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RAB40AL Gene

protein-coding   GIFtS: 43
GCID: GC0XP102192

RAB40A, Member RAS Oncogene Family-Like

  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
RAB40A, Member RAS Oncogene Family-Like1 2     MRXSMP2 5
RLGP2 3 5     RAR22
Ras Like GTPase1 2     Ras-Related Protein Rab-40A-Like2
Ras-Like GTPase2 3     SOCS Box Containing Protein RAR22

External Ids:    HGNC: 254101   Entrez Gene: 2828082   Ensembl: ENSG000001021287   OMIM: 3004055   UniProtKB: P0C0E43   

Export aliases for RAB40AL gene to outside databases

Previous GC identifers: GC00U921648 GC0XP102079 GC0XP091857


(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 RAB40AL 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. Disruptions in this gene are associated with Duchenne muscular dystrophy.
(provided by RefSeq, Apr 2010)

GeneCards Summary for RAB40AL Gene:
RAB40AL (RAB40A, member RAS oncogene family-like) is a protein-coding gene. Diseases associated with RAB40AL include mental retardation, x-linked, syndromic, martin-probst type, and duchenne muscular dystrophy. GO annotations related to this gene include GTP binding. An important paralog of this gene is RAB40A.

UniProtKB/Swiss-Prot: RB40L_HUMAN, P0C0E4
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 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_011651.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the RAB40AL gene promoter:
         GR   p53   p300   NRSF form 1   POU6F1 (c2)   NRSF form 2   C/EBPalpha   AREB6   GR-alpha   ITF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRAB40AL promoter sequence
   Search Chromatin IP Primers for RAB40AL

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RAB40AL


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

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

RAB40AL Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RAB40AL gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP102192:  view genomic region     (about GC identifiers)

Start:
102,192,200 bp from pter      End:
102,193,228 bp from pter
Size:
1,029 bases      Orientation:
plus 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RB40L_HUMAN, P0C0E4 (See protein sequence)
Recommended Name: Ras-related protein Rab-40A-like  
Size: 278 amino acids; 31239 Da
Secondary accessions: Q495H3

Explore the universe of human proteins at neXtProt for RAB40AL: NX_P0C0E4

Explore proteomics data for RAB40AL at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RAB40AL Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001027004.1  
    ENSEMBL proteins: 
     ENSP00000218249  

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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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    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 P0C0E4

    ProtoNet protein and cluster: P0C0E4

    1 Blocks protein domain: IPB001496 SOCS protein

    UniProtKB/Swiss-Prot: RB40L_HUMAN, P0C0E4
    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


    RAB40AL 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: RB40L_HUMAN, P0C0E4
    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--
         
    RAB40AL for ontologies           About GeneDecksing


    Animal Models:
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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
    RB40L_HUMAN, P0C0E4: Cell membrane; Lipid-anchor; Cytoplasmic side. Mitochondrion
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion5
    plasma membrane5
    cytosol3
    cytoskeleton1
    extracellular1
    nucleus1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005737cytoplasm IDA--
    GO:0005739mitochondrion IDA--
    GO:0005886plasma membrane IEA--
    GO:0016020membrane ----

    RAB40AL 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: RB40L_HUMAN, P0C0E4
    Pathway: Protein modification; protein ubiquitination

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RAB40AL
    Interactions:

        Search GeneGlobe Interaction Network for RAB40AL

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

    Selected Interacting proteins for RAB40AL (ENSP000002182494) via UniProtKB, MINT, STRING, and/or I2D (see all 35)

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

    RAB40AL 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
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    Browse Tocris compounds for RAB40AL (RB40L)



    (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,
    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 RAB40AL gene: 
    NM_001031834.1  

    Unigene Cluster for RAB40AL:

    RAB40A, member RAS oncogene family-like
    Hs.449517
    Unigene Representative Sequence: BC101170
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000218249(uc004ejs.3)
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      QuantiFast Probe-based Assays in human, mouse, rat RAB40AL

    Additional mRNA sequence: 

    BC101169.1 BC101170.2 BC101171.1 BC101172.1 

    1 DOTS entry:

    DT.121305595 

    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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    RAB40AL expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGAACAATGC
    RAB40AL Expression
    About this image

    RAB40AL Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RAB40AL Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.449517

    UniProtKB/Swiss-Prot: RB40L_HUMAN, P0C0E4
    Tissue specificity: Expressed in brain, lung, heart, skeletal muscle, kidney and liver. Highest expression in
    brain. Expressed in fetal brain and kidney

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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 RAB40AL 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
    73(a)
    1 → many
    18(3340422-3363541)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    74(a)
    1 → many
    2(103680964-103703579)
    zebrafish
    (Danio rerio)
    Actinopterygii rab40b6
    RAB40B, member RAS oncogene family
    78(a)
    1 → many
    12(33726278-33753571) ENSDARG00000042410
    fruit fly
    (Drosophila melanogaster)
    Insecta Rab406
    Rab40
    57(a)
    1 → many
    X(12353823-12357141)
            Species with no ortholog for RAB40AL

