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RAB5B Gene

protein-coding   GIFtS: 62

GC12P054654
RAB5B, member RAS oncogene family
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Descriptions
RAB5B, member RAS oncogene family 2
External Ids
HGNC: 97841
Entrez Gene: 58692
UniProtKB: P610203
Ensembl: ENSG000001115407
Search outside databases for aliases for RAB5B gene

Previous GC identifers: GC12M056195 GC12P056944 GC12P056084

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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UniProtKB/Swiss-Prot: RAB5B_HUMAN, P61020
Function: Protein transport. Probably involved in vesicular traffic (By similarity)

Gene Wiki entry for RAB5B

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the RAB5B gene  

Entrez Gene cytogenetic band: 12q13   Ensembl cytogenetic band:  12q13.2   HGNC cytogenetic band: 12q13

RAB5B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P054654:     (about GC identifiers)

Start:
54,654,125 bp from pter
End:
54,674,757 bp from pter
Size:
20,633 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000012.10  NT_029419.11  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: RAB5B_HUMAN, P61020 (See protein sequence)
Recommended Name: Ras-related protein Rab-5B  
Size: 215 amino acids; 23707 Da
Subunit: Binds EEA1. Interacts with RIN2 and RIN3, which probably regulate its pathway, possibly by
acting as GEFs
Subcellular location: Cell membrane; Lipid-anchor; Cytoplasmic side. Early endosome membrane;
Lipid-anchor. Melanosome. Note=Enriched in stage I melanosomes
PDB structures from and Proteopedia :
2HEI (3D)    
Secondary accessions: P35239 P35277 Q6PIK9 Q86TH0 Q8IXL2

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_002859.1  

    ENSEMBL proteins: 
    ENSP00000353444 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (Rab5b)
    Human Recombinant Proteins from Abnova (RAB5B)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    5/7 Gene Ontology (GO) cellular component terms (links to tree view) (see all 7 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622 intracellular IDA11256614
    GO:0005624 membrane fraction TAS1541686
    GO:0005768 endosome IDA10491193
    GO:0005886 plasma membrane TAS1541686
    GO:0030139 endocytic vesicle IEA--
    About this table

    Antibodies for RAB5B: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse Antibodies at Sigma-Aldrich
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (Rab5b), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for RAB5B

    Assays for RAB5B: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    5 InterPro domains/families:
     IPR001806 Ras_GTPase
     IPR005225 Small_GTP_bd
     IPR003579 GTPase_Rab
     IPR013753 Ras
     IPR015599 Rab5-like


       GeneDecks  RAB5B for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry P61020

    ProtoNet protein and cluster: P61020

    3 Blocks protein families:
    IPB002041 GTP-binding nuclear protein Ran
    IPB003577 Ras small GTPase
    IPB003578 Ras small GTPase


    UniProtKB/Swiss-Prot: RAB5B_HUMAN, P61020
    Similarity: Belongs to the small GTPase superfamily. Rab family

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (RAB5B)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002868

                  Applied Biosystems Silencer® siRNAs for RAB5B

                  Sigma-Aldrich siRNA for RAB5B  
                         Sigma-Aldrich shRNA for RAB5B  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_002868
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_002868
                                     untagged cDNA clone in CMV expression vector: NM_002868 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_002868

    UniProtKB/Swiss-Prot: RAB5B_HUMAN, P61020
    Function: Protein transport. Probably involved in vesicular traffic (By similarity)
    Enzyme regulation: Regulated by guanine nucleotide exchange factors (GEFs) which promote the
    exchange of bound GDP for free GTP

    Genatlas biochemistry entry for RAB5B:
    RAB5B,Ras oncogene superfamily member,involved in endocytosis,expressed in skeletal muscle

    4 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166 nucleotide binding IEA--
    GO:0003924 GTPase activity TAS1541686
    GO:0005525 GTP binding IEA--
    GO:0030742 GTP-dependent protein binding IDA10491193
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


