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Protein

Retinoic acid receptor beta

Gene

RARB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi88 – 153Nuclear receptorPROSITE-ProRule annotationAdd BLAST66
Zinc fingeri88 – 108NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri124 – 148NR C4-typePROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

  • DNA binding Source: ProtInc
  • drug binding Source: Ensembl
  • retinoic acid receptor activity Source: ProtInc
  • RNA polymerase II regulatory region sequence-specific DNA binding Source: Ensembl
  • steroid hormone receptor activity Source: InterPro
  • zinc ion binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000077092-MONOMER.
ReactomeiR-HSA-383280. Nuclear Receptor transcription pathway.
R-HSA-5362517. Signaling by Retinoic Acid.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
SignaLinkiP10826.
SIGNORiP10826.

Names & Taxonomyi

Protein namesi
Recommended name:
Retinoic acid receptor beta
Short name:
RAR-beta
Alternative name(s):
HBV-activated protein
Nuclear receptor subfamily 1 group B member 2
RAR-epsilon
Gene namesi
Name:RARB
Synonyms:HAP, NR1B2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:9865. RARB.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Microphthalmia, syndromic, 12 (MCOPS12)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:615524
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_070780394R → C in MCOPS12; increases transcriptional response to retinoic acid. 1 Publication1
Natural variantiVAR_070781394R → S in MCOPS12; increases transcriptional response to retinoic acid. 1 Publication1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi188T → I: No effect on transcriptional activation in the absence of hormone. 1 Publication1
Mutagenesisi191I → V: No effect on transcriptional activation in the absence of hormone. 1 Publication1
Mutagenesisi222L → I: Reduced transcriptional activation in the absence of hormone. Even greater reduction in transcriptional activation in the absence of hormone; when associated with D-223 or S-232. Great reduction in transcriptional activation in the absence of hormone; when associated with D-223 and S-232. 1 Publication1
Mutagenesisi223G → D: Greatly reduced transcriptional activation in the absence of hormone. Even greater reduction in transcriptional activation in the absence of hormone; when associated with I-222 or S-232. Great reduction in transcriptional activation in the absence of hormone; when associated with I-222 and S-232. 1 Publication1
Mutagenesisi232A → S: Reduced transcriptional activation in the absence of hormone. Some further reduction of transcriptional activity in the absence of hormone; when associated with I-222 or D-223. Great reduction in transcriptional activation in the absence of hormone; when associated with I-222 and D-223. 1 Publication1

Keywords - Diseasei

Disease mutation, Microphthalmia, Proto-oncogene

Organism-specific databases

DisGeNETi5915.
MalaCardsiRARB.
MIMi615524. phenotype.
OpenTargetsiENSG00000077092.
Orphaneti2470. Matthew-Wood syndrome.
PharmGKBiPA34226.

Chemistry databases

ChEMBLiCHEMBL2008.
DrugBankiDB00459. Acitretin.
DB00210. Adapalene.
DB00523. Alitretinoin.
DB04942. Tamibarotene.
DB00799. Tazarotene.
GuidetoPHARMACOLOGYi591.

Polymorphism and mutation databases

BioMutaiRARB.
DMDMi17380507.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000534671 – 455Retinoic acid receptor betaAdd BLAST455

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei77PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP10826.
PeptideAtlasiP10826.
PRIDEiP10826.

PTM databases

iPTMnetiP10826.
PhosphoSitePlusiP10826.

Expressioni

Gene expression databases

BgeeiENSG00000077092.
CleanExiHS_RARB.
ExpressionAtlasiP10826. baseline and differential.
GenevisibleiP10826. HS.

Organism-specific databases

HPAiCAB002617.
HPA004174.

Interactioni

Subunit structurei

Homodimer (By similarity). Heterodimer; with a RXR molecule. Binds DNA preferentially as a RAR/RXR heterodimer (By similarity). Interacts weakly with NCOR2.By similarity1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
P032552EBI-8583223,EBI-2603114From a different organism.
MEOX2A4D1273EBI-8583223,EBI-10172134
RXRBP287024EBI-8583223,EBI-748576
RXRBQ5STP94EBI-8583223,EBI-10197393
RXRGP484433EBI-8583223,EBI-712405

Protein-protein interaction databases

BioGridi111850. 22 interactors.
IntActiP10826. 16 interactors.
MINTiMINT-1180428.
STRINGi9606.ENSP00000332296.

Chemistry databases

BindingDBiP10826.

