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

RARB Gene

protein-coding   GIFtS: 72
GCID: GC03P025194

Retinoic Acid Receptor, Beta

Microbiology & Infectious Diseases Congress
  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)
About This Section

Aliases
Retinoic Acid Receptor, Beta1 2     Hepatitis B Virus Activated Protein2
HAP2 3 5     Retinoic Acid Receptor Beta2
Nuclear Receptor Subfamily 1 Group B Member 22 3     Retinoic Acid Receptor Beta 22
NR1B22 3     Retinoic Acid Receptor Beta 42
RAR-beta2 3     Retinoic Acid Receptor Beta 52
RAR-epsilon2 3     Retinoic Acid Receptor Beta Variant 12
HBV-Activated Protein2 3     Retinoic Acid Receptor Beta Variant 22
RRB22     Retinoic Acid Receptor, Beta Polypeptide2

External Ids:    HGNC: 98651   Entrez Gene: 59152   Ensembl: ENSG000000770927   OMIM: 1802205   UniProtKB: P108263   

Export aliases for RARB gene to outside databases

Previous GC identifers: GC03P025167 GC03P025066 GC03P025191 GC03P025192 GC03P025444


(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 RARB Gene:
This gene encodes retinoic acid receptor beta, a member of the thyroid-steroid hormone receptor superfamily of
nuclear transcriptional regulators. This receptor localizes to the cytoplasm and to subnuclear compartments. It
binds retinoic acid, the biologically active form of vitamin A which mediates cellular signalling in embryonic
morphogenesis, cell growth and differentiation. It is thought that this protein limits growth of many cell types
by regulating gene expression. The gene was first identified in a hepatocellular carcinoma where it flanks a
hepatitis B virus integration site. The gene expresses at least two transcript variants; one additional
transcript has been described, but its full length nature has not been determined. (provided by RefSeq, Jul 2008)

GeneCards Summary for RARB Gene: 
RARB (retinoic acid receptor, beta) is a protein-coding gene. Diseases associated with RARB include chromosome 3p deletion, and hepatitis b, and among its related super-pathways are Nuclear Receptors and Gene Expression. GO annotations related to this gene include sequence-specific DNA binding and retinoic acid receptor activity. An important paralog of this gene is VDR.

UniProtKB/Swiss-Prot: RARB_HUMAN, P10826
Function: Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response
elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various
biological processes. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of
tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence or presence of hormone ligand, acts mainly as an
activator of gene expression due to weak binding to corepressors. In concert with RARG, required for skeletal
growth, matrix homeostasis and growth plate function

summary for RARB Gene:
Retinoic acid receptors (RARs) are nuclear hormone receptors of the NRB1 class, which function as
heterodimers with retinoid X receptors (RXRs). There are three distinct RAR subtypes; RARalpha, RARbeta and
RARgamma. RARalpha is present in most tissue types, whereas RARbeta and RARgamma expression is more
selective. RXR-RAR heterodimers act as ligand-dependent transcriptional regulators by binding to the
specific retinoic acid response element (RARE) found in the promoter regions of target genes. In the absence
of an RAR agonist, RXR-RAR recruits co-repressor proteins such as NCoR and associated factors such as
histone deacetylase to maintain a condensed chromatin structure. RAR agonist binding stimulates co-repressor
release and co-activator complexes, such as histone acetyltransferase, are recruited to activate
transcription. RARs transduce retinoid signals in vivo, which mediates proper embryogenesis, differentiation
and growth arrest. Specifically, RXRalpha-RARgamma heterodimers are necessary for growth arrest and viseral
and primitive endodermal differentiation, whereas RXRalpha-RARalpha is required for cAMP-dependent parietal
endodermal differentiation. In vitro it has been difficult to elucidate the roles of individual subtypes as
functional RAR knockouts generate artificial redundancies that are thought not to exist under normal
conditions.

