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

RAB40B Gene

protein-coding   GIFtS: 53
GCID: GC17M080614

RAB40B, member RAS oncogene family

 Explore 1 disease affiliated with
RAB40B via our new
 Human Malady Compendium 
Biological research products
for RAB40B
    

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

Aliases
RAB40B, Member RAS Oncogene Family1 2     SOCS Box-Containing Protein RAR2 3
SEC4L1 2 3     GTP-Binding Protein Homologous To Saccharomyces Cerevisiae SEC42
RAR1 2     Ras-Related Protein Rab-40B2
Protein Rar2 3     

External Ids:    HGNC: 182841   Entrez Gene: 109662   Ensembl: ENSG000001415427   UniProtKB: Q128293   

Export aliases for RAB40B gene to outside databases

Previous GC identifers: GC17M079683 GC17M083584 GC17M081144 GC17M081293 GC17M078208 GC17M076014


(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 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, Jul 2008)

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 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_000017.10  NC_018928.1  NT_010663.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RAB40B gene promoter:
         NF-YB   CBF-B   CBF-A   NF-YA   NF-YC   CP1C   CP1A   NF-Y   CBF-C   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): RAB40B promoter sequence
   Search SABiosciences Chromatin IP Primers for RAB40B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RAB40B


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

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)
RAB40B gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M080614:  view genomic region     (about GC identifiers)

Start:
80,612,849 bp from pter      End:
80,656,604 bp from pter
Size:
43,756 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: 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

Explore the universe of human proteins at neXtProt for RAB40B: NX_Q12829

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q12829

  • RAB40B Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_006813.1  
    ENSEMBL proteins: 
     ENSP00000461785   ENSP00000269347   ENSP00000438897   ENSP00000458638  

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    Uscn Proteins for RAB40B

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

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


    RAB40B 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

    RAB40B for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR005225 Small_GTP-bd_dom
     IPR001806 Small_GTPase
     IPR003579 Small_GTPase_Rab_type
     IPR001496 SOCS_C

    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 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: 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)

    miRNA
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    8/28 QIAGEN miScript miRNA Assays for microRNAs that regulate RAB40B (see all 28):
    hsa-miR-623 hsa-miR-15a hsa-miR-1271 hsa-let-7a-2* hsa-miR-103a hsa-miR-374a* hsa-miR-9 hsa-miR-424
    SwitchGear 3'UTR luciferase reporter plasmidRAB40B 3' UTR sequence
    Inhib. RNA
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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--


    RAB40B for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for RAB40B:
     Increased cell death HMECs cel 


    (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



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

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RAB40B

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

    5/6 Interacting proteins for RAB40B (Q128293 ENSP000002693474) via UniProtKB, MINT, STRING, and/or I2D (see all 6)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    TCEB1Q153693, ENSP000002848114I2D: score=1 STRING: ENSP00000284811
    CCDC64BA1A5D93I2D: score=1 
    TCEB2ENSP000002623064STRING: ENSP00000262306
    FHITENSP000003420874STRING: ENSP00000342087
    WFDC1ENSP000002194544STRING: ENSP00000219454
    About this table

    Gene Ontology (GO): 3 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:0016567protein ubiquitination IEA--


    RAB40B 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 RAB40B
    Search CenterWatch for drugs/clinical trials and news about RAB40B / RB40B 

    (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 RAB40B gene: 
    NM_006822.2  

    Unigene Cluster for RAB40B:

    RAB40B, member RAS oncogene family
    Hs.484068  [show with all ESTs]
    Unigene Representative Sequence: AK095782
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000571995(uc002kft.3) ENST00000571880 ENST00000269347(uc002kfs.3 uc010wvq.1)
    ENST00000576359 ENST00000574132 ENST00000570676 ENST00000538809 ENST00000576148
    ENST00000573395 ENST00000571554 ENST00000572603

    miRNA
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    8/28 QIAGEN miScript miRNA Assays for microRNAs that regulate RAB40B (see all 28):
    hsa-miR-623 hsa-miR-15a hsa-miR-1271 hsa-let-7a-2* hsa-miR-103a hsa-miR-374a* hsa-miR-9 hsa-miR-424
    SwitchGear 3'UTR luciferase reporter plasmidRAB40B 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AB209711.1 AK095782.1 AK124376.1 AK124627.1 BC018039.1 BC035814.1 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):

    CR619045 AW467132 BC035814 CF142144 AW195204 CR604923 BM842538 BM799558 
    BX644764 BG260032 AL047483 AU099462 CR598763 BE810332 CD677749 T16827 
    U05227 AI884971 BI551467 BE671564 AW005667 BM931598 BM720666 AL552252 

    GeneLoc Exon Structure

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

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


    ECgene alternative splicing isoforms for RAB40B

    (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

    RAB40B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATTGCACTGC

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

    About this image

    RAB40B expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    TestisSeminiferous TubulesSertoli cellsTestis
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See RAB40B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RAB40B

    SOURCE GeneReport for Unigene cluster: Hs.484068
        SABiosciences Custom PCR Arrays for RAB40B
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAB40B

    (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 RAB40B gene from 5/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves RAB40B1 RAB40B, member RAS oncogene family 78.9(n)
    90.29(a)
      417338  XM_415603.2  XP_415603.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    81(a)
    1 → many
    2(103680964-103703579)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.238872 Xenopus laevis transcribed sequence with moderate similarity to protein refNP_006813.1 (H.sapiens) GTP-binding protein homologous to Saccharomyces cerevisiae SEC4 [Homo sapiens] less 77.69(n)    CA974571.1 
    zebrafish
    (Danio rerio)
    Actinopterygii rab40b1 RAB40B, member RAS oncogene family 74.22(n)
    83.45(a)
      436797  NM_001002524.1  NP_001002524.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG19003 RAB small monomeric GTPase 60(a)   11A11   --


    ENSEMBL Gene Tree for RAB40B (if available)
    TreeFam Gene Tree for RAB40B (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RAB40B gene
    RAB40A2  RAB40C2  RAB40AL2  
    18/54 SIMAP similar genes for RAB40B using alignment to 4 protein entries:     RB40B_HUMAN (see all proteins) (see all similar genes):
    RAB40AL    RAB40A    RAB40C    rab1b    RAB10    RAB19
    DKFZp686J06205    RAB15    RAB8A    RAB8B    RAB4B    RAB13
    RAB26    RAB35    RAB43    DKFZp686J07132    RAB11A    RAB37

    RAB40B 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

    10/1057 NCBI SNPs in RAB40B are shown (see all 1057    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1132129611,2
    C,--76028172(+) GCGTCC/TCGTGT 1 -- us2k13Minor allele frequency- T:0.10NA EA 242
    rs1865605341,2
    --80614581(+) AAGTAA/GAGGGC 1 -- ds50010--------
    rs1925633571,2
    --80614667(+) GGTGGA/GTCACC 1 -- ds50010--------
    rs1845291761,2
    --80614684(+) TAGGAG/TTTCAA 1 -- ds50010--------
    rs1891219621,2
    --80614742(+) AAAATA/TAGCCG 1 -- ds50010--------
    rs1928866671,2
    --80614751(+) CGGGCA/GTGGTG 1 -- ds50010--------
    rs1121839121,2
    --80614808(+) TCGCTG/TGAACC 1 -- ds50011Minor allele frequency- T:0.50CSA 2
    rs1850252171,2
    --80614877(+) AAGAGC/TGAAAC 1 -- ds50010--------
    rs37947251,2
    C,F,A,H,--80614933(+) ACCGGC/TCGCCA 1 -- ds500125Minor allele frequency- T:0.31NS EA NA WA CSA 2341
    rs1894896491,2
    --80615149(+) ATTTAC/TAGAAA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for RAB40B (80612849 - 80656604 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 14 variations for RAB40B
         10 CNVs: 88662 88663 88660 77765 73078 67280 73074 102562 73077 88661
         4 Indels: 41851 25959 25961 25960

    SABiosciences Cancer Mutation PCR Assays
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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

    RAB40B for disorders           About GeneDecksing

    1 disease for RAB40B:    About MalaCards
    thyroiditis


    Export disorders for RAB40B 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 RAB40B gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with RAB40B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    2. Evolution of the Rab family of small GTP-binding proteins. (PubMed id 11697911)1, 3 Pereira-Leal J.B. and Seabra M.C. (2001)
    3. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    4. Dynamics of cullin-RING ubiquitin ligase network revea led by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (2010)
    5. Array MAPPIT: high-throughput interactome analysis in mammalian cells. (PubMed id 19159283)1 Lievens S....Tavernier J. (2009)
    6. Characterization of Cullin-box sequences that direct recruitment of Cul2-Rbx1 and Cul5-Rbx2 modules to Elongin BC-based ubiquitin ligases. (PubMed id 18187417)1 Mahrour N....Conaway J.W. (2008)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
    8. 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. (2002)
    9. The SOCS box: a tale of destruction and degradation. (PubMed id 12076535)1 Kile B.T....Hilton D.J. (2002)
    10. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, 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 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 RAB40B Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RAB40B 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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    Patent Information for RAB40B gene:
    Search GeneIP for patents involving RAB40B

    GeneCards and IP:
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