Structurei

Secondary structure

1455
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi87 – 91Combined sources5
Beta strandi100 – 102Combined sources3
Helixi107 – 118Combined sources12
Beta strandi133 – 135Combined sources3
Helixi141 – 148Combined sources8
Helixi149 – 151Combined sources3
Helixi182 – 198Combined sources17
Beta strandi202 – 205Combined sources4
Helixi222 – 244Combined sources23
Helixi249 – 251Combined sources3
Helixi254 – 274Combined sources21
Beta strandi276 – 278Combined sources3
Turni279 – 282Combined sources4
Beta strandi283 – 285Combined sources3
Beta strandi289 – 293Combined sources5
Helixi294 – 300Combined sources7
Helixi303 – 305Combined sources3
Helixi306 – 316Combined sources11
Helixi317 – 319Combined sources3
Helixi323 – 334Combined sources12
Helixi345 – 366Combined sources22
Beta strandi368 – 370Combined sources3
Helixi373 – 401Combined sources29
Beta strandi402 – 404Combined sources3
Helixi408 – 414Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HRANMR-A82-160[»]
1XAPX-ray2.10A176-421[»]
4DM6X-ray1.90A/B176-421[»]
4DM8X-ray2.30A/B176-421[»]
4JYGX-ray2.35A/B176-421[»]
4JYHX-ray2.60A/B176-421[»]
4JYIX-ray1.90A/B176-421[»]
ProteinModelPortaliP10826.
SMRiP10826.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP10826.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 87ModulatingAdd BLAST87
Regioni154 – 199HingeAdd BLAST46
Regioni200 – 419Ligand-bindingAdd BLAST220

Domaini

Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.

Sequence similaritiesi

Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri88 – 108NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri124 – 148NR C4-typePROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00850000132242.
HOGENOMiHOG000010312.
HOVERGENiHBG005606.
InParanoidiP10826.
KOiK08528.
OMAiCINIPHC.
OrthoDBiEOG091G0XCQ.
PhylomeDBiP10826.
TreeFamiTF328382.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR003078. Retinoic_acid_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR01292. RETNOICACIDR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform Beta-1 (identifier: P10826-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MTTSGHACPV PAVNGHMTHY PATPYPLLFP PVIGGLSLPP LHGLHGHPPP
60 70 80 90 100
SGCSTPSPAT IETQSTSSEE LVPSPPSPLP PPRVYKPCFV CQDKSSGYHY
110 120 130 140 150
GVSACEGCKG FFRRSIQKNM IYTCHRDKNC VINKVTRNRC QYCRLQKCFE
160 170 180 190 200
VGMSKESVRN DRNKKKKETS KQECTESYEM TAELDDLTEK IRKAHQETFP
210 220 230 240 250
SLCQLGKYTT NSSADHRVRL DLGLWDKFSE LATKCIIKIV EFAKRLPGFT
260 270 280 290 300
GLTIADQITL LKAACLDILI LRICTRYTPE QDTMTFSDGL TLNRTQMHNA
310 320 330 340 350
GFGPLTDLVF TFANQLLPLE MDDTETGLLS AICLICGDRQ DLEEPTKVDK
360 370 380 390 400
LQEPLLEALK IYIRKRRPSK PHMFPKILMK ITDLRSISAK GAERVITLKM
410 420 430 440 450
EIPGSMPPLI QEMLENSEGH EPLTPSSSGN TAEHSPSISP SSVENSGVSQ

SPLVQ
Length:455
Mass (Da):50,489
Last modified:November 16, 2001 - v2
Checksum:i8813263AD0495D5A
GO
Isoform Beta-2 (identifier: P10826-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-60: MTTSGHACPV...SGCSTPSPAT → MFDCMDVLSV...EWQHRHTAQS

Show »
Length:448
Mass (Da):50,344
Checksum:i844A298AD32F46A8
GO
Isoform Beta-3 (identifier: P10826-4)
Sequence is not available
Length:
Mass (Da):
Isoform Beta-4 (identifier: P10826-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-119: Missing.

Show »
Length:336
Mass (Da):37,932
Checksum:iD248E5CAB87DA44E
GO

Sequence cautioni

The sequence CAA27637 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti206G → A in CAA68398 (PubMed:2825037).Curated1
Sequence conflicti317L → Q in CAA30262 (PubMed:2836738).Curated1
Sequence conflicti414L → M in CAA68398 (PubMed:2825037).Curated1
Sequence conflicti454V → L in CAA30262 (PubMed:2836738).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03606090V → I in a colorectal cancer sample; somatic mutation. 1 Publication1
Natural variantiVAR_070780394R → C in MCOPS12; increases transcriptional response to retinoic acid. 1 Publication1
Natural variantiVAR_070781394R → S in MCOPS12; increases transcriptional response to retinoic acid. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0036351 – 119Missing in isoform Beta-4. 1 PublicationAdd BLAST119
Alternative sequenceiVSP_0036341 – 60MTTSG…PSPAT → MFDCMDVLSVSPGQILDFYT ASPSSCMLQEKALKACFSGL TQTEWQHRHTAQS in isoform Beta-2. 3 PublicationsAdd BLAST60

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07282 mRNA. Translation: CAA30262.1.
Y00291 mRNA. Translation: CAA68398.1.
AF157483 mRNA. Translation: AAD45688.1.
BC060794 mRNA. Translation: AAH60794.1.
X56849 Genomic DNA. No translation available.
X77664 Genomic DNA. Translation: CAA54740.1.
X04014 Genomic DNA. Translation: CAA27637.1. Sequence problems.
M57445 Genomic DNA. Translation: AAA58728.1.
CCDSiCCDS2642.1. [P10826-2]
CCDS46775.1. [P10826-3]
PIRiS02827.
S49021.
RefSeqiNP_000956.2. NM_000965.4. [P10826-2]
NP_001277145.1. NM_001290216.2. [P10826-1]
NP_001277146.1. NM_001290217.1. [P10826-3]
NP_001277195.1. NM_001290266.1.
NP_001277205.1. NM_001290276.1. [P10826-3]
NP_057236.1. NM_016152.3. [P10826-3]
UniGeneiHs.543218.
Hs.581530.
Hs.654490.
Hs.733004.