Gene Wiki entry for RARB (Retinoic acid receptor beta) 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000003.11  NT_022517.18  NC_018914.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RARB gene promoter:
         C/EBPbeta   CBF-B   
         Other transcription factors

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

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


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

Entrez Gene cytogenetic band: 3p24.2   Ensembl cytogenetic band:  3p24.2   HGNC cytogenetic band: 3p24

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

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P025194:  view genomic region     (about GC identifiers)

Start:
25,215,823 bp from pter      End:
25,639,423 bp from pter
Size:
423,601 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RARB_HUMAN, P10826 (See protein sequence)
Recommended Name: Retinoic acid receptor beta  
Size: 455 amino acids; 50489 Da
Subunit: Homodimer (By similarity). Heterodimer; with a RXR molecule. Binds DNA preferentially as a RAR/RXR
heterodimer (By similarity). Interacts weakly with NCOR2
Subcellular location: Isoform Beta-1: Nucleus
Subcellular location: Isoform Beta-2: Nucleus
Subcellular location: Isoform Beta-4: Cytoplasm
Sequence caution: Sequence=CAA27637.1; Type=Erroneous gene model prediction;
4 PDB 3D structures from and Proteopedia for RARB:
1HRA (3D)        1XAP (3D)        4DM6 (3D)        4DM8 (3D)    
Secondary accessions: P12891 Q00989 Q15298 Q9UN48
Alternative splicing: 4 isoforms:  P10826-1   P10826-2   P10826-4   P10826-3   

Explore the universe of human proteins at neXtProt for RARB: NX_P10826

Explore proteomics data for RARB at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P10826

  • RARB Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RARB Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_000956.2  NP_057236.1  

    ENSEMBL proteins: 
     ENSP00000373282   ENSP00000398840   ENSP00000332296   ENSP00000391391   ENSP00000385865  
    Reactome Protein details: P10826
    Human Recombinant Protein Products for RARB: 
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    Novus Biologicals RARB Proteins
    Novus Biologicals RARB Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA18845237
    GO:0005654nucleoplasm TAS--
    GO:0005737cytoplasm IEA--

    RARB for ontologies           About GeneDecksing



    RARB Antibody Products: 
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    NR: Nuclear hormone receptors

    IUPHAR Guide to PHARMACOLOGY protein family classification: Retinoic acid receptor-&beta 
    1B. Retinoic acid receptors

    5/6 InterPro protein domains (see all 6):
     IPR008946 Nucl_hormone_rcpt_ligand-bd
     IPR001723 Str_hrmn_rcpt
     IPR003078 Retinoic_acid_rcpt
     IPR013088 Znf_NHR/GATA
     IPR000536 Nucl_hrmn_rcpt_lig-bd_core

    Graphical View of Domain Structure for InterPro Entry P10826

    ProtoNet protein and cluster: P10826

    2 Blocks protein domains:
    IPB001723 Steroid hormone receptor signature
    IPB003078 Retinoic acid receptor (1B nuclear receptor) signature


    UniProtKB/Swiss-Prot: RARB_HUMAN, P10826
    Domain: Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal
    ligand-binding domain
    Similarity: Belongs to the nuclear hormone receptor family. NR1 subfamily
    Similarity: Contains 1 nuclear receptor DNA-binding domain


    RARB 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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RARB_HUMAN, P10826
    Function: Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response
    elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various
    biological processes. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of
    tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence or presence of hormone ligand, acts mainly as an
    activator of gene expression due to weak binding to corepressors. In concert with RARG, required for skeletal
    growth, matrix homeostasis and growth plate function

         Genatlas biochemistry entry for RARB:
    retinoic acid receptor binding and activated by both all-trans (T-RA) and its 9-cis isomer (9-cis-RA) retinoic
    acids,beta subunit ,steroid/thyroid hormone receptor superfamily

         Gene Ontology (GO): 5/7 molecular function terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding TAS2153268
    GO:0003700sequence-specific DNA binding transcription factor activity ----
    GO:0003707steroid hormone receptor activity IEA--
    GO:0003708retinoic acid receptor activity IEA--
    GO:0005515protein binding IPI7565739
         
    RARB for ontologies           About GeneDecksing


    Phenotypes:
         15/20 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Rarb) (see all 20):
     behavior/neurological  cardiovascular system  craniofacial  digestive/alimentary  embryogenesis 
     endocrine/exocrine gland  growth/size  hearing/vestibular/ear  hematopoietic system  immune system 
     limbs/digits/tail  mortality/aging  muscle  nervous system  normal 