    ENSEMBL Gene Tree for RAB40AL (if available)
    TreeFam Gene Tree for RAB40AL (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RAB40AL gene
    RAB40A2  RAB40C2  RAB40B2  
    Selected SIMAP similar genes for RAB40AL using alignment to 1 protein entry:     RB40L_HUMAN(see all similar genes):
    RAB40A    RAB40B    RAB40C    RAB10    RAB13    RAB8A
    RAB8B    RAB15    RAB11B    RAB19    RAB43    RAB11A
    RAB30    RAB26    RAB1B    RAB35    RAB37    RAB3C

    RAB40AL 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 RAB40AL (see all 81)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0689164
    Mental retardation, X-linked, syndromic, Martin-Probst type (MRXSMP)4--see VAR_0689162 D G mis40--------
    rs70656791,2
    C,F,H--102159914(+) AGCACC/TTCCCT 1 -- us2k1 tfbs3 trp315Minor allele frequency- T:0.15NS EA NA WA CSA 1280
    rs1888741581,2
    --102160105(+) TAGCAA/CATAAC 1 -- us2k10--------
    rs1812782291,2
    --102160142(+) GAAAAA/CTGTTT 1 -- us2k10--------
    rs59874981,2
    C,F,A,H--102160290(+) ACTGAG/TAAGTG 1 -- us2k1 tfbs39Minor allele frequency- T:0.27NS EA NA 897
    rs1848581341,2
    --102160392(+) AAAAAA/CAAATT 1 -- us2k10--------
    rs1120036951,2
    C--102160434(+) TCAAAA/C/TGATAG 1 -- us2k11CSA 1
    rs59459081,2
    C,F,A,H--102160534(+) ATTTCA/GTCATC 1 -- us2k1 tfbs328Minor allele frequency- G:0.54NS EA NA WA CSA 2831
    rs1896982501,2
    --102160541(+) CATCCA/GTGAAC 1 -- us2k10--------
    rs1808841351,2
    --102160660(+) GGCTGA/CATATT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for RAB40AL (102192200 - 102193228 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for RAB40AL: --
    Human Gene Mutation Database (HGMD): RAB40AL
    Locus Specific Mutation Databases (LSDB): RAB40AL

    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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 300405   
    OMIM disorders: 300519  
    UniProtKB/Swiss-Prot: RB40L_HUMAN, P0C0E4
  • Mental retardation, X-linked, syndromic, Martin-Probst type (MRXSMP) [MIM:300519]: A rare
    neurodevelopmental disorder characterized by mental retardation, sensorineural hearing loss, short stature and
    craniofacial dysmorphisms. Patients also exhibit abnormal teeth, widely spaced nipples, abnormal dermatoglyphics,
    renal insufficiency, and impaired haematopoiesis. Mental retardation is defined as significantly below average
    general intellectual functioning associated with impairments in adaptive behavior and manifested during the
    developmental period. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 13 diseases for RAB40AL:    
    About MalaCards
    mental retardation, x-linked, syndromic, martin-probst type    duchenne muscular dystrophy    vitelliform macular dystrophy    sensorineural hearing loss
    cerebral palsy    macular dystrophy    muscular dystrophy    mental retardation, x-linked
    short stature    mental retardation    cerebritis    multiple myeloma
    myeloma


    RAB40AL for disorders           About GeneDecksing


    Export disorders for RAB40AL 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 RAB40AL gene integrated from 10 sources:
    (articles sorted by number of sources associating them with RAB40AL)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The Xq22 inversion breakpoint interrupted a novel Ras-like GTPase gene in a patient with Duchenne muscular dystrophy and profound mental retardation. (PubMed id 12145744)1, 2, 9 Saito-Ohara F.... Inazawa J. (Am. J. Hum. Genet. 2002)
    2. Disruption of RAB40AL function leads to Martin--Probst syndrome, a rare X-linked multisystem neurodevelopmental human disorder. (PubMed id 22581972)1, 2 Bedoyan J.K.... Martin D.M. (J. Med. Genet. 2012)
    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. 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)
    6. 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)
    7. The SOCS box: a tale of destruction and degradation. (PubMed id 12076535)1 Kile B.T....Hilton D.J. (Trends Biochem. Sci. 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: 282808 HGNC: 25410 Ensembl:ENSG00000102128 euGenes: HUgn282808 ECgene: RAB40AL
    H-InvDB: RAB40AL

    (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 RAB40AL Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RAB40AL 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 RAB40AL gene:
    Search GeneIP for patents involving RAB40AL

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



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    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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