Genome annotation databases

EnsembliENST00000330688; ENSP00000332296; ENSG00000077092. [P10826-2]
ENST00000437042; ENSP00000398840; ENSG00000077092. [P10826-3]
ENST00000458646; ENSP00000391391; ENSG00000077092. [P10826-3]
GeneIDi5915.
KEGGihsa:5915.
UCSCiuc003cdh.4. human. [P10826-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07282 mRNA. Translation: CAA30262.1.
Y00291 mRNA. Translation: CAA68398.1.
AF157483 mRNA. Translation: AAD45688.1.
BC060794 mRNA. Translation: AAH60794.1.
X56849 Genomic DNA. No translation available.
X77664 Genomic DNA. Translation: CAA54740.1.
X04014 Genomic DNA. Translation: CAA27637.1. Sequence problems.
M57445 Genomic DNA. Translation: AAA58728.1.
CCDSiCCDS2642.1. [P10826-2]
CCDS46775.1. [P10826-3]
PIRiS02827.
S49021.
RefSeqiNP_000956.2. NM_000965.4. [P10826-2]
NP_001277145.1. NM_001290216.2. [P10826-1]
NP_001277146.1. NM_001290217.1. [P10826-3]
NP_001277195.1. NM_001290266.1.
NP_001277205.1. NM_001290276.1. [P10826-3]
NP_057236.1. NM_016152.3. [P10826-3]
UniGeneiHs.543218.
Hs.581530.
Hs.654490.
Hs.733004.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HRANMR-A82-160[»]
1XAPX-ray2.10A176-421[»]
4DM6X-ray1.90A/B176-421[»]
4DM8X-ray2.30A/B176-421[»]
4JYGX-ray2.35A/B176-421[»]
4JYHX-ray2.60A/B176-421[»]
4JYIX-ray1.90A/B176-421[»]
ProteinModelPortaliP10826.
SMRiP10826.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111850. 22 interactors.
IntActiP10826. 16 interactors.
MINTiMINT-1180428.
STRINGi9606.ENSP00000332296.

Chemistry databases

BindingDBiP10826.
ChEMBLiCHEMBL2008.
DrugBankiDB00459. Acitretin.
DB00210. Adapalene.
DB00523. Alitretinoin.
DB04942. Tamibarotene.
DB00799. Tazarotene.
GuidetoPHARMACOLOGYi591.

PTM databases

iPTMnetiP10826.
PhosphoSitePlusiP10826.

Polymorphism and mutation databases

BioMutaiRARB.
DMDMi17380507.

Proteomic databases

PaxDbiP10826.
PeptideAtlasiP10826.
PRIDEiP10826.

Protocols and materials databases

DNASUi5915.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000330688; ENSP00000332296; ENSG00000077092. [P10826-2]
ENST00000437042; ENSP00000398840; ENSG00000077092. [P10826-3]
ENST00000458646; ENSP00000391391; ENSG00000077092. [P10826-3]
GeneIDi5915.
KEGGihsa:5915.
UCSCiuc003cdh.4. human. [P10826-1]

Organism-specific databases

CTDi5915.
DisGeNETi5915.
GeneCardsiRARB.
HGNCiHGNC:9865. RARB.
HPAiCAB002617.
HPA004174.
MalaCardsiRARB.
MIMi180220. gene.
615524. phenotype.
neXtProtiNX_P10826.
OpenTargetsiENSG00000077092.
Orphaneti2470. Matthew-Wood syndrome.
PharmGKBiPA34226.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00850000132242.
HOGENOMiHOG000010312.
HOVERGENiHBG005606.
InParanoidiP10826.
KOiK08528.
OMAiCINIPHC.
OrthoDBiEOG091G0XCQ.
PhylomeDBiP10826.
TreeFamiTF328382.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000077092-MONOMER.
ReactomeiR-HSA-383280. Nuclear Receptor transcription pathway.
R-HSA-5362517. Signaling by Retinoic Acid.
R-HSA-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
SignaLinkiP10826.
SIGNORiP10826.

Miscellaneous databases

EvolutionaryTraceiP10826.
GeneWikiiRetinoic_acid_receptor_beta.
GenomeRNAii5915.
PROiP10826.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000077092.
CleanExiHS_RARB.
ExpressionAtlasiP10826. baseline and differential.
GenevisibleiP10826. HS.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR003078. Retinoic_acid_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR01292. RETNOICACIDR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRARB_HUMAN
AccessioniPrimary (citable) accession number: P10826
Secondary accession number(s): P12891
, Q00989, Q15298, Q9UN48
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: November 16, 2001
Last modified: November 30, 2016
This is version 206 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.