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Q8R1B8 (RORB_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 110. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nuclear receptor ROR-beta
Alternative name(s):
Nuclear receptor RZR-beta
Nuclear receptor subfamily 1 group F member 2
Retinoid-related orphan receptor-beta
Gene names
Name:Rorb
Synonyms:Nr1f2
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length470 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Nuclear receptor that binds DNA as a monomer to ROR response elements (RORE) containing a single core motif half-site 5'-AGGTCA-3' preceded by a short A-T-rich sequence. Considered to have intrinsic transcriptional activity, have some natural ligands such as all-trans retinoic acid (ATRA) and other retinoids which act as inverse agonists repressing the transcriptional activity. Required for normal postnatal development of rod and cone photoreceptor cells. Modulates rod photoreceptors differentiation at least by inducing the transcription factor NRL-mediated pathway. In cone photoreceptor cells, regulates transcription of OPN1SW. Involved in the regulation of the period length and stability of the circadian rhythm. May control cytoarchitectural patterning of neocortical neurons during development. May act in a dose-dependent manner to regulate barrel formation upon innervation of layer IV neurons by thalamocortical axons. May play a role in the suppression of osteoblastic differentiation through the inhibition of RUNX2 transcriptional activity. Ref.1 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9

Isoform 1 is critical for hindlimb motor control and for the differentiation of amacrine and horizontal cells in the retina. Regulates the expression of PTF1A synergistically with FOXN4. Ref.1 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9

Subunit structure

Monomer. Interacts with CRX.

Subcellular location

Nucleus Ref.1.

Tissue specificity

Expressed in inner and outer neuroblastic layer as well as in the ganglion cell layer of the developing retina. Expressed in bone marrow osteoprogenitor cells. Ref.1 Ref.4 Ref.7 Ref.8 Ref.9

Developmental stage

Expressed in the lateral cortical plate at E18.5 and only very weakly expressed by cortical neurons at E15.5. Expression progressively increases in layer IV neurons of the prospective somatosensory, visual and auditory cortices. At much lower levels, also expressed by scattered neurons in layer V in these areas. By P4, expression is striking in the whisker barrel cortex of the somatosensory cortex. During retinal development, isoform 1 is broadly expressed in between E13.5 and P5 then declines and is maintained at lower levels into adulthood. At E15.5, is expressed in the immature cochlea, brainstem, spinal cord and cerebral cortex. Isoform 2 is first detected at low levels at late embryonic stages (E18.5), the expression highly increases during the first postnatal week and is maintained during the adulthood. Ref.1 Ref.7 Ref.9

Induction

Induced by aging in bone marrow. Ref.8

Domain

AF-2 (activation function-2) motif is required for recruiting coregulators containing the LXXLL motif, such as NCOA1, and control the transactivational activity By similarity.

Disruption phenotype

Mice are blind, show juvenile ataxia, duck gait, hind paw clasping reflex as well as delayed onset of male fertility. They suffer a degeneration of the retina during postnatal development with severe defects in photoreceptor cell morphology. Mice display reduced anxiety and learned helplessness-related behaviors. They also show a significant increase of the circadian period. Knockouts for isoform 1 display duck gait and lack amacrine and horizontal cells with an excess of ganglion cells in the retina. Ref.1 Ref.4 Ref.5 Ref.6 Ref.9

Sequence similarities