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RAB3D Gene

protein-coding   GIFtS: 56

GC19M011296
RAB3D, member RAS oncogene family
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: GOV)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
D2-2 1, 2
GOV 2, 3, 5
RAB16 1, 2, 3
RAD3D 1, 2, 5
Descriptions
RAB3D, member RAS oncogene family 2
Rab3D upregulated with myeloid differentiation 2
glioblastoma overexpressed 2
External Ids
HGNC: 97791
Entrez Gene: 95452
UniProtKB: O957163
Ensembl: ENSG000001055147
Search outside databases for aliases for RAB3D gene

Previous GC identifers: GC19M011566 GC19M011655 GC19M011280

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: RAB3D_HUMAN, O95716
Function: Protein transport. Probably involved in regulated exocytosis (By similarity)

Gene Wiki entry for RAB3D

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the RAB3D gene  

Entrez Gene cytogenetic band: 19p13.2   Ensembl cytogenetic band:  19p13.2   HGNC cytogenetic band: 19p13.2

RAB3D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M011296:     (about GC identifiers)

Start:
11,296,093 bp from pter
End:
11,311,321 bp from pter
Size:
15,229 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000019.8  NT_011295.10  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: RAB3D_HUMAN, O95716 (See protein sequence)
Recommended Name: Ras-related protein Rab-3D  
Size: 219 amino acids; 24267 Da
Subunit: Binds RIMS1. Interacts with RAB3IP (By similarity)
Subcellular location: Cell membrane; Lipid-anchor; Cytoplasmic side (Potential)
PDB structures from and Proteopedia :
2GF9 (3D)    

REFSEQ proteins: NP_004274.1  

ENSEMBL proteins: 
ENSP00000222120 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Sigma-Aldrich AQUA Peptides for RAB3D  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (Rab3A + Rab3B + Rab3C + Rab3D, Rab3D)
Human Recombinant Proteins from Abnova (RAB3D)
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

1 Gene Ontology (GO) cellular component term (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005886 plasma membrane IEA--
About this table

Antibodies for RAB3D: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for RAB3D
Browse R&D Systems for Antibodies
Antibodies from Abcam (Rab3A + Rab3B + Rab3C + Rab3D, Rab3D), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (RAB3D)
Novus Biologicals Antibody for RAB3D

Assays for RAB3D: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

5 InterPro domains/families:
 IPR015596 Rab3
 IPR001806 Ras_GTPase
 IPR005225 Small_GTP_bd
 IPR003579 GTPase_Rab
 IPR013753 Ras


   GeneDecks  RAB3D for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry O95716

ProtoNet protein and cluster: O95716

1 Blocks protein family: IPB001806 Transforming protein P21 RAS signature

UniProtKB/Swiss-Prot: RAB3D_HUMAN, O95716
Similarity: Belongs to the small GTPase superfamily. Rab family

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (RAB3D)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (RAB3D)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004283

              Applied Biosystems Silencer® siRNAs for RAB3D

              Sigma-Aldrich siRNA for RAB3D  
                     Sigma-Aldrich shRNA for RAB3D  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Browse Clone Ranger at Invitrogen for clones
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_004283
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_004283
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_004283 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_004283

UniProtKB/Swiss-Prot: RAB3D_HUMAN, O95716
Function: Protein transport. Probably involved in regulated exocytosis (By similarity)
Induction: Activated in myeloid differentiation

7 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rab3d):

behavior/neurologicalgrowth/sizehomeostasis/metabolismlethality-prenatal/perinatalnervous system
normalrespiratory system

4 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0000166 nucleotide binding IEA--
GO:0003924 GTPase activity TAS10023084
GO:0005515 protein binding ISS--
GO:0005525 GTP binding IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section


 Gene Network CentralTM Interacting Genes and Proteins Network for  RAB3D 


5/9 Interacting proteins for RAB3D (ENSP000002221203) via UniProtKB, MINT, and/or STRING (see all 9 )
InteractantInteraction Details
GeneCardExternal ID(s)
RAB3IPENSP000003233493STRING (score=.968)
RIMS1ENSP000002648393STRING (score=.949)
RPH3ALENSP000003192103STRING (score=.912)
S100A10ENSP000003577993STRING (score=.877)
ANXA2ENSP000003460323STRING (score=.847)
About this table

3 Gene Ontology (GO) biological process terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006887 exocytosis IEA--
GO:0007264 small GTPase mediated signal transduction IEA--
GO:0015031 protein transport IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Enzo Life Sciences drugs & compounds for RAB3D
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for RAB3D

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (RAB3D)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (RAB3D)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004283

              Sigma-Aldrich siRNA for RAB3D  
                     Sigma-Aldrich shRNA for RAB3D  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_004283  

REFSEQ mRNAs for RAB3D gene: 

NM_004283.2   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_004283  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_004283
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_004283
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_004283 

Additional cDNA sequence: 

AF019226.1 AF081353.1 AF498933.1 AK313538.1 BC007960.2 BC016471.1 BC035309.1 

7 DOTS entries:

DT.95167487  DT.91754714  DT.121497451  DT.121497438  DT.75107864  DT.100661499  DT.92440280 

24/424 AceView cDNA sequences (see all 424 ):

AI280176 AA402328 AI559369 BX091064 AI192573 BM764630 CD671556 BU179008 
BE889078 AA303056 CA943917 BM709889 BM853995 CK299243 AI434953 AA298311 
AA411457 BX509018 AI140421 AI937180 AA595980 W67281 BM974589 BE645743 

highest scoring ESTs for RAB3D:

