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RAB40A Gene

protein-coding   GIFtS: 46
GCID: GC0XM102754

RAB40A, Member RAS Oncogene Family

  Search for RAB40A
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
RAB40A, Member RAS Oncogene Family1 2     Ras-Related Protein Rab-40A2
Protein Rar-22 3     SOCS Box Containing Protein RAR2A2
SOCS Box-Containing Protein RAR2A2 3     MRXSMP5
RAR22     RAB40AL5
RAR2A2     RLGP5

External Ids:    HGNC: 182831   Entrez Gene: 1426842   Ensembl: ENSG000001724767   OMIM: 3004055   UniProtKB: Q8WXH63   

Export aliases for RAB40A gene to outside databases

Previous GC identifers: GC0XM098056 GC0XM099663 GC0XM100787 GC0XM101526 GC0XM102560 GC0XM102641 GC0XM092410


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RAB40A Gene:
This gene encodes a member of the Rab40 subfamily of Rab small GTP-binding proteins that contains a C-terminal
suppressors of cytokine signaling box. (provided by RefSeq, Apr 2010)

GeneCards Summary for RAB40A Gene:
RAB40A (RAB40A, member RAS oncogene family) is a protein-coding gene. GO annotations related to this gene include GTP binding. An important paralog of this gene is RAB40C.

UniProtKB/Swiss-Prot: RB40A_HUMAN, Q8WXH6
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)

Gene Wiki entry for RAB40A Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the RAB40A gene promoter:
         AP-2rep   LHX3b/Lhx3b   HNF-1A   POU2F1   POU2F1b   POU2F1a   HNF-1   LHX3a/Lhx3a   Cart-1   POU2F1c   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRAB40A promoter sequence
   Search Chromatin IP Primers for RAB40A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RAB40A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq22.1   Ensembl cytogenetic band:  Xq22.2   HGNC cytogenetic band: Xq22.1

RAB40A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RAB40A gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM102754:  view genomic region     (about GC identifiers)

Start:
102,754,678 bp from pter      End:
102,774,417 bp from pter
Size:
19,740 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: RB40A_HUMAN, Q8WXH6 (See protein sequence)
Recommended Name: Ras-related protein Rab-40A precursor  
Size: 277 amino acids; 31076 Da
Secondary accessions: O00407 Q17RQ5 Q6DK06 Q8TF06

Explore the universe of human proteins at neXtProt for RAB40A: NX_Q8WXH6

Explore proteomics data for RAB40A at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RAB40A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_543155.2  
    ENSEMBL proteins: 
     ENSP00000361716   ENSP00000305648  

    RAB40A Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    RAB: RAB, member RAS oncogene

    5 InterPro protein domains:
     IPR005225 Small_GTP-bd_dom
     IPR001806 Small_GTPase
     IPR003579 Small_GTPase_Rab_type
     IPR027417 P-loop_NTPase
     IPR001496 SOCS_C

    Graphical View of Domain Structure for InterPro Entry Q8WXH6

    ProtoNet protein and cluster: Q8WXH6

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


    UniProtKB/Swiss-Prot: RB40A_HUMAN, Q8WXH6
    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


    RAB40A for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RB40A_HUMAN, Q8WXH6
    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)

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003924GTPase activity ----
    GO:0005525GTP binding IEA--
         
    RAB40A for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RAB40A
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    miRNA
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    miRTarBase miRNAs that target RAB40A:
    hsa-mir-335-5p (MIRT017532)

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    Sino Biological Human cDNA Clone for RAB40A
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RB40A_HUMAN, Q8WXH6: Cell membrane; Lipid-anchor; Cytoplasmic side (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    cytosol3
    extracellular1
    peroxisome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005886plasma membrane IEA--
    GO:0016020membrane ----

    RAB40A for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    UniProtKB/Swiss-Prot: RB40A_HUMAN, Q8WXH6
    Pathway: Protein modification; protein ubiquitination

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RAB40A
    Interactions:

        Search GeneGlobe Interaction Network for RAB40A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for RAB40A (Q8WXH62 ENSP000003056484) via UniProtKB, MINT, STRING, and/or I2D (see all 26)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    EXOC2ENSP000002304494STRING: ENSP00000230449
    EXOC4ENSP000002538614STRING: ENSP00000253861
    EXOC7ENSP000003341004STRING: ENSP00000334100
    EXOC6ENSP000002607624STRING: ENSP00000260762
    EXOC6BENSP000002724274STRING: ENSP00000272427
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006184GTP catabolic process ----
    GO:0006886intracellular protein transport ----
    GO:0006913nucleocytoplasmic transport ----
    GO:0007165signal transduction ----
    GO:0007264small GTPase mediated signal transduction IEA--

