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Protein

Retinoic acid receptor beta

Gene

Rarb

Organism
Mus musculus (Mouse)
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 RAR/RXR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence of ligand, acts mainly as an activator of gene expression due to weak binding to corepressors (By similarity). In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function.By similarity1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi115 – 180Nuclear receptorPROSITE-ProRule annotationAdd BLAST66
Zinc fingeri115 – 135NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri151 – 175NR C4-typePROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

GO - Biological processi

  • bone development Source: MGI
  • embryonic digestive tract development Source: MGI
  • embryonic eye morphogenesis Source: MGI
  • embryonic hindlimb morphogenesis Source: MGI
  • glandular epithelial cell development Source: MGI
  • growth plate cartilage development Source: MGI
  • multicellular organism growth Source: MGI
  • negative regulation of apoptotic process Source: MGI
  • negative regulation of cartilage development Source: MGI
  • negative regulation of cell proliferation Source: MGI
  • negative regulation of chondrocyte differentiation Source: MGI
  • negative regulation of transcription from RNA polymerase II promoter Source: MGI
  • neurogenesis Source: MGI
  • outflow tract septum morphogenesis Source: MGI
  • positive regulation of apoptotic process Source: MGI
  • positive regulation of cell proliferation Source: MGI
  • positive regulation of neuron differentiation Source: Ensembl
  • positive regulation of programmed cell death Source: MGI
  • positive regulation of transcription from RNA polymerase II promoter Source: MGI
  • regulation of myelination Source: Ensembl
  • retina development in camera-type eye Source: MGI
  • retinal pigment epithelium development Source: MGI
  • striatum development Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
  • ureteric bud development Source: MGI
  • ventricular cardiac muscle cell differentiation Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-383280. Nuclear Receptor transcription pathway.
R-MMU-5362517. Signaling by Retinoic Acid.
R-MMU-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
SIGNORiP22605.

Names & Taxonomyi

Protein namesi
Recommended name:
Retinoic acid receptor beta
Short name:
RAR-beta
Alternative name(s):
Nuclear receptor subfamily 1 group B member 2
Gene namesi
Name:Rarb
Synonyms:Nr1b2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 14

Organism-specific databases

MGIiMGI:97857. Rarb.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Rarb and Rarg, but not Rarb and Rara, double null mice exhibit growth retardation 3 weeks after birth. Defects are found in the growth plates with deficiency in cartilage. Growth retardation was noticable in limb sketal elements such as femurs. Early lethality and male sterility due to squamous metaplasia of the seminal vesicles and prostate are also observed. Isoform 2 mutants appear normal.1 Publication

Chemistry databases

ChEMBLiCHEMBL3266.
GuidetoPHARMACOLOGYi591.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000534681 – 482Retinoic acid receptor betaAdd BLAST482

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei104PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP22605.
PRIDEiP22605.

PTM databases

iPTMnetiP22605.
PhosphoSitePlusiP22605.

Expressioni

Gene expression databases

BgeeiENSMUSG00000017491.
CleanExiMM_RARB.
ExpressionAtlasiP22605. baseline and differential.
GenevisibleiP22605. MM.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi230063. 3 interactors.
IntActiP22605. 2 interactors.
STRINGi10090.ENSMUSP00000067694.

Chemistry databases

BindingDBiP22605.

Structurei

Secondary structure

1482
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi212 – 225Combined sources14
Beta strandi229 – 232Combined sources4
Helixi249 – 271Combined sources23
Turni274 – 276Combined sources3
Beta strandi277 – 279Combined sources3
Helixi281 – 301Combined sources21
Turni306 – 309Combined sources4
Beta strandi310 – 312Combined sources3
Beta strandi317 – 320Combined sources4
Helixi321 – 326Combined sources6
Turni327 – 329Combined sources3
Helixi330 – 332Combined sources3
Helixi333 – 343Combined sources11
Helixi344 – 346Combined sources3
Helixi350 – 361Combined sources12
Beta strandi366 – 368Combined sources3
Helixi372 – 378Combined sources7
Helixi380 – 393Combined sources14
Helixi400 – 405Combined sources6
Helixi407 – 425Combined sources19
Turni426 – 428Combined sources3
Helixi435 – 441Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1XDKX-ray2.90B/F180-482[»]
ProteinModelPortaliP22605.
SMRiP22605.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22605.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 114ModulatingAdd BLAST114
Regioni181 – 226HingeAdd BLAST46
Regioni227 – 446Ligand-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 fingeri115 – 135NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri151 – 175NR C4-typePROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00850000132242.
HOGENOMiHOG000010312.
HOVERGENiHBG005606.
InParanoidiP22605.
KOiK08528.
OMAiCINIPHC.
PhylomeDBiP22605.
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-3 (identifier: P22605-1) [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
MSTSSHACPV PAVRGHMTHY PAAPYPLLFP PVIRGLSLPP LHGLHGHPPP
60 70 80 90 100
SGCSTPSPAS VGQACQRTTG GSQFAASTKW TPSLNAAIET QSTSSEELVP
110 120 130 140 150
SPPSPLPPPR VYKPCFVCQD KSSGYHYGVS ACEGCKGFFR RSIQKNMIYT
160 170 180 190 200
CHRDKNCVIN KVTRNRCQYC RLQKCFEVGM SKESVRNDRN KKKKEPSKQE
210 220 230 240 250
CTESYEMTAE LDDLTEKIRK AHQETFPSLC QLGKYTTNSS ADHRVRLDLG
260 270 280 290 300
LWDKFSELAT KCIIKIVEFA KRLPGFTGLT IADQITLLKA ACLDILILRI
310 320 330 340 350
CTRYTPEQDT MTFSDGLTLN RTQMHNAGFG PLTDLVFTFA NQLLPLEMDD
360 370 380 390 400
TETGLLSAIC LICGDRQDLE EPTKVDKLQE PLLEALKIYI RKRRPSKPHM
410 420 430 440 450
FPKILMKITD LRSISAKGAE RVITLKMEIP GSMPPLIQEM LENSEGHEPL
460 470 480
TPSSSGNIAE HSPSVSPSSV ENSGVSQSPL LQ
Length:482
Mass (Da):53,331
Last modified:August 1, 1991 - v1
Checksum:i48E78E6C7D012515
GO
Isoform Beta-1 (identifier: P22605-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     60-60: S → T
     61-87: Missing.