    RARB for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for RARB: Rarbtm1Vgi Rarbtm2.1Ipc Rarbtm1Ipc Rarbtm1Mma

       inGenious Targeting Laboratory - Custom generated mouse model solutions for RARB 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for RARB

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RARB 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for RARB 

    miRNA
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    miRTarBase miRNAs that target RARB:
    hsa-mir-16-2 (MIRT004488)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat RARB
    8/55 QIAGEN miScript miRNA Assays for microRNAs that regulate RARB (see all 55):
    hsa-miR-520f hsa-miR-106a hsa-miR-15a hsa-miR-200a hsa-miR-29a hsa-miR-30d hsa-miR-449a hsa-miR-548m
    SwitchGear 3'UTR luciferase reporter plasmidRARB 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RARB


    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for RARB About   (see all 13)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Nuclear Receptor transcription pathway
    Nuclear Receptor transcription pathway0.68
    Nuclear Receptors0.68
    2Generic Transcription Pathway
    Gene Expression0.47
    Generic Transcription Pathway0.47
    3PEDF Induced Signaling
    all-trans-Retinoic Acid Signaling in Brain0.71
    4Apoptotic Pathways in Synovial Fibroblasts
    Nuclear Receptor Activation by Vitamin-A0.57
    5Glioma
    Non-small cell lung cancer0.51

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 EMD Millipore Pathway for RARB
        Transcription Sin3 and NuRD in transcription regulation

    4 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for RARB
        Nuclear Receptor Activation by Vitamin-A
    Molecular Mechanisms of Cancer
    all-trans-Retinoic Acid Signaling in Brain
    all-trans-Retinoic Acid Mediated Apoptosis

    1 GeneGo (Thomson Reuters) Pathway for RARB
        Transcription Sin3 and NuRD in transcription regulation

    4 BioSystems Pathways for RARB
        Vitamin A and carotenoid metabolism
    Nuclear Receptors
    Nuclear receptors in lipid metabolism and toxicity
    Integrated Pancreatic Cancer Pathway

    3        Reactome Pathways for RARB
        Generic Transcription Pathway
    Nuclear Receptor transcription pathway
    Gene Expression


    3         Kegg Pathways  (Kegg details for RARB):
        Pathways in cancer
    Small cell lung cancer
    Non-small cell lung cancer


    RARB for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for RARB

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

    5/62 Interacting proteins for RARB (P108262, 3 ENSP000003322964) via UniProtKB, MINT, STRING, and/or I2D (see all 62)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SMAD2Q157962, 3MINT-61612 I2D: score=3 
    PRKD2Q9BZL62, 3MINT-61761 I2D: score=2 
    ENSG00000227322P287023, ENSP000004025904I2D: score=2 STRING: ENSP00000402590
    RXRBP287023, ENSP000003638124I2D: score=2 STRING: ENSP00000363812
    ENSG00000206289P287023I2D: score=2 
    About this table

    Gene Ontology (GO): 5/21 biological process terms (GO ID links to tree view) (see all 21):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0001657ureteric bud development IEA--
    GO:0003417growth plate cartilage development IEA--
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0006367transcription initiation from RNA polymerase II promoter TAS--

    RARB for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    RARB for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Compounds for RARB available from Tocris Bioscience    About this table
    CompoundAction CAS #
    Liarozole hydrochlorideBlocks retinoic acid metabolism[145858-50-0]
    BMS 195614Selective RARalpha antagonist[253310-42-8]
    FenretinideSynthetic retinoid. Potent anticancer agent[65646-68-6]
    BMS 493Pan-RAR inverse agonist[215030-90-3]
    CD 1530Potent and selective RARgamma agonist[107430-66-0]

    1 HMDB Compound for RARB    About this table
    CompoundSynonyms CAS #PubMed Ids
    Retinoic acidRetinoate (see all 21)302-79-4--

    7 DrugBank Compounds for RARB    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Alitretinoin9-cis-Retinoic acid (see all 4)5300-03-8targetagonist16253547 19678713 16128742 16531051 16297713 16316409
    AdapaleneAdapaleno [INN-Spanish] (see all 2)106685-40-9targetagonist9990413 11752352 9557255 9204085
    TamibaroteneAm 80 (see all 2)94497-51-5targetagonist17611697 17925887 15563242 15843826
    Tazarotene-- 118292-40-3targetagonist18034539 12942109 15102095 9035701
    Acitretin-- 55079-83-9targetagonist7755585 19144697 11586072
    Etretinate-- 54350-48-0targetagonist9298126 8301142
    TTNPB(E)-4-[2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthylenyl)-1 -propenyl] benzoic acid (see all 8)71441-28-6target--15546741 10592235

