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Aliases for RARB Gene

Aliases for RARB Gene

  • Retinoic Acid Receptor Beta 2 3 5
  • Nuclear Receptor Subfamily 1 Group B Member 2 3 4
  • HBV-Activated Protein 3 4
  • RAR-Epsilon 3 4
  • RAR-Beta 3 4
  • NR1B2 3 4
  • HAP 3 4
  • Retinoic Acid Receptor, Beta Polypeptide 3
  • Hepatitis B Virus Activated Protein 3
  • Retinoic Acid Receptor, Beta 2
  • RARbeta1 3
  • MCOPS12 3
  • RRB2 3

External Ids for RARB Gene

Previous GeneCards Identifiers for RARB Gene

  • GC03P025167
  • GC03P025066
  • GC03P025191
  • GC03P025192
  • GC03P025444

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 Microphthalmia, Syndromic 12 and Chromosome 3P Deletion. Among its related pathways are Nuclear Receptor transcription pathway and Pathways in cancer. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and protein complex binding. An important paralog of this gene is RARA.

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 NR1B class, which function as heterodimers with retinoid X receptors (RXRs). There are three distinct RAR subtypes: RARalpha, present in most tissue types; and RARbeta and RARgamma, with more selective expression.

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

Regulatory Elements for RARB Gene

Enhancers for RARB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around RARB on UCSC Golden Path with GeneCards custom track

Genomic Location for RARB Gene

Chromosome:
3
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

Genes around RARB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RARB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RARB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

Post-translational modifications for RARB Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RARB Gene

Domains & Families for RARB Gene

Gene Families for RARB Gene

Graphical View of Domain Structure for InterPro Entry

P10826

UniProtKB/Swiss-Prot:

RARB_HUMAN :
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
Domain:
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
  • Contains 1 nuclear receptor DNA-binding domain.
Family:
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
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 transcription factor activity, sequence-specific DNA binding IEA --
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

Human Phenotype Ontology for RARB Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RARB Gene

MGI Knock Outs for RARB:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets 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
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 IDA,TAS --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with RARB: view

Pathways & Interactions for RARB Gene

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

SIGNOR curated interactions for RARB Gene

Activates:
Is activated by:

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

Drugs & Compounds for RARB Gene

(73) Drugs for RARB Gene - From: DrugBank, ApexBio, DGIdb, IUPHAR, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adapalene Approved Pharma binder, Target, agonist RAR尾 and RAR纬 agonist 75
Tazarotene Approved, Investigational Pharma binder, Target, agonist Topical retinoid;antiproliferative;inducer of TIG3 tumor suppressor 39
Acitretin Approved Pharma Target, agonist Metabolite of etretinate 30
Tamibarotene Approved, Investigational Pharma Agonist, binder, Target, agonist RARα agonist 0
Alitretinoin Approved, Investigational Pharma agonist, Target 15

(34) Additional Compounds for RARB Gene - From: IUPHAR, HMDB, Novoseek, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
all-trans-retinoic acid
  • (all-E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoate
  • (all-E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid
  • 3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoate
  • 3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid
  • Acide retinoique (French)
Full agonist, Agonist 302-79-4
Am 580
102121-60-8
retinoic acid
302-79-4
9-cis-retinoic acid
  • 15-Apo-beta-caroten-15-oate
  • 15-Apo-beta-caroten-15-oic acid
  • 9-cis-Retinoate
  • 9-cis-Retinoic acid
  • 9-cis-Tretinoin
Agonist

(5) Tocris Compounds for RARB Gene

Compound Action Cas Number
AM 580 Retinoic acid analog; RARalpha agonist 102121-60-8
BMS 493 Pan-RAR inverse agonist 215030-90-3
CD 2665 Selective RARbeta/gamma antagonist 170355-78-9
ER 50891 Selective RARalpha antagonist 187400-85-7
Retinoic acid Endogenous retinoic acid receptor agonist 302-79-4

(25) ApexBio Compounds for RARB Gene

Compound Action Cas Number
AC 261066 Potent RARβ2 agonist 870773-76-5
AC 55649 RARβ2 agonist,potent and iso-form selective 59662-49-6
Acitretin Metabolite of etretinate 55079-83-9
Acitretin sodium 925701-88-8
Adapalene RAR尾 and RAR纬 agonist 106685-40-9
Adarotene Apoptosis inducer/DNA damage agent 496868-77-0
AGN 194310 pan-RAR antagonist 229961-45-9
AGN 195183 RARαagonist,potent and selective 191469-29-1
AGN 205327 Potent RARs agonist
BMS 453 RAR agonist 166977-43-1
BMS 493 Pan-RAR inverse agonist 215030-90-3
CD 2314 RARβ agonist,potent and selective 170355-37-0
CD 2665 Selective RARβ/γ antagonist 170355-78-9
Ch 55 110368-33-7
EC 23 104561-41-3
ER 50891 187400-85-7
Fenretinide Synthetic retinoid agonist 65646-68-6
LE 135 155877-83-1
MM 11253 345952-44-5
Palovarotene 410528-02-8
Talarozole Cytochrome P450 inhibitor 201410-53-9
Tazarotene Topical retinoid;antiproliferative;inducer of TIG3 tumor suppressor 118292-40-3
Tretinoin (Aberela) 302-79-4
TTNPB (Arotinoid Acid) Potent RAR agonist 71441-28-6
Vitamin A Acetate Unsaturated nutritional hydrocarbons 127-47-9
genes like me logo Genes that share compounds with RARB: view

Drug Products

Transcripts for RARB Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RARB Gene

This gene is overexpressed in Placenta (68.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RARB Gene



Protein tissue co-expression partners for RARB Gene

NURSA nuclear receptor signaling pathways regulating expression of RARB Gene:

RARB

SOURCE GeneReport for Unigene cluster for RARB Gene:

Hs.654490
genes like me logo Genes that share expression patterns with RARB: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for RARB Gene

Orthologs for RARB Gene

This gene was present in the common ancestor of animals.

