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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RAB39B Gene

protein-coding   GIFtS: 50
GCID: GC0XM154487

RAB39B, member RAS oncogene family

 Explore 2 diseases affiliated with
RAB39B via our new
 Human Malady Compendium 
Biological research products
for RAB39B
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
RAB39B, Member RAS Oncogene Family1 2
MRX722 5
Ras-Related Protein Rab-39B2

External Ids:    HGNC: 164991   Entrez Gene: 1164422   Ensembl: ENSG000001559617   OMIM: 3007745   UniProtKB: Q96DA23   

Export aliases for RAB39B gene to outside databases

Previous GC identifers: GC00U991112 GC0XM150941 GC0XM152004 GC0XM152909 GC0XM152900 GC0XM154051 GC0XM154140 GC0XM143031


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

Entrez Gene summary for RAB39B:
This gene encodes a member of the Rab family of proteins. Rab proteins are small GTPases that are involved in vesicular
trafficking. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: RB39B_HUMAN, Q96DA2
Function: May be involved in vesicular trafficking. Plays a role in synapse formation (By similarity)

Gene Wiki entry for RAB39B


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.1  NT_167198.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RAB39B gene promoter:
         POU2F2 (Oct-2.1)   p53   HTF   CUTL1   POU2F2   C/EBPalpha   POU2F2C   POU2F1a   IRF-7A   POU2F2B   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRAB39B promoter sequence
   Search SABiosciences Chromatin IP Primers for RAB39B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RAB39B


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

Entrez Gene cytogenetic band: Xq28   Ensembl cytogenetic band:  Xq28   HGNC cytogenetic band: Xq28

RAB39B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RAB39B gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM154487:  view genomic region     (about GC identifiers)

Start:
154,487,526 bp from pter      End:
154,493,874 bp from pter
Size:
6,349 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: RB39B_HUMAN, Q96DA2 (See protein sequence)
Recommended Name: Ras-related protein Rab-39B  
Size: 213 amino acids; 24622 Da
Subcellular location: Cell membrane; Lipid-anchor; Cytoplasmic side (Potential). Golgi apparatus. Note=Partial
colocalization with markers that cycle from the cell surface to the trans-Golgi network (By similarity)
Secondary accessions: Q5JT79 Q8NEX3

Explore the universe of human proteins at neXtProt for RAB39B: NX_Q96DA2

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96DA2

  • RAB39B Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_741995.1  
    ENSEMBL proteins: 
     ENSP00000358466  

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    Uscn Proteins for RAB39B

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular IDA--
    GO:0005737cytoplasm ----
    GO:0005794Golgi apparatus IDA--
    GO:0005886plasma membrane IEA--


    RAB39B for ontologies           About GeneDecksing



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

    RAB39B for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR005225 Small_GTP-bd_dom
     IPR001806 Small_GTPase
     IPR003579 Small_GTPase_Rab_type

    Graphical View of Domain Structure for InterPro Entry Q96DA2

    ProtoNet protein and cluster: Q96DA2

    1 Blocks protein family: IPB001806 Transforming protein P21 RAS signature

    UniProtKB/Swiss-Prot: RB39B_HUMAN, Q96DA2
    Similarity: Belongs to the small GTPase superfamily. Rab family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: RB39B_HUMAN, Q96DA2
    Function: May be involved in vesicular trafficking. Plays a role in synapse formation (By similarity)

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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005525GTP binding IEA--


    RAB39B for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RAB39B

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for RAB39B (ENSP000003584664) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SIRT2ENSP000002493964STRING: ENSP00000249396
    GDI1ENSP000003940714STRING: ENSP00000394071
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007264small GTPase mediated signal transduction IEA--
    GO:0015031protein transport IEA--
    GO:0016192vesicle-mediated transport ISS--
    GO:0050808synapse organization ISS--


    RAB39B for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RAB39B
    Search CenterWatch for drugs/clinical trials and news about RAB39B / RB39B 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RAB39B gene: 
    NM_171998.2  

    Unigene Cluster for RAB39B:

    RAB39B, member RAS oncogene family
    Hs.632832  [show with all ESTs]
    Unigene Representative Sequence: NM_171998
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000369454(uc004fne.3)

    miRNA
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    hsa-miR-21* hsa-miR-345 hsa-miR-300 hsa-miR-218-1* hsa-miR-30d hsa-miR-548l hsa-miR-10b* hsa-miR-30a
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    Inhib. RNA
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    Additional cDNA sequence: 

    AK056209.1 AL834460.1 AY052478.1 BC009714.1 

    2 DOTS entries:

    DT.308598  DT.121283435 

    24/67 AceView cDNA sequences (see all 67):

    BX108796 AA705288 AI022744 NM_171998 AK056209 AI929317 AA804525 AL834460 
    BM069528 AA744827 BX419147 BU634476 BC009714 CK819082 BM069764 AA356937 
    BM677208 BE503571 N36723 AA280648 BG057699 AA805950 AI218721 AI057628 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RAB39B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTGGATTAGA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    RAB39B expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Line H9 (WA09) (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See RAB39B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RAB39B

