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RAB40B Gene

protein-coding   GIFtS: 54

GC17M078208
RAB40B, member RAS oncogene family
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
FLJ42385 2
RAR 1, 2
SEC4L 1, 2, 3
Descriptions
GTP-binding protein homologous to Saccharomyces cerevisiae
SEC4 2
RAB40B, member RAS oncogene family 2
Rar protein 3
SOCS box-containing protein RAR 3
External Ids
HGNC: 182841
Entrez Gene: 109662
UniProtKB: Q128293
Ensembl: ENSG000001415427
Search outside databases for aliases for RAB40B gene

Previous GC identifers: GC17M079683 GC17M083584 GC17M081144 GC17M081293

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

EntrezGene summary for RAB40B:
The protein encoded by this gene has similarity to a yeast protein which suggests a role of the
gene product in regulating secretory vesicles. [provided by RefSeq]

UniProtKB/Swiss-Prot: RB40B_HUMAN, Q12829
Function: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box
protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal
degradation of target proteins (By similarity)

(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 RAB40B gene  

Entrez Gene cytogenetic band: 17q25.3   Ensembl cytogenetic band:  17q25.3   HGNC cytogenetic band: 17q25.3

RAB40B 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 17         GeneLoc Exon Structure

GeneLoc location for GC17M078208:     (about GC identifiers)

Start:
78,208,238 bp from pter
End:
78,249,802 bp from pter
Size:
41,565 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000017.9  NT_010663.14  
(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: RB40B_HUMAN, Q12829 (See protein sequence)
Recommended Name: Ras-related protein Rab-40B  
Size: 278 amino acids; 30956 Da
Subcellular location: Cell membrane; Lipid-anchor; Cytoplasmic side (Potential)
Secondary accessions: Q8WVG3

REFSEQ proteins: NP_006813.1  

ENSEMBL proteins: 
ENSP00000269347 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (RAB40B)
Human Recombinant Proteins from Abnova (RAB40B)
              OriGene Purified Recombinant Human Protein: RAB40B 

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005886 plasma membrane IEA--
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Antibodies for RAB40B: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Browse Antibodies at Sigma-Aldrich
Browse R&D Systems for Antibodies
Antibodies from Abcam (RAB40B), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (RAB40B)
Novus Biologicals Antibody for RAB40B

Assays for RAB40B: 
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:
 IPR001806 Ras_GTPase
 IPR005225 Small_GTP_bd
 IPR003579 GTPase_Rab
 IPR013753 Ras
 IPR001496 SOCS_C


   GeneDecks  RAB40B for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry Q12829

ProtoNet protein and cluster: Q12829

2 Blocks protein families:
IPB001496 SOCS protein
IPB001806 Transforming protein P21 RAS signature


UniProtKB/Swiss-Prot: RB40B_HUMAN, Q12829
Domain: The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module
in different E3 ubiquitin ligase complexes (By similarity)
Similarity: Belongs to the small GTPase superfamily. Rab family
Similarity: Contains 1 SOCS box domain

(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 (RAB40B)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006822

              Applied Biosystems Silencer® siRNAs for RAB40B

              Sigma-Aldrich siRNA and siRNA Panels for RAB40B  
                     Sigma-Aldrich shRNA for RAB40B  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for RAB40B
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_006822
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_006822
                                 untagged cDNA clone in CMV expression vector: NM_006822 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_006822

UniProtKB/Swiss-Prot: RB40B_HUMAN, Q12829
Function: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box
protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal
degradation of target proteins (By similarity)

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

GO IDQualified GO termEvidencePubMed IDs
GO:0000166 nucleotide binding IEA--
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


UniProtKB/Swiss-Prot: RB40B_HUMAN, Q12829
Pathway: Protein modification; protein ubiquitination

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

GO IDQualified GO termEvidencePubMed IDs
GO:0007264 small GTPase mediated signal transduction IEA--
GO:0015031 protein transport IEA--
GO:0019941 modification-dependent protein catabolic process 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 RAB40B
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for RAB40B

(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 (RAB40B)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006822

              Sigma-Aldrich siRNA and siRNA Panels for RAB40B  
                     Sigma-Aldrich shRNA for RAB40B  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_006822  

REFSEQ mRNAs for RAB40B gene: 

NM_006822.2   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_006822  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_006822
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_006822
                                 untagged cDNA clone in CMV expression vector: NM_006822 

Additional cDNA sequence: 

AB209711.1 AK095782.1 AK124376.1 AK124627.1 BC018039.1 BC035814.1 CR598763.1 CR604923.1 
CR619045.1 U05227.1 

11 DOTS entries:

DT.413737  DT.97840658  DT.99989296  DT.101959901  DT.91750469  DT.86854763  DT.100812050  DT.100832293 
DT.120953715  DT.92032377  DT.95293819 

24/122 AceView cDNA sequences (see all 122 ):

AW467132 BX644764 AW195204 CR604923 BC035814 AU099462 AL047483 CR598763 
BG260032 BM799558 CR619045 CF142144 BM842538 AW005667 AL575602 BM720666 
BX444456 CD677749 BM679368 BI552559 F21913 BI913545 BI822864 BQ882900 

highest scoring ESTs for RAB40B:

U05227 AL047483 AL552252 AU099462 BC018039 BC035814 BG715999 BG716709 BI549516 BI551467 

Unigene Cluster for RAB40B:

RAB40B, member RAS oncogene family
Hs.484068  [show with all ESTs]
Unigene Representative Sequence: AK095782


GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for RAB40B

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c
SP1:              -     -                       -                                 
SP2:              -     -                       -     -                           
SP3:                                            -                                 
SP4:                    -                                                         
SP5:                                                                              

About this scheme

ECgene alternative splicing isoforms for RAB40B

1 Ensembl transcript including schematic representation:
ENST00000269347  
(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

RAB40B expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for RAB40B

1 / 2 / 3

4 probe-sets matching RAB40B gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
555_at2, 3 U95-A 2 1.00 0.91 0.98 0.94 U05227 1.00 1.00 1.00 1
108_g_at2, 3 U95-A 4 1.00 0.32 0.97 1.06 Z95624 0.20 0.33 0.27 1

204547_at2, 3 U133-A 1 1.00 1.00 -- -- NM_006822 0.60 1.00 0.82 1

204547_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  RAB40B 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: ATTGCACTGC

SOURCE GeneReport for Unigene cluster: Hs.484068

Expression variation in blood from EXPOLDB for RAB40B

(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 RAB40B gene from 5/11 species (see all 11 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
RAB40B1   -- RAB40B, member RAS oncogene family 88.25(n)
94.29(a)
608295  XM_845270.1  XP_850363.1 
chimpanzee
(Pan troglodytes)
RAB40B1   -- RAB40B, member RAS oncogene family 99.43(n)
99.57(a)
454998  XM_511769.2  XP_511769.2 
cow
(Bos taurus)
RAB40B1   -- RAB40B, member RAS oncogene family 88.37(n)
89.57(a)
534237  XM_613938.3  XP_613938.2 
rat
(Rattus norvegicus)
Rab40b1   -- Rab40b, member RAS oncogene family 86.81(n)
94.24(a)
303754  XM_221213.4  XP_221213.2 
mouse
(Mus musculus)
Rab40b1, 5 115
Rab40b, member RAS oncogene family1, 5 87.41(n)1
92.81(a)1
2173711  NM_139147.21  NP_631886.11 
 AB2326385  AF4256435  (see all 9)
About this table        Species with no ortholog for RAB40B

ENSEMBL Gene Tree for RAB40B
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for RAB40B gene
RAB40A2  RAB40C2  RAB40AL2  

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


10/397 NCBI SNPs in RAB40B are shown (see all 397 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 85)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 17 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs111051,2
A,C,F,H78208579(-) AAAGCA/GCCAAT 1 -- ut319Minor allele frequency- G:0.38MN NA EU EA WA 926
--
rs38984311,2
A,C,F,H78251628(+) GTGGAC/TGCTAG 1 -- ng3112Minor allele frequency- T:0.06EU EA WA 1258
rs37947251,2
A,C,F,H78208222(+) ACCGGC/TCGCCA 1 -- ng514Minor allele frequency- T:0.32EU EA WA 412
--
rs22436061,2
A,C,F78249905(+) GCGCAG/TCCCCG 1 -- ng311Minor allele frequency- T:0.14EA 1292
--
rs22643731,2
A,C78250712(-) acacaC/Tagatg 1 -- ng310--------
rs37519111,2
C,F78208932(+) TCGCCG/AAGAGG 1 -- ut31 ese39Minor allele frequency- A:0.15EA NA EU WA 1544
rs72242261,2
C,H78208329(+) TTGACC/ATGTCG 1 -- ut31 ese34Minor allele frequency- A:0.00EU EA WA 418
rs37519101,2
H78208906(+) GCGTCG/ACACAC 1 -- ut31 ese34Minor allele frequency- A:0.00EU EA WA 414
rs37519121,2
F78209007(+) CCGCCG/ATGTTT 1 -- ut31 ese31Minor allele frequency- A:0.04EA 1494
--
rs341893041,2
F78209077(-) CCCCCA/C/GCCAGA 2 P/H P/R mis11NA 76
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HapMap Linkage Disequilibrium images for RAB40B (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

  --

(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

7 PubMed articles for RAB40B gene:
(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: 10966 HGNC: 18284 AceView: RAB40B Ensembl:ENSG00000141542 euGenes: HUgn10966
ECgene: RAB40B H-InvDB: RAB40B
(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 RAB40B 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 RAB40B:
 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
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 Millipore Preclinical / Clinical Development Services
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 Millipore Target Screening & Profiling Services


 Predesigned and custom siRNAs for RAB40B Browse antibodies at Sigma-Aldrich
 Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
 Lentivirus-delivered shRNAs for RAB40B Browse small molecules at Sigma-Aldrich
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 Tagged/untagged cDNA clones
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 Purified proteins from HEK293T cells
 Western blot validated antibodies
 shRNA in GFP-retroviral vector
 Search Tocris compounds for RAB40B




 Drugs for RAB40B
 Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
 Antibodies for RAB40B

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