Orthologs for RARB Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia RARB 34
  • 96.5 (n)
  • 99.55 (a)
RARB 35
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rarb 34
  • 91 (n)
  • 98.44 (a)
Rarb 16
Rarb 35
  • 98 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RARB 34
  • 99.7 (n)
  • 100 (a)
RARB 35
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rarb 34
  • 90.77 (n)
  • 98.21 (a)
cow
(Bos Taurus)
Mammalia RARB 35
  • 90 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RARB 35
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RARB 35
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves RARB 34
  • 86.45 (n)
  • 96.21 (a)
RARB 35
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RARB 35
  • 94 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rarb 34
  • 81.28 (n)
  • 90.83 (a)
Str.2838 34
African clawed frog
(Xenopus laevis)
Amphibia LOC397983 34
zebrafish
(Danio rerio)
Actinopterygii rarga 34
  • 68.44 (n)
  • 75.93 (a)
fruit fly
(Drosophila melanogaster)
Insecta Eip75B 36
  • 32 (a)
worm
(Caenorhabditis elegans)
Secernentea sex-1 36
  • 28 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8261 35
  • 40 (a)
OneToMany
Species where no ortholog for RARB was found in the sources mined by GeneCards:
  • 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
VAR_036060 A colorectal cancer sample
VAR_070780 Microphthalmia, syndromic, 12 (MCOPS12)
VAR_070781 Microphthalmia, syndromic, 12 (MCOPS12)
rs868367 -- 25,582,160(+) GACAA(A/T)GTGGG intron-variant
rs868368 -- 25,582,249(+) AGAAC(C/T)TAAAA intron-variant

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

Variant ID Type Subtype PubMed ID
dgv4704n100 CNV loss 25217958
dgv4705n100 CNV gain 25217958
dgv4706n100 CNV gain 25217958
dgv4707n100 CNV loss 25217958
dgv767e201 CNV deletion 23290073
esv1074268 CNV insertion 17803354
esv2725051 CNV deletion 23290073
esv2725053 CNV deletion 23290073
esv2743257 CNV deletion 23290073
esv3307540 CNV mobile element insertion 20981092
esv3308202 CNV mobile element insertion 20981092
esv3322280 CNV insertion 20981092
esv3347567 CNV insertion 20981092
esv3357765 CNV insertion 20981092
esv3423309 CNV insertion 20981092
esv3450200 CNV insertion 20981092
esv3595598 CNV loss 21293372
esv3595600 CNV loss 21293372
esv3595604 CNV loss 21293372
esv3595607 CNV loss 21293372
esv3595608 CNV loss 21293372
esv3893676 CNV loss 25118596
nsv1013446 CNV loss 25217958
nsv1127946 CNV deletion 24896259
nsv1143047 CNV tandem duplication 24896259
nsv1160922 CNV duplication 26073780
nsv1160923 CNV deletion 26073780
nsv3735 CNV deletion 18451855
nsv508213 CNV deletion 20534489
nsv524030 CNV loss 19592680
nsv528280 CNV gain 19592680
nsv528608 CNV gain 19592680
nsv834645 CNV gain 17160897
nsv966997 CNV duplication 23825009

Variation tolerance for RARB Gene

Residual Variation Intolerance Score: 11.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.64; 13.64% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RARB Gene

Human Gene Mutation Database (HGMD)
RARB
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RARB

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RARB Gene

Disorders for RARB Gene

MalaCards: The human disease database

(17) MalaCards diseases for RARB Gene - From: OMIM, ClinVar, GeneTests, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
microphthalmia, syndromic 12
  • microphthalmia with or without pulmonary hypoplasia, diaphragmatic hernia and/or cardiac defects
chromosome 3p deletion
  • 3p- syndrome
hepatitis b
  • chronic hepatitis b
teratocarcinoma
  • mixed embryonal carcinoma and teratoma
lung adenoma
  • adenoma of lung
- elite association - COSMIC cancer census association via MalaCards
Search RARB in MalaCards View complete list of genes associated with diseases

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.

Relevant External Links for RARB

Genetic Association Database (GAD)
RARB
Human Genome Epidemiology (HuGE) Navigator
RARB
Tumor Gene Database (TGDB):
RARB
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RARB
genes like me logo Genes that share disorders with RARB: view

No data available for Genatlas for RARB Gene

Publications for RARB Gene

  1. 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 22 46 65
  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 22 65
  3. Recessive and dominant mutations in retinoic acid receptor beta in cases with microphthalmia and diaphragmatic hernia. (PMID: 24075189) Srour M. … Michaud J.L. (Am. J. Hum. Genet. 2013) 3 4 65
  4. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. (PMID: 21946350) Soler Artigas M. … Tobin M.D. (Nat. Genet. 2011) 3 46 65
  5. High incidence of MGMT and RARbeta promoter methylation in primary glioblastomas: association with histopathological characteristics, inflammatory mediators and clinical outcome. (PMID: 19809523) Piperi C. … Papavassiliou A.G. (Mol. Med. 2010) 3 22 65

Products for RARB Gene

Sources for RARB Gene

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