    9 IUPHAR Ligands for RARB (Retinoic acid receptor-&beta)    About this table 
    LigandTypeActionAffinityPubmed IDs
    9-cis-retinoic acid
    Agonist9.77791761 10964567
    all-trans-retinoic acid
    AgonistAgonist9.410637371 8264595 10964567 7791761
    AGN193109
    AntagonistInverse agonist8.710777502 10637371 8798442
    BMS641
    AgonistAgonist8.615319780
    BMS493
    AntagonistInverse agonist8.5411805839
    AC261066
    AgonistFull agonist7.9 - 8.116302793
    TTNPB
    AgonistAgonist810637371 8264595 10964567 7791761
    AC55649
    AgonistFull agonist6.5 - 7.316302793
    CD666
    AgonistAgonist5.641323296

    10/71 Novoseek inferred chemical compound relationships for RARB gene (see all 71)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoic acid 95.9 1504 8707417 (10), 8034721 (7), 10866321 (7), 7998926 (7) (see all 99)
    retinoid 94.2 166 10369704 (4), 12767074 (4), 9425148 (3), 8954130 (3) (see all 98)
    ch 55 86.6 4 7556191 (1), 2154975 (1), 10747926 (1), 11769677 (1)
    ttnpb 82.8 3 2175182 (1), 9006080 (1)
    cd 2019 82.7 5 8216300 (2), 19800972 (1), 10374844 (1), 11726401 (1)
    am 580 80.3 12 18271925 (3), 8216300 (2), 12504905 (1), 11726401 (1) (see all 6)
    ttnn 79.2 1 7812950 (1)
    cd 437 78.7 5 8216300 (2), 10953043 (1), 10374844 (1), 9516142 (1)
    am80 76.6 1 2154975 (1)
    sr 11217 74.5 1 7812950 (1)

    Search CenterWatch for drugs/clinical trials and news about RARB

    (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,
    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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RARB gene (2 alternative transcripts): 
    NM_000965.3  NM_016152.3  

    Unigene Clusters for RARB:

    Retinoic acid receptor, beta
    Hs.654490  [show with all ESTs], Hs.733004
    Unigene Representative Sequences: NM_000965, S82362
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000383772 ENST00000437042(uc003cdi.2) ENST00000330688(uc003cdh.3)
    ENST00000489694 ENST00000480001 ENST00000462272 ENST00000479097 ENST00000458646(uc011awl.2)
    ENST00000404969
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    8/55 QIAGEN miScript miRNA Assays for microRNAs that regulate RARB (see all 55):
    hsa-miR-520f hsa-miR-106a hsa-miR-15a hsa-miR-200a hsa-miR-29a hsa-miR-30d hsa-miR-449a hsa-miR-548m
    SwitchGear 3'UTR luciferase reporter plasmidRARB 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 2): RARB (NM_016152)
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    Additional mRNA sequence: S82362.1 

    6 DOTS entries:

    DT.100748508  DT.414721  DT.120925299  DT.120925216  DT.100679239  DT.91797951 

    24/91 AceView cDNA sequences (see all 91):

    CR536558 AA917936 AL547687 CA392074 CD679225 CA447720 BM719146 CD014020 
    AA147673 BX390267 BU740742 BC030234 AF157483 CA390471 BF062606 BM722961 
    CR621137 CD014021 BM727498 N66800 AA419238 CD014022 BX350055 BX107734 

    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

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


    RARB expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/24 selected tissues (see all 24) fully expand
     
     Brain (Nervous System)    fully expand to see all 18 entries
             Thalamus
             Septum   
     
     Cartilage (Muscoskeletal System)    fully expand to see all 5 entries
             Prechondrocytic Mesenchymal Cells Stylopod
             HyStem+TGFbeta3+GDF5-induced MEL2 cells
     