    SOURCE GeneReport for Unigene cluster: Hs.632832

    UniProtKB/Swiss-Prot: RB39B_HUMAN, Q96DA2
    Tissue specificity: Highly expressed in the brain

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAB39B

    (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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for RAB39B gene from 5/21 species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves RAB39B1 RAB39B, member RAS oncogene family 84.35(n)
    97.65(a)
      422354  XM_420326.3  XP_420326.3 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.132912 Transcribed sequence with weak similarity to protein more 78.45(n)    BX726620.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.290852 Danio rerio RAB39B, member RAS oncogene family, mRNA more 72.86(n)    BC060898.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Rab391 CG12156-PA 57.28(n)
    53.52(a)
      31684  NM_132177.3  NP_572405.2 
    worm
    (Caenorhabditis elegans)
    Secernentea rab-391 Protein RAB-39 55.05(n)
    55.56(a)
      183941  NM_063583.2  NP_495984.2 


    ENSEMBL Gene Tree for RAB39B (if available)
    TreeFam Gene Tree for RAB39B (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RAB39B gene
    RAB39A2  RAB2A2  RAB252  RAB142  RAB4B2  RAB11B2  RAB422  RAB4A2  
    RAB11A2  RAB2B2  
    18/84 SIMAP similar genes for RAB39B using alignment to 1 protein entry:     RB39B_HUMAN(see all similar genes):
    RAB39A    RAB30    DKFZp313C1541    DKFZp686J07132    RAB13    RAB26
    RAB43    RAB10    RAB4B    RAB8A    RAB8B    RAB19
    RAB2B    RAB37    RAB5C    RAB15    RAB5B    RAB11B

    RAB39B for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/94 NCBI SNPs in RAB39B are shown (see all 94    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1928173531,2
    --154487065(+) TGTACC/TATCAA 1 -- ds50010--------
    rs1845623031,2
    --154487267(+) ATCATC/GATGAT 1 -- ds50010--------
    rs1889308801,2
    --154487317(+) GCATAG/TGCTCA 1 -- ds50010--------
    rs1468333431,2
    --154487358(+) GATATC/GATGGT 1 -- ds50010--------
    rs1819857641,2
    --154487462(+) TGGTAC/GTAGTT 1 -- ds50010--------
    rs37473261,2
    C,F,H,--154487472(+) TGCTAC/TGCTGT 1 -- ds50018Minor allele frequency- T:0.01NS EA NA 840
    rs413117101,2
    C,--154487473(+) GCTACA/GCTGTA 1 -- ds50010--------
    rs128561251,2
    C--154488030(+) TCCAGC/TCGACT 1 -- ut31 ese30--------
    rs128482901,2
    C,H--154488071(+) AGAATC/TTTCTA 1 -- ut31 ese34Minor allele frequency- T:0.00NS EA 418
    rs128562021,2
    H--154488101(+) GTTGAT/AGAAAT 1 -- ut31 ese34Minor allele frequency- A:0.00NS EA 418

    HapMap Linkage Disequilibrium report for RAB39B (154487526 - 154493874 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for RAB39B
         2 CNVs: 103296 23331
    Human Gene Mutation Database (HGMD): RAB39B

    Locus Specific Mutation Databases (LSDB): RAB39B

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    RAB39B for disorders           About GeneDecksing

    OMIM gene information: 300774   
    OMIM disorders: 300271  
    UniProtKB/Swiss-Prot: RB39B_HUMAN, Q96DA2
  • Defects in RAB39B are the cause of mental retardation X-linked type 72 (MRX72) [MIM:300271]. Mental
  • retardation is characterized by significantly below average general intellectual functioning associated with
    impairments in adaptative behavior and manifested during the developmental period. MRX72 patients can manifest autism
    spectrum disorder, seizures and macrocephaly as additional features

    2 diseases for RAB39B:    About MalaCards
    mental retardation, x-linked    malaria


    Export disorders for RAB39B 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)
    About This Section

    PubMed articles for RAB39B gene, integrated from 9 sources (see all 17):
    (articles sorted by number of sources associating them with RAB39B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of a human novel RAB (RAB39B) gene. (PubMed id 12438742)1, 2, 3 Cheng H.... Mao Y. (2002)
    2. Mutations in the small GTPase gene RAB39B are respons ible for X-linked mental retardation associated with autism, epilepsy, and macr ocephaly. (PubMed id 20159109)1, 2 Giannandrea M....D'Adamo P. (2010)
    3. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (2005)
    4. 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. (2004)
    5. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    6. Functional dissection of lysine deacetylases reveals t hat HDAC1 and p300 regulate AMPK. (PubMed id 22318606)1 Lin Y.Y....Boeke J.D. (2012)
    7. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    8. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    9. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    10. Screening for target Rabs of TBC (Tre-2/Bub2/Cdc16) domain-containing proteins based on their Rab-binding activity. (PubMed id 16923123)1 Itoh T.... Fukuda M. (2006)

    (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, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 116442 HGNC: 16499 AceView: RAB39B Ensembl:ENSG00000155961 euGenes: HUgn116442
    ECgene: RAB39B H-InvDB: RAB39B

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RAB39B Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RAB39B Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for RAB39B gene:
    Search GeneIP for patents involving RAB39B

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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