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Protein

Retinoic acid receptor beta

Gene

Rarb

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionDNA-binding, Receptor
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-383280 Nuclear Receptor transcription pathway
R-MMU-5362517 Signaling by Retinoic Acid

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 14

Organism-specific databases

MGIiMGI:97857 Rarb

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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 Expressed in 277 organ(s), highest expression level in caudate-putamen
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

GO - Molecular functioni

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

3D structure databases

ProteinModelPortaliP22605
SMRiP22605
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22605

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini210 – 444NR LBDPROSITE-ProRule annotationAdd BLAST235

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 114ModulatingAdd BLAST114
Regioni181 – 209HingeAdd BLAST29

Domaini

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

Sequence similaritiesi

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
GeneTreeiENSGT00870000136372
HOGENOMiHOG000010312
HOVERGENiHBG005606
InParanoidiP22605
KOiK08528
OMAiSVPGFKM
PhylomeDBiP22605
TreeFamiTF328382

Family and domain databases

Gene3Di3.30.50.10, 1 hit
InterProiView protein in InterPro
IPR035500 NHR_like_dom_sf
IPR000536 Nucl_hrmn_rcpt_lig-bd
IPR001723 Nuclear_hrmn_rcpt
IPR003078 Retinoic_acid_rcpt
IPR001628 Znf_hrmn_rcpt
IPR013088 Znf_NHR/GATA
PfamiView protein in Pfam
PF00104 Hormone_recep, 1 hit
PF00105 zf-C4, 1 hit
PRINTSiPR01292 RETNOICACIDR
PR00398 STRDHORMONER
PR00047 STROIDFINGER
SMARTiView protein in SMART
SM00430 HOLI, 1 hit
SM00399 ZnF_C4, 1 hit
SUPFAMiSSF48508 SSF48508, 1 hit
PROSITEiView protein in PROSITE
PS51843 NR_LBD, 1 hit
PS00031 NUCLEAR_REC_DBD_1, 1 hit
PS51030 NUCLEAR_REC_DBD_2, 1 hit

Sequences (4+)i

Sequence statusi: Complete.

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

This entry has 4 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A286YCH1A0A286YCH1_MOUSE
Retinoic acid receptor beta
Rarb
402Annotation score:
A0A286YCX1A0A286YCX1_MOUSE
Retinoic acid receptor beta
Rarb
164Annotation score:
A0A286YDP5A0A286YDP5_MOUSE
Retinoic acid receptor beta
Rarb
139Annotation score:
A0A286YE15A0A286YE15_MOUSE
Retinoic acid receptor beta
Rarb
74Annotation score:
A0A286YCR2A0A286YCR2_MOUSE
Retinoic acid receptor beta
Rarb
61Annotation score:

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

Similar proteinsi

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
GeneTreeiENSGT00870000136372
HOGENOMiHOG000010312
HOVERGENiHBG005606
InParanoidiP22605
KOiK08528
OMAiSVPGFKM
PhylomeDBiP22605
TreeFamiTF328382

Enzyme and pathway databases

ReactomeiR-MMU-383280 Nuclear Receptor transcription pathway
R-MMU-5362517 Signaling by Retinoic Acid

Miscellaneous databases

EvolutionaryTraceiP22605
PROiPR:P22605
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000017491 Expressed in 277 organ(s), highest expression level in caudate-putamen
CleanExiMM_RARB
ExpressionAtlasiP22605 baseline and differential
GenevisibleiP22605 MM

Family and domain databases

Gene3Di3.30.50.10, 1 hit
InterProiView protein in InterPro
IPR035500 NHR_like_dom_sf
IPR000536 Nucl_hrmn_rcpt_lig-bd
IPR001723 Nuclear_hrmn_rcpt
IPR003078 Retinoic_acid_rcpt
IPR001628 Znf_hrmn_rcpt
IPR013088 Znf_NHR/GATA
PfamiView protein in Pfam
PF00104 Hormone_recep, 1 hit
PF00105 zf-C4, 1 hit
PRINTSiPR01292 RETNOICACIDR
PR00398 STRDHORMONER
PR00047 STROIDFINGER
SMARTiView protein in SMART
SM00430 HOLI, 1 hit
SM00399 ZnF_C4, 1 hit
SUPFAMiSSF48508 SSF48508, 1 hit
PROSITEiView protein in PROSITE
PS51843 NR_LBD, 1 hit
PS00031 NUCLEAR_REC_DBD_1, 1 hit
PS51030 NUCLEAR_REC_DBD_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRARB_MOUSE
AccessioniPrimary (citable) accession number: P22605
Secondary accession number(s): P11417, P22604
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: September 12, 2018
This is version 180 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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