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RAB39B Gene

protein-coding   GIFtS: 52
GCID: GC0XM154487

RAB39B, Member RAS Oncogene Family

(Previous names: mental retardation, X-linked 72)
(Previous symbol: MRX72)
  See related diseases
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
RAB39B, Member RAS Oncogene Family1 2
MRX721 2 5
Mental Retardation, X-Linked 721
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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RAB39B Gene:
This gene encodes a member of the Rab family of proteins. Rab proteins are small GTPases that are involved in
vesicular trafficking. Mutations in this gene are associated with X-linked mental retardation. (provided by
RefSeq, Aug 2013)

GeneCards Summary for RAB39B Gene:
RAB39B (RAB39B, member RAS oncogene family) is a protein-coding gene. Diseases associated with RAB39B include distal xq28 microduplication syndrome, and mental retardation, x-linked 17/31, microduplication. GO annotations related to this gene include GTP binding. An important paralog of this gene is RAB19.

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 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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RefSeq DNA sequence:
NC_000023.11  NC_018934.2  NT_011681.17  
Regulatory elements:
   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 Chromatin IP Primers for RAB39B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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, 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: RB39B_HUMAN, Q96DA2 (See protein sequence)
Recommended Name: Ras-related protein Rab-39B  
Size: 213 amino acids; 24622 Da
Secondary accessions: Q5JT79 Q8NEX3

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

Explore proteomics data for RAB39B at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys140
  • Modification sites at PhosphoSitePlus

  • See RAB39B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_741995.1  
    ENSEMBL proteins: 
     ENSP00000358466  

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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

    4 InterPro protein domains:
     IPR005225 Small_GTP-bd_dom
     IPR001806 Small_GTPase
     IPR003579 Small_GTPase_Rab_type
     IPR027417 P-loop_NTPase

    Graphical View of Domain Structure for InterPro Entry Q96DA2

    ProtoNet protein and cluster: Q96DA2

    1 Blocks protein domain: IPB001806 Transforming protein P21 RAS signature

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


    RAB39B 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: RB39B_HUMAN, Q96DA2
    Function: May be involved in vesicular trafficking. Plays a role in synapse formation (By similarity)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003924GTPase activity ----
    GO:0005525GTP binding IEA--
         
    RAB39B for ontologies           About GeneDecksing


    Animal Models:
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    hsa-mir-1 (MIRT024007)

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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
    SwitchGear 3'UTR luciferase reporter plasmidRAB39B 3' UTR sequence
    Inhib. RNA
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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
    RB39B_HUMAN, Q96DA2: 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)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    golgi apparatus5
    plasma membrane5
    cytoskeleton3
    cytosol3
    nucleus3
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular IDA--
    GO:0005634nucleus ----
    GO:0005737cytoplasm ----
    GO:0005794Golgi apparatus IDA--
    GO:0005886plasma membrane IEA--

    RAB39B 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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RAB39B
    Interactions:

        Search GeneGlobe Interaction Network for RAB39B

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    Selected Interacting proteins for RAB39B (ENSP000003584664) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SIRT2ENSP000002493964STRING: ENSP00000249396
    GAPVD1ENSP000003776654STRING: ENSP00000377665
    RABGEF1ENSP000002849574STRING: ENSP00000284957
    SLC25A3ENSP000002283184STRING: ENSP00000228318
    ECI2ENSP000003547374STRING: ENSP00000354737
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    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--

    RAB39B 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 RAB39B (RB39B)



    (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 RAB39B gene: 
    NM_171998.3  

    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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      QuantiTect SYBR Green Assays in human, mouse, rat RAB39B
      QuantiFast Probe-based Assays in human, mouse, rat RAB39B

    Additional mRNA sequence: 

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

    2 DOTS entries:

    DT.308598  DT.121283435 

    Selected AceView cDNA sequences (see all 67):

    NM_171998 AA804525 AA356937 CK819082 BX419147 AK056209 BM069528 AL834460 
    BE503571 BU634476 AA705288 BC009714 AI022744 AA744827 BX108796 BM069764 
    BM677208 AI929317 AA280648 BM126536 AW015673 BX461685 AY052478 AI929251 

    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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    RAB39B expression in normal human tissues (normalized intensities)      RAB39B embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGGATTAGA
    RAB39B Expression
    About this image


    RAB39B expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
             Human embryonic stem cells (family)
    RAB39B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RAB39B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.632832

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

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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 RAB39B gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rab39b1 , 5 RAB39B, member RAS oncogene family1, 5 97.65(n)1
    99.53(a)1
      X (38.26 cM)5
    677901  NM_175122.61  NP_780331.11 
     755720465 
    chicken
    (Gallus gallus)
    Aves RAB39B1 RAB39B, member RAS oncogene family 84.35(n)
    97.65(a)
      422354  XM_420326.4  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 Rab39 57.28(n)
    53.52(a)
      31684  NM_001258639.2  NP_001245568.1 
    worm
    (Caenorhabditis elegans)
    Secernentea rab-391 rab-39 54.79(n)
    54.46(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)
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    Paralogs for RAB39B gene
    RAB192  RAB39A2  RAB2A2  RAB252  RAB432  RAB142  RAB4B2  RAB11B2  
    RAB11A2  RAB422  RAB4A2  RAB302  RAB4B-EGLN22  RAB2B2  
    Selected 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    RAB8A    RAB8B    RAB19    RAB2B
    RAB37    RAB5C    RAB15    RAB5B    RAB11B    RAB17

    RAB39B 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 RAB39B (see all 114)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2004145531,2
    C--154487028(+) TTTCC-/TTTTTT 1 -- ds50010--------
    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

    HapMap Linkage Disequilibrium report for RAB39B (154487526 - 154493874 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RAB39B:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2543058CNV Deletion19546169
    esv29972CNV Gain17803354
    esv33784CNV Gain+Loss17666407

    Human Gene Mutation Database (HGMD): RAB39B
    Locus Specific Mutation Databases (LSDB): RAB39B

    Site Specific Mutation Identification with PCR Assays
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    (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: 300774   
    OMIM disorders: 300271  
    UniProtKB/Swiss-Prot: RB39B_HUMAN, Q96DA2
  • Mental retardation, X-linked 72 (MRX72) [MIM:300271]: A disorder characterized by significantly below
    average general intellectual functioning associated with impairments in adaptive behavior and manifested during
    the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked mental
    retardation, while syndromic mental retardation presents with associated physical, neurological and/or
    psychiatric manifestations. MRX72 patients can manifest autism spectrum disorder, seizures and macrocephaly as
    additional features. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 9 diseases for RAB39B:    About MalaCards
    distal xq28 microduplication syndrome    mental retardation, x-linked 17/31, microduplication    autism spectrum disorder    mental retardation
    mental retardation, x-linked    glaucoma    malaria    multiple myeloma
    myeloma


    RAB39B for disorders           About GeneDecksing


    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)
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    PubMed articles for RAB39B gene, integrated from 10 sources (see all 22):
    (articles sorted by number of sources associating them with RAB39B)
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    1. Mutations in the small GTPase gene RAB39B are responsible for X- linked mental retardation associated with autism, epilepsy, and macrocephaly. (PubMed id 20159109)1, 2, 3 Giannandrea M.... D'Adamo P. (Am. J. Hum. Genet. 2010)
    2. Isolation and characterization of a human novel RAB (RAB39B) gene. (PubMed id 12438742)1, 2, 3 Cheng H.... Mao Y. (Cytogenet. Genome Res. 2002)
    3. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 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. (Genome Res. 2004)
    5. XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing. (PubMed id 23871722)1 Piton A....Mandel J.L. (Am. J. Hum. Genet. 2013)
    6. Cystatin a, a potential common link for mutant myocilin causative glaucoma. (PubMed id 22615763)1 Kennedy K.D....BorrA!s T. (PLoS ONE 2012)
    7. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    8. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    9. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    10. A de novo paradigm for mental retardation. (PubMed id 21076407)1 Vissers L.E.... Veltman J.A. (Nat. Genet. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 116442 HGNC: 16499 AceView: RAB39B Ensembl:ENSG00000155961 euGenes: HUgn116442
    ECgene: RAB39B H-InvDB: RAB39B

    (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 RAB39B Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RAB39B Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RAB39B gene:
    Search GeneIP for patents involving RAB39B

    GeneCards and IP:
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