    3 Sigma-Aldrich "Your Favorite Gene" Pathways for  RAB5B  (Your Favorite Gene powered by Ingenuity) 
     Clathrin-mediated Endocytosis
     Caveolar-mediated Endocytosis
     Amyotrophic Lateral Sclerosis Signaling

       GeneDecks  RAB5B for the pathways selected above  
    About GeneDecksing

     Gene Network CentralTM Interacting Genes and Proteins Network for  RAB5B 


    5 Interacting proteins for RAB5B (P610201 ENSP000003534443) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EEA1Q150751, ENSP000003179553EBI-399401, EBI-298113 STRING (score=.994)
    RIN2ENSP000002550063STRING (score=.912)
    RIN3ENSP000002164873STRING (score=.852)
    EPS8ENSP000002811723STRING (score=.746)
    TFRCENSP000003532243STRING (score=.732)
    About this table

    4 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007032 endosome organization IEA--
    GO:0007264 small GTPase mediated signal transduction IEA--
    GO:0015031 protein transport IEA--
    GO:0030100 regulation of endocytosis IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Enzo Life Sciences drugs & compounds for RAB5B
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for RAB5B

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (RAB5B)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_002868

                  Sigma-Aldrich siRNA for RAB5B  
                         Sigma-Aldrich shRNA for RAB5B  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_002868  

    REFSEQ mRNAs for RAB5B gene: 

    NM_002868.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_002868  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_002868
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_002868
                                     untagged cDNA clone in CMV expression vector: NM_002868 

    Additional cDNA sequence: 

    AF267863.1 AF498937.1 AK292597.1 AK296517.1 AK307468.1 BC032740.1 BC040143.1 BC050558.1 
    BC056422.1 BC065298.1 BX537408.1 BX647808.1 CR536482.1 CR541690.1 CR594499.1 CR597002.1 
    CR614791.1 CR621175.1 X54871.1 

    16 DOTS entries:

    DT.95163364  DT.449878  DT.91753780  DT.95310391  DT.100884665  DT.100884674  DT.101988020  DT.102831914 
    DT.100884668  DT.101988019  DT.121176035  DT.91753772  DT.92049768  DT.97782336  DT.100830065  DT.95163374 

    24/451 AceView cDNA sequences (see all 451 ):

    BM727209 BU184297 BE350213 BC065298 D25759 CB139940 NM_002868 AI203761 
    BX537408 BU193195 AL709073 AL708561 T31857 CF242896 BC040143 AI201796 
    AL597347 AA782248 BF725398 CB138948 BX384213 BQ216670 BM548884 BM842983 

    highest scoring ESTs for RAB5B:

    X54871 AA058838 AA059355 AA099203 AA099663 AA214320 AA214440 AA219377 AA310272 AA322846 

    Unigene Cluster for RAB5B:

    RAB5B, member RAS oncogene family
    Hs.567328  [show with all ESTs]
    Unigene Representative Sequence: BX537408


    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for RAB5B (see all 7 )

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b · 9c · 9d
    SP1:                                                                                          
    SP2:                                                        -     -     -                     
    SP3:                          -     -                                                         
    SP4:                                                                                          
    SP5:                                      -                                                   

    About this scheme

    ECgene alternative splicing isoforms for RAB5B

    1 Ensembl transcript including schematic representation:
    ENST00000360299  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    RAB5B expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for RAB5B

    1 / 2 / 3

    4 probe-sets matching RAB5B gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    37362_at2, 3 U95-A 1 1.00 1.00 0.79 1.26 X54871 1.00 1.00 1.00 1

