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Aliases for RARB Gene

Aliases for RARB Gene

  • Retinoic Acid Receptor, Beta 2 3
  • HAP 3 4 6
  • Nuclear Receptor Subfamily 1 Group B Member 2 3 4
  • HBV-Activated Protein 3 4
  • RAR-Epsilon 3 4
  • RAR-Beta 3 4
  • MCOPS12 3 6
  • NR1B2 3 4
  • Retinoic Acid Receptor, Beta Polypeptide 3
  • Hepatitis B Virus Activated Protein 3
  • Retinoic Acid Receptor Beta 3
  • RRB2 3

External Ids for RARB Gene

Summaries for RARB Gene

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. Alternate promoter usage and differential splicing result in multiple transcript variants. [provided by RefSeq, Mar 2014]

GeneCards Summary for RARB Gene

RARB (Retinoic Acid Receptor, Beta) is a Protein Coding gene. Diseases associated with RARB include hepatitis b and microphthalmia, syndromic 12. Among its related pathways are Pathways in cancer and ERK Signaling. GO annotations related to this gene include sequence-specific DNA binding and retinoic acid receptor activity. An important paralog of this gene is NR1I2.

UniProtKB/Swiss-Prot for RARB Gene

  • 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.

Tocris 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 Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RARB Gene

Genomics for RARB Gene

Genomic Location for RARB Gene

Start:
25,174,332 bp from pter
End:
25,597,932 bp from pter
Size:
423,601 bases
Orientation:
Plus strand

Genomic View for RARB Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for RARB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RARB Gene

Regulatory Elements for RARB Gene

Proteins for RARB Gene

  • Protein details for RARB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P10826-RARB_HUMAN
    Recommended name:
    Retinoic acid receptor beta
    Protein Accession:
    P10826
    Secondary Accessions:
    • P12891
    • Q00989
    • Q15298
    • Q9UN48

    Protein attributes for RARB Gene

    Size:
    455 amino acids
    Molecular mass:
    50489 Da
    Quaternary structure:
    • Homodimer (By similarity). Heterodimer; with a RXR molecule. Binds DNA preferentially as a RAR/RXR heterodimer (By similarity). Interacts weakly with NCOR2.
    SequenceCaution:
    • Sequence=CAA27637.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RARB Gene

    Alternative splice isoforms for RARB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RARB Gene

Proteomics data for RARB Gene at MOPED

Post-translational modifications for RARB Gene

No Post-translational modifications

No data available for DME Specific Peptides for RARB Gene

Domains for RARB Gene

Gene Families for RARB Gene

HGNC:
  • NR :Nuclear hormone receptors
IUPHAR :

UniProtKB/Swiss-Prot:

RARB_HUMAN
Domain:
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain:
    • P10826
  • Contains 1 nuclear receptor DNA-binding domain.:
    • P10826
Family:
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.:
    • P10826
genes like me logo Genes that share domains with RARB: view

Function for RARB Gene

Molecular function for RARB Gene

GENATLAS Biochemistry: 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
UniProtKB/Swiss-Prot 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.

Gene Ontology (GO) - Molecular Function for RARB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0003677 DNA binding TAS 2153268
GO:0003700 sequence-specific DNA binding transcription factor activity --
GO:0003707 steroid hormone receptor activity IEA --
GO:0003708 retinoic acid receptor activity IEA --
genes like me logo Genes that share ontologies with RARB: view
genes like me logo Genes that share phenotypes with RARB: view

Animal Models for RARB Gene

MGI Knock Outs for RARB:

miRNA for RARB Gene

miRTarBase miRNAs that target RARB

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for RARB Gene

Localization for RARB Gene

Subcellular locations from UniProtKB/Swiss-Prot for RARB Gene

Isoform Beta-1: Nucleus.
Isoform Beta-2: Nucleus.
Isoform Beta-4: Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RARB Gene COMPARTMENTS Subcellular localization image for RARB gene
Compartment Confidence
nucleus 5
cytoskeleton 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for RARB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 18845237
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with RARB: view

Pathways for RARB Gene

genes like me logo Genes that share pathways with RARB: view

Gene Ontology (GO) - Biological Process for RARB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0001657 ureteric bud development IEA --
GO:0002068 glandular epithelial cell development IEA --
GO:0003148 outflow tract septum morphogenesis IEA --
GO:0003406 retinal pigment epithelium development IEA --
genes like me logo Genes that share ontologies with RARB: view

Compounds for RARB Gene

(5) Tocris Compounds for RARB Gene

Compound Action Cas Number
BMS 195614 Selective RARalpha antagonist [253310-42-8]
BMS 493 Pan-RAR inverse agonist [215030-90-3]
CD 1530 Potent and selective RARgamma agonist [107430-66-0]
Fenretinide Synthetic retinoid. Potent anticancer agent [65646-68-6]
Liarozole hydrochloride Blocks retinoic acid metabolism [145858-50-0]

(1) HMDB Compounds for RARB Gene

Compound Synonyms Cas Number PubMed IDs
Retinoic acid
  • Retinoate
302-79-4

(7) Drugbank Compounds for RARB Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Acitretin
55079-83-9 target agonist
Adapalene
  • Adapaleno [INN-Spanish]
106685-40-9 target agonist
Alitretinoin
  • 9-cis-Retinoic acid
5300-03-8 target agonist
Etretinate
54350-48-0 target agonist
Tamibarotene
  • Am 80
94497-51-5 target agonist