Show »
Length:455
Mass (Da):50,624
Checksum:iBADB158A2BFDDF38
GO
Isoform Beta-2 (identifier: P22605-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-87: MSTSSHACPV...TKWTPSLNAA → MFDCMDVLSV...EWQHRHTAQS

Show »
Length:448
Mass (Da):50,322
Checksum:iFA4EA32326EAB900
GO
Isoform Beta-4 (identifier: P22605-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-83: Missing.
     84-86: LNA → MEN

Show »
Length:399
Mass (Da):44,889
Checksum:i574409A46F525B84
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0036361 – 87MSTSS…SLNAA → MFDCMDVLSVSPGQILDFYT ASPSSCMLQEKALKACLSGF TQAEWQHRHTAQS in isoform Beta-2. 4 PublicationsAdd BLAST87
Alternative sequenceiVSP_0036371 – 83Missing in isoform Beta-4. 1 PublicationAdd BLAST83
Alternative sequenceiVSP_00363960S → T in isoform Beta-1. 1 Publication1
Alternative sequenceiVSP_00364061 – 87Missing in isoform Beta-1. 1 PublicationAdd BLAST27
Alternative sequenceiVSP_00363884 – 86LNA → MEN in isoform Beta-4. 1 Publication3

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56574 mRNA. Translation: CAA39921.1.
X56569 mRNA. Translation: CAA39918.1.
X56573 mRNA. Translation: CAA39920.1.
S56660 mRNA. Translation: AAB25784.2.
S92180 mRNA. No translation available.
CCDSiCCDS26834.1. [P22605-3]
PIRiS05051.
RefSeqiNP_001276689.1. NM_001289760.1. [P22605-1]
NP_001276690.1. NM_001289761.1. [P22605-2]
NP_001276691.1. NM_001289762.1. [P22605-4]
NP_035373.1. NM_011243.2. [P22605-3]
UniGeneiMm.259318.

Genome annotation databases

EnsembliENSMUST00000063750; ENSMUSP00000067694; ENSMUSG00000017491. [P22605-3]
GeneIDi218772.
KEGGimmu:218772.
UCSCiuc007shh.2. mouse. [P22605-4]
uc007shi.2. mouse. [P22605-2]
uc007shj.2. mouse. [P22605-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56574 mRNA. Translation: CAA39921.1.
X56569 mRNA. Translation: CAA39918.1.
X56573 mRNA. Translation: CAA39920.1.
S56660 mRNA. Translation: AAB25784.2.
S92180 mRNA. No translation available.
CCDSiCCDS26834.1. [P22605-3]
PIRiS05051.
RefSeqiNP_001276689.1. NM_001289760.1. [P22605-1]
NP_001276690.1. NM_001289761.1. [P22605-2]
NP_001276691.1. NM_001289762.1. [P22605-4]
NP_035373.1. NM_011243.2. [P22605-3]
UniGeneiMm.259318.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1XDKX-ray2.90B/F180-482[»]
ProteinModelPortaliP22605.
SMRiP22605.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi230063. 3 interactors.
IntActiP22605. 2 interactors.
STRINGi10090.ENSMUSP00000067694.

Chemistry databases

BindingDBiP22605.
ChEMBLiCHEMBL3266.
GuidetoPHARMACOLOGYi591.

PTM databases

iPTMnetiP22605.
PhosphoSitePlusiP22605.

Proteomic databases

PaxDbiP22605.
PRIDEiP22605.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000063750; ENSMUSP00000067694; ENSMUSG00000017491. [P22605-3]
GeneIDi218772.
KEGGimmu:218772.
UCSCiuc007shh.2. mouse. [P22605-4]
uc007shi.2. mouse. [P22605-2]
uc007shj.2. mouse. [P22605-1]

Organism-specific databases

CTDi5915.
MGIiMGI:97857. Rarb.

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00850000132242.
HOGENOMiHOG000010312.
HOVERGENiHBG005606.
InParanoidiP22605.
KOiK08528.
OMAiCINIPHC.
PhylomeDBiP22605.
TreeFamiTF328382.

Enzyme and pathway databases

ReactomeiR-MMU-383280. Nuclear Receptor transcription pathway.
R-MMU-5362517. Signaling by Retinoic Acid.
R-MMU-5617472. Activation of anterior HOX genes in hindbrain development during early embryogenesis.
SIGNORiP22605.

Miscellaneous databases

EvolutionaryTraceiP22605.
PROiP22605.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000017491.
CleanExiMM_RARB.
ExpressionAtlasiP22605. baseline and differential.
GenevisibleiP22605. MM.

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_MOUSE
AccessioniPrimary (citable) accession number: P22605
Secondary accession number(s): P11417, P22604
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: November 2, 2016
This is version 166 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.