    1221_at2, 3 U95-A 1 1.00 1.00 0.93 0.74 X54871 1.00 1.00 1.00 1

    201276_at2, 3 U133-A 1 1.00 1.00 -- -- AF267863 0.80 1.00 0.91 1

    201276_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: GCCCTGAAAC

    SOURCE GeneReport for Unigene cluster: Hs.567328

    Expression variation in blood from EXPOLDB for RAB5B

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for RAB5B gene from 5/16 species (see all 16 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    RAB5B1   -- RAB5B, member RAS oncogene family 95.35(n)
    100(a)
    474394  XM_531627.2  XP_531627.2 
    chimpanzee
    (Pan troglodytes)
    RAB5B1   -- RAB5B, member RAS oncogene family 99.84(n)
    100(a)
    746457  XM_001153865.1  XP_001153865.1 
    cow
    (Bos taurus)
    RAB5B1   -- RAB5B, member RAS oncogene family 94.57(n)
    99.53(a)
    539150  XM_866612.2  XP_871705.1 
    rat
    (Rattus norvegicus)
    Rab5b1   -- RAB5B, member RAS oncogene family 92.56(n)
    99.07(a)
    288779  XM_213824.4  XP_213824.3 
    mouse
    (Mus musculus)
    Rab5b1, 5 105
    RAB5B, member RAS oncogene family1, 5 92.87(n)1
    100(a)1
    193441  NM_011229.11  NP_035359.11 
     AB2325945  AK0812515  (see all 19)
    About this table        Species with no ortholog for RAB5B

    ENSEMBL Gene Tree for RAB5B
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for RAB5B gene
    RAB5C2  RAB5A2  RAB172  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/35 NCBI SNPs in RAB5B are shown (see all 35 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 67)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 12 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs32131291,2
    F,H54653653(+) GGGGGA/TGGGGC 1 -- ng51 tfbs3 trp34Minor allele frequency- T:0.00NS EU EA 472
    rs22711931,2
    F,H54653609(-) CTTCTA/GTGACA 1 -- ng515Minor allele frequency- G:0.01EA EU WA 1914
    rs7731081,2
    A,C,F,H,O54656178(+) GAAGTA/GTAAAT 1 -- int110Minor allele frequency- G:0.21EU EA WA NA 794
    rs7731071,2
    C,F,H,O54655773(+) AGCCTA/GTTGGA 1 -- int14Minor allele frequency- G:0.11EU EA WA 418
    rs175287361,2
    C,F,H54654785(+) TTAATC/TTAGAA 1 -- int111Minor allele frequency- T:0.02NA EU EA WA 982
    rs111717101,2
    C,F,H54654345(+) CTAATG/AGGGGT 1 -- int18Minor allele frequency- A:0.41EU EA WA 834
    rs128176711,2
    F,H54655491(+) ATCTGG/AGGAAG 1 -- int14Minor allele frequency- A:0.01EU EA WA 414
    --
    rs116134421,2
    H54656099(+) cccggC/GcATCA 1 -- int14Minor allele frequency- G:0.00EU EA WA 408
    --
    rs358308901,2
    --54658826(+) CAGTC-/TTTTTT 1 -- int10--------
    --
    rs344573451,2
    --54654976(+) AGTAA-/TTTTTT 1 -- int10--------
    About this table

    HapMap Linkage Disequilibrium images for RAB5B (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 179514

    Human Genome Epidemiology Navigator: RAB5B (1 document)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/23 PubMed articles for RAB5B gene (see all 23 ):
    (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, and/or H-InvDB)
    About This Section

    Entrez Gene: 5869 HGNC: 9784 AceView: RAB5B Ensembl:ENSG00000111540 euGenes: HUgn5869
    ECgene: RAB5B H-InvDB: RAB5B
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for RAB5B Genetics and Cytogenetics in Oncology and Haematology
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for RAB5B:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
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     Millipore Immunoassay Services
     Millipore Target Screening & Profiling Services


     Predesigned and custom siRNAs for RAB5B Browse antibodies at Sigma-Aldrich
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for RAB5B Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Search Novus for antibodies for RAB5B

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