     Bone (Muscoskeletal System)    fully expand to see all 5 entries
             Prechondrocytic Mesenchymal Cells Stylopod
             HyStem+TGFbeta3+GDF5-induced MEL2 cells
     
     Adipose (Muscoskeletal System)    fully expand to see all 3 entries
             HyStem+BMP4-induced E15 cells
     
     Endothelium (Cardiovascular System)    fully expand to see all 2 entries
             Peripheral blood-derived endothelial progenitor cells
             cd31+ cells   

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

    SOURCE GeneReport for Unigene clusters: Hs.654490 Hs.733004
        SABiosciences Expression via Pathway-Focused PCR Arrays including RARB (see all 6): 
              Lung Cancer in human mouse rat
              Breast Cancer in human mouse rat
              Polycomb & Trithorax Target Genes in human mouse rat
              Prostate Cancer in human mouse rat
              Nuclear Receptors & Coregulators in human mouse rat

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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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for RARB gene from 5/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rarb1 , 5 retinoic acid receptor, beta1, 5 91(n)1
    98.44(a)1
      14 (7.08 cM)5
    2187721  NM_011243.11  NP_035373.11 
     164308395 
    chicken
    (Gallus gallus)
    Aves RARB1 retinoic acid receptor, beta 86.45(n)
    96.21(a)
      396266  NM_205326.1  NP_990657.1 
    lizard
    (Anolis carolinensis)
    Reptilia RARB6
    Uncharacterized protein
    94(a)
    1 ↔ 1
    GL343380.1(790801-902499)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3979832 retinoic acid receptor gamma isoform 2.1 77.79(n)    S82173.1 
    zebrafish
    (Danio rerio)
    Actinopterygii rarga1 retinoic acid receptor gamma a 68.29(n)
    75.93(a)
      30606  NM_131339.1  NP_571414.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RARB gene
    VDR2  NR4A32  RARG2  NR4A12  NR1I22  NR1I32  THRB2  RARA2  
    NR4A22  NR1H42  NR1H22  THRA2  NR1H32  
    18/48 SIMAP similar genes for RARB using alignment to 6 protein entries:     RARB_HUMAN (see all proteins) (see all similar genes):
    NR1B2    RARG    BCOR-RARA    RARA    PML-RAR    NR1B3
    NR1B1    HNF4G    NR6A1    PRKAR1A/RARA fusion    RORA    DKFZp761C0417
    NR5A1    HNF4alpha    NR2C2    ESR1    NR3C2    DKFZp779O0162

    RARB 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) 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

    10/4103 SNPs in RARB are shown (see all 4103)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0360604
    A colorectal cancer sample4--see VAR_0360602 V I mis40--------
    rs1503497311,2
    C--25406945(+) AAACAC/GAGATT 1 -- us2k10--------
    rs1815379781,2
    --25406992(+) TCAATA/GGCAAG 2 -- us2k10--------
    rs1438928241,2
    C--25407083(+) ACTTTC/TCATGT 2 -- us2k10--------
    rs1870260581,2
    --25407178(+) AGGCCC/TGGATG 2 -- us2k10--------
    rs1465614541,2
    --25407220(+) GGAGAC/TTGGAG 2 -- us2k10--------
    rs1911141731,2
    --25407451(+) TCTCCA/CTCCGG 2 -- us2k10--------
    rs1390066171,2
    C--25407583(+) TACTGG/TATTTT 2 -- us2k10--------
    rs759539701,2
    C--25407679(+) TATGCG/ATTTAA 2 -- us2k12Minor allele frequency- A:0.09CSA WA 120
    rs1833804511,2
    --25407729(+) CAACCA/GACATG 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for RARB (25215823 - 25465823 bp, first 250kb of RARB)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for RARB:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2743257CNV Deletion23290073
    esv2725053CNV Deletion23290073
    dgv814e201CNV Deletion23290073
    nsv3735CNV Loss18451855
    nsv528608CNV Gain19592680
    nsv834645CNV Gain17160897
    nsv528280CNV Gain19592680

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 180220    OMIM disorders: --