(9) IUPHAR Ligand for RARB Gene

Ligand Type Action Affinity Pubmed IDs
9-cis-retinoic acid Agonist Agonist 9.7
all-trans-retinoic acid Agonist Agonist 9.4
AGN193109 Antagonist Inverse agonist 8.7
BMS641 Agonist Agonist 8.6
BMS493 Antagonist Inverse agonist 8.54
AC261066 Agonist Full agonist 8.1
TTNPB Agonist Agonist 8
AC55649 Agonist Full agonist 7.3
CD666 Agonist Agonist 5.64

(71) Novoseek inferred chemical compound relationships for RARB Gene

Compound -log(P) Hits PubMed IDs
retinoic acid 95.9 358
retinoid 94.2 125
ch 55 86.6 4
ttnpb 82.8 2
cd 2019 82.7 5
genes like me logo Genes that share compounds with RARB: view

Transcripts for RARB Gene

Alternative Splicing Database (ASD) splice patterns (SP) for RARB Gene

No ASD Table

Relevant External Links for RARB Gene

GeneLoc Exon Structure for
RARB
ECgene alternative splicing isoforms for
RARB

Expression for RARB Gene

mRNA expression in normal human tissues for RARB Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for RARB Gene

SOURCE GeneReport for Unigene cluster for RARB Gene Hs.654490

genes like me logo Genes that share expressions with RARB: view

Orthologs for RARB Gene

This gene was present in the common ancestor of animals.

Orthologs for RARB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RARB 36
  • 99.7 (n)
  • 100 (a)
RARB 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RARB 37
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RARB 36
  • 96.5 (n)
  • 99.55 (a)
RARB 37
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rarb 36
  • 91 (n)
  • 98.44 (a)
Rarb 16
Rarb 37
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RARB 37
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RARB 37
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rarb 36
  • 90.77 (n)
  • 98.21 (a)
chicken
(Gallus gallus)
Aves RARB 36
  • 86.45 (n)
  • 96.21 (a)
RARB 37
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RARB 37
  • 94 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia LOC397983 36
tropical clawed frog
(Silurana tropicalis)
Amphibia rarb 36
  • 81.28 (n)
  • 90.83 (a)
Str.2838 36
zebrafish
(Danio rerio)
Actinopterygii rarga 36
  • 68.44 (n)
  • 75.93 (a)
fruit fly
(Drosophila melanogaster)
Insecta Eip75B 38
  • 32 (a)
worm
(Caenorhabditis elegans)
Secernentea sex-1 38
  • 28 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8261 37
  • 40 (a)
OneToMany
Species with no ortholog for RARB:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RARB Gene

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

Paralogs for RARB Gene

genes like me logo Genes that share paralogs with RARB: view

Variants for RARB Gene

Sequence variations from dbSNP and Humsavar for RARB Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs167731 -- 25,279,998(-) CAGCC(A/G)CAAAT intron-variant
rs167732 -- 25,300,305(-) AGACA(G/T)TGTGC intron-variant
rs167733 -- 25,297,467(-) CCAGT(C/T)TAAAT intron-variant
rs167734 -- 25,246,995(-) aaagg(C/T)agcag intron-variant
rs170396 -- 25,182,974(-) CCATG(C/T)CTCTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RARB Gene

Variant ID Type Subtype PubMed ID
nsv834645 CNV Gain 17160897
nsv528608 CNV Gain 19592680
esv2725053 CNV Deletion 23290073
esv2743257 CNV Deletion 23290073
dgv814e201 CNV Deletion 23290073
nsv3735 CNV Loss 18451855
nsv528280 CNV Gain 19592680

Relevant External Links for RARB Gene

HapMap Linkage Disequilibrium report
RARB
Human Gene Mutation Database (HGMD)
RARB

Disorders for RARB Gene

(1) OMIM Diseases for RARB Gene (180220)

UniProtKB/Swiss-Prot

RARB_HUMAN
  • Microphthalmia, syndromic, 12 (MCOPS12) [MIM:615524]: A form of microphthalmia, a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. MCOPS12 patients manifest variable features, including diaphragmatic hernia, pulmonary hypoplasia, and cardiac abnormalities. {ECO:0000269 PubMed:24075189}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(1) University of Copenhagen DISEASES for RARB Gene

(88) Novoseek inferred disease relationships for RARB Gene

Disease -log(P) Hits PubMed IDs
teratocarcinoma 71 5
carcinoma embryonal 70.4 5
premalignant 67 20
leukemia promyelocytic acute 62.1 3
tumors 56.8 124

Relevant External Links for RARB

Genetic Association Database (GAD)
RARB
Human Genome Epidemiology (HuGE) Navigator
RARB
Tumor Gene Database (TGDB):
RARB
genes like me logo Genes that share disorders with RARB: view

Publications for RARB Gene

  1. Elevated retinoic acid receptor beta(4) protein in human breast tumor cells with nuclear and cytoplasmic localization. (PMID: 10411930) Sommer K.M. … Swisshelm K. (Proc. Natl. Acad. Sci. U.S.A. 1999) 3 4 23
  2. Mouse and human retinoic acid receptor beta 2 promoters: sequence comparison and localization of retinoic acid responsiveness. (PMID: 1663808) Shen S. … Kruijer W. (DNA Seq. 1991) 3 4 23
  3. Fetal isoform of human retinoic acid receptor beta expressed in small cell lung cancer lines. (PMID: 8275470) Houle B. … Bradley W.E. (Cancer Res. 1994) 3 4 23
  4. Association analysis of retinoic acid receptor beta (RARbeta) gene with high myopia in Chinese subjects. (PMID: 20508731) Ding Y. … Zhou X. (Mol. Vis. 2010) 3 23 49
  5. 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. (PMID: 16128742) Mizuiri H. … Yasui W. (Cancer Sci. 2005) 3 23 25

Products for RARB Gene

Sources for RARB Gene

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