AF081353 BC016471 BF038343 BI910348 BX281152 CB960016 CB960882 CB989112 CD109583 CN285981 

Unigene Cluster for RAB3D:

RAB3D, member RAS oncogene family
Hs.655274  [show with all ESTs]
Unigene Representative Sequence: AF019226


GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:
ENST00000222120  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

RAB3D expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for RAB3D

1 / 2 / 3

6 probe-sets matching RAB3D gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
55027_at2, 3 U95-B 1 1.00 1.00 0.90 1.19 N26076 0.40 0.50 0.45 1
69449_r_at2, 3 U95-E 1 1.00 1.00 0.67 0.82 R19240 0.60 0.83 0.73 1

208466_at2, 3 U133-A 1 1.00 1.00 -- -- NM_004283 0.60 0.83 0.73 1

225001_at2, 3 U133-B 1 1.00 1.00 -- -- AI744658 0.20 0.25 0.23 2

208466_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

225001_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  RAB3D for binary patterns associated with the probe-sets selected above  
About GeneDecksing
About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: ACCACAGGGG

SOURCE GeneReport for Unigene cluster: Hs.655274

UniProtKB/Swiss-Prot: RAB3D_HUMAN, O95716
Tissue specificity: Highly expressed in granulocytes of peripheral blood. Constitutively expressed
at low levels in all hematopoietic cell lines invstigated

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for RAB3D gene from 5/10 species (see all 10 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
RAB3D1   -- RAB3D, member RAS oncogene family 88.89(n)
94.98(a)
476708  XM_533913.2  XP_533913.1 
chimpanzee
(Pan troglodytes)
RAB3D1   -- RAB3D, member RAS oncogene family 99.09(n)
99.54(a)
746353  XM_001167816.1  XP_001167816.1 
rat
(Rattus norvegicus)
Rab3d1   -- RAB3D, member RAS oncogene family 87.37(n)
92.69(a)
140665  NM_080580.2  NP_542147.1 
mouse
(Mus musculus)
Rab3d1, 5 95
RAB3D, member RAS oncogene family1, 5 87.21(n)1
94.52(a)1
193401  NM_031874.41  NP_114080.21 
 AB2325905  AF2633655  (see all 22)
zebrafish
(Danio rerio)
wu:fi17a031   -- wu:fi17a03 72.6(n)
79.91(a)
567288  XM_690580.2  XP_695672.2 
About this table        Species with no ortholog for RAB3D

ENSEMBL Gene Tree for RAB3D
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for RAB3D gene
RAB3A2  RAB3B2  RAB122  RAB3C2  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/83 NCBI SNPs in RAB3D are shown (see all 83 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 41)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 19 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
--
rs39698601,2
C,F,H11308886(+) GTAGAC/TGGTCT 1 V/I mis1 ese312Minor allele frequency- T:0.23EU EA WA NA 1032
--
rs116664781,2
A,C11312163(+) aaaaaC/Tacaaa 1 -- ng310--------
rs118832621,2
C11311464(+) TAGCCA/CAGCAA 1 -- ng310--------
--
rs72520211,2
A11312586(+) cgagaC/Tcgcgc 1 -- ng310--------
rs340536411,2
F11308932(+) GCGGGA/CGTGAA 1 T/T syn11Minor allele frequency- C:0.07NA 70
rs8964121,2
A,C,F,H11305131(-) ACACAG/CATGTT 1 -- int116Minor allele frequency- C:0.25EU EA WA NA 1398
rs1727311,2
A,C,F,H11307951(+) TTCCCT/CGTTGG 1 -- int14Minor allele frequency- C:0.37EU EA WA 410
rs38168641,2
A,C,F,H11307520(+) TGTCTT/GAGAGG 1 -- int14Minor allele frequency- G:0.26EU EA WA 412
--
rs3807641,2
A,C,F11303525(+) GCTGGA/TGTTGC 1 -- int13Minor allele frequency- T:0.11NA 118
rs72508301,2
F,H11304425(+) tagctG/Aggatt 1 -- int14Minor allele frequency- A:0.08EU EA WA 416
About this table

HapMap Linkage Disequilibrium images for RAB3D (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 604350

(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
About This Section

10/25 PubMed articles for RAB3D gene (see all 25 ):
(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)
(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 9545 HGNC: 9779 AceView: RAB3DandUNQ501 Ensembl:ENSG00000105514 euGenes: HUgn9545
ECgene: RAB3D H-InvDB: RAB3D
(According to HUGE)
About This Section

  --
(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

NameDescription
ATLAS Chromosomes in Cancer entry for RAB3D Genetics and Cytogenetics in Oncology and Haematology
(Available from WIS Yeda, Salk, Tufts)
About This Section

  --
(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for RAB3D:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



  Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
  Invitrogen Antibodies  Invitrogen Assays
  Invitrogen Clones  Invitrogen Q-PCR Products
  Invitrogen Human Recombinant Kinases  Invitrogen Custom Antibody and Peptide Service
  Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for RAB3D-related products

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 Predesigned and custom siRNAs for RAB3D Antibodies for RAB3D
 Explore super-pooled esiRNAs Proteins for RAB3D
 Lentivirus-delivered shRNAs for RAB3D Browse small molecules at Sigma-Aldrich
 "Your Favorite Gene" Pathwaysfeedback


  
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 Recombinant Proteins
(Rab3A + Rab3B + Rab3C + Rab3D, Rab3D)
 Antibodies (Rab3A + Rab3B + Rab3C + Rab3D, Rab3D)
 Search OriGene for RAB3D
 Search Tocris compounds for RAB3D




 Drugs for RAB3D
 Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
 Antibodies for RAB3D

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