    20/100 diseases for RARB (see all 100):    About MalaCards
    chromosome 3p deletion    hepatitis b    progesterone-receptor negative breast cancer    variant creutzfeldt-jakob disease
    lichen sclerosus    lung adenoma    craniopharyngioma    choroid plexus papilloma
    leukoplakia    familial partial lipodystrophy    esophageal cancer    von hippel-lindau disease
    hepatitis    oral leukoplakia    teratocarcinoma    refractory anemia
    papillary carcinoma    chromophobe renal cell carcinoma    silicosis    esophagitis

    1 disease from the University of Copenhagen DISEASES database for RARB:
    Lung cancer

    RARB for disorders           About GeneDecksing

    10/88 Novoseek inferred disease relationships for RARB gene (see all 88)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    teratocarcinoma 71 5 1323569 (1), 9419418 (1), 8353043 (1), 9457077 (1) (see all 5)
    carcinoma embryonal 70.4 5 9140065 (1), 2162058 (1), 1379266 (1), 7731708 (1) (see all 5)
    premalignant 67 26 11848477 (5), 7723796 (3), 15010078 (2), 15173091 (1) (see all 13)
    leukemia promyelocytic acute 62.1 4 8801177 (1), 15189119 (1), 19317219 (1)
    tumors 56.8 206 8180126 (3), 12469153 (3), 14715861 (3), 17998817 (3) (see all 99)
    cancer lung 56.6 73 9426695 (4), 1717924 (4), 7923214 (3), 16841329 (2) (see all 33)
    carcinoma squamous cell 54.7 40 11173543 (4), 9426070 (3), 12839965 (2), 10416619 (2) (see all 24)
    hnscc 54.7 28 15959780 (5), 8012985 (3), 19885608 (2), 11687961 (2) (see all 8)
    squamous cell lung cancer 53 1 8381540 (1)
    cancer 52.9 76 10629053 (5), 12516107 (3), 8657191 (3), 9255592 (2) (see all 49)

    Genetic Association Database (GAD): RARB
    Human Genome Epidemiology (HuGE) Navigator: RARB (20 documents)
    Tumor Gene Database (TGDB): RARB

    Export disorders for RARB 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 RARB gene, integrated from 9 sources (see all 736):
    (articles sorted by number of sources associating them with RARB)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Association analysis of retinoic acid receptor beta ( RARbeta) gene with high myopia in Chinese subjects. (PubMed id 20508731)1, 4, 9 Ding Y....Zhou X. (2010)
    2. DNA methylation of genes linked to retinoid signaling in squamous cell carcinoma of the esophagus: DNA methylation of CRBP1 and TIG1 is associated with tumor stage. (PubMed id 16128742)1, 7, 9 Mizuiri H....Yasui W. (2005)
    3. Retinoic acid receptors beta and gamma do not repress, but instead activate target gene transcription in both the absence and presence of hormone ligand. (PubMed id 12554770)1, 2, 9 Hauksdottir H....Privalsky M.L. (2003)
    4. Mouse and human retinoic acid receptor beta 2 promoters: sequence comparison and localization of retinoic acid responsiveness. (PubMed id 1663808)1, 2, 9 Shen S.... Kruijer W. (1991)
    5. Elevated retinoic acid receptor beta(4) protein in human breast tumor cells with nuclear and cytoplasmic localization. (PubMed id 10411930)1, 2, 9 Sommer K.M.... Swisshelm K. (1999)
    6. Fetal isoform of human retinoic acid receptor beta expressed in small cell lung cancer lines. (PubMed id 8275470)1, 2, 9 Houle B.... Bradley W.E. (1994)
    7. Genome-wide association and large-scale follow up iden tifies 16 new loci influencing lung function. (PubMed id 21946350)1, 4 Soler Artigas M....Tobin M.D. (2011)
    8. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
    9. Physiogenomic analysis of statin-treated patients: do main-specific counter effects within the ACACB gene on low-density lipoprotein cholesterol? (PubMed id 20602615)1, 4 RuaA+o G....Wu A.H. (2010)
    10. Rubella vaccine-induced cellular immunity: evidence o f associations with polymorphisms in the Toll-like, vitamin A and D receptors, and innate immune response genes. (PubMed id 19902255)1, 4 Ovsyannikova I.G....Poland G.A. (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    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: 5915 HGNC: 9865 AceView: RARB Ensembl:ENSG00000077092 euGenes: HUgn5915
    ECgene: RARB Kegg: 5915 H-InvDB: RARB

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

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



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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