    RAB40A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for RAB40A (RB40A)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for RAB40A gene: 
    NM_080879.2  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372633(uc022cbs.1) ENST00000304236(uc004ekk.3)
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat RAB40A
      QuantiFast Probe-based Assays in human, mouse, rat RAB40A

    15 AceView cDNA sequences:

    AF132748 Z43570 BC074855 BC074854 AK056859 H24206 NM_080879 BC045674 
    AF422143 H24205 Z39635 AW300309 CF264884 BI562054 R48513 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    RAB40A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    RAB40A Expression
    About this image

    RAB40A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RAB40A Protein Expression
        Custom PCR Arrays for RAB40A
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for RAB40A gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves RAB40B6
    ras-related protein Rab-40B
    72(a)
    1 → many
    18(3340422-3363541)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    73(a)
    1 → many
    2(103680964-103703579)
    zebrafish
    (Danio rerio)
    Actinopterygii rab40b6
    RAB40B, member RAS oncogene family
    77(a)
    1 → many
    12(33726278-33753571) ENSDARG00000042410
    fruit fly
    (Drosophila melanogaster)
    Insecta CG19003 RAB small monomeric GTPase 58(a)   11A11   --
            Species with no ortholog for RAB40A

    ENSEMBL Gene Tree for RAB40A (if available)
    TreeFam Gene Tree for RAB40A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RAB40A gene
    RAB40C2  RAB40AL2  RAB40B2  
    Selected SIMAP similar genes for RAB40A using alignment to 1 protein entry:     RB40A_HUMAN(see all similar genes):
    RAB40AL    RAB40B    RAB40C    RAB10    RAB13    DKFZp686J07132
    RAB8A    RAB8B    RAB15    RAB11B    RAB19    RAB43
    RAB11A    RAB30    RAB1B    RAB35    RAB37    RAB3C

    RAB40A for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for RAB40A (see all 272)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs59032161,2
    C--92424574(+) GAAAGG/-AAAAT 1 -- int11Minor allele frequency- -:0.00CSA 2
    rs556707391,2
    C--102723736(+) CTGTTA/GTATAC 1 -- ds50010--------
    rs1911289161,2
    --102723876(+) GAATTC/TATACT 1 -- ds50010--------
    rs1405111131,2
    C,F--102724306(+) GATCTC/TCACTT 2 K E mis11Minor allele frequency- T:0.00NA 4532
    rs1996697441,2
    C--102724341(+) AGCTGC/GTGGTG 2 T S mis10--------
    rs1823684691,2
    C--102724366(+) GCCTCA/GCATCA 2 R * stg10--------
    rs617355251,2
    C,F--102724403(+) GAGAAG/AGACTT 2 /S syn12Minor allele frequency- A:0.00NS NA 4624
    rs617355241,2
    C,F--102724404(+) AGAAGG/AACTTG 2 /S /F mis13Minor allele frequency- A:0.10NS WA NA 4630
    rs1393895791,2
    C--102724417(+) GTGGCC/TTCTTA 2 S G mis10--------
    rs2014665011,2
    C--102724426(+) TAAGGC/TACTGG 2 T A mis10--------

    HapMap Linkage Disequilibrium report for RAB40A (102754678 - 102774417 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for RAB40A: --
    Locus Specific Mutation Databases (LSDB): RAB40A

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RAB40A
    DNA2.0 Custom Variant and Variant Library Synthesis for RAB40A

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 300405   
    OMIM disorders: 300519  

    RAB40A for disorders           About GeneDecksing


    Export disorders for RAB40A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for RAB40A gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with RAB40A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Screening for target Rabs of TBC (Tre-2/Bub2/Cdc16) domain-containing proteins based on their Rab-binding activity. (PubMed id 16923123)1, 2 Itoh T.... Fukuda M. (Genes Cells 2006)
    2. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. Evolution of the Rab family of small GTP-binding proteins. (PubMed id 11697911)1, 3 Pereira-Leal J.B. and Seabra M.C. (J. Mol. Biol. 2001)
    5. Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition. (PubMed id 22939624)1 Taipale M....Lindquist S. (Cell 2012)
    6. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    7. Pericentrosomal targeting of Rab6 secretory vesicles by Bicaudal-D-related protein 1 (BICDR-1) regulates neuritogenesis. (PubMed id 20360680)1 Schlager M.A....Hoogenraad C.C. (EMBO J. 2010)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. Distinct Rab binding specificity of Rim1, Rim2, rabphilin, and Noc2. Identification of a critical determinant of Rab3A/Rab27A recognition by Rim2. (PubMed id 12578829)1 Fukuda M. (J. Biol. Chem. 2003)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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, Kegg, and/or H-InvDB)
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    Entrez Gene: 142684 HGNC: 18283 AceView: RAB40A Ensembl:ENSG00000172476 euGenes: HUgn142684
    ECgene: RAB40A H-InvDB: RAB40A

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RAB40A Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RAB40A Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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