lung(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 30 31
  • 99.09 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia RAB3D 30 31
  • 90.56 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia RAB3D 30 31
  • 88.89 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia RAB3D 31
  • 88 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Rab3d 30
  • 87.37 (n)
Mouse
(Mus musculus)
 Mammalia Rab3d 30 17 31
  • 87.21 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia RAB3D 31
  • 61 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia RAB3D 31
  • 80 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia rab3d 30
  • 75.77 (n)
Str.4787 30
Zebrafish
(Danio rerio)
 Actinopterygii rab3db 31
  • 76 (a)
 OneToMany
rab3da 30 31
  • 72.6 (n)
 OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.4063 30
Fruit Fly
(Drosophila melanogaster)
 Insecta Rab3 31 32
  • 75 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea rab-3 31 32
  • 67 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 74 (a)
 OneToMany
Species where no ortholog for RAB3D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RAB3D: view image

Paralogs for RAB3D Gene

Paralogs for RAB3D Gene

(86) SIMAP similar genes for RAB3D Gene using alignment to 1 proteins:

  • RAB3D_HUMAN
genes like me logo Genes that share paralogs with RAB3D: view

Variants for RAB3D Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RAB3D Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
785611 Benign: not provided 11,335,657(-) G/T INTRON_VARIANT
rs3969860 - p.Val64Ile

Additional dbSNP identifiers (rs#s) for RAB3D Gene

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

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

Disorder Aliases PubMed IDs
esophageal varix
  • bleeding esophageal varices
scleral staphyloma
  • scleral ectasia
meckel diverticulum
  • meckel's diverticulum
shoulder impingement syndrome
  • impingement syndrome of shoulder region
vein disease
  • disorder of vein
- 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
Open Targets Platform
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 23
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 41
  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
  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 23
  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

ExternalLinks

View latest publications for RAB3D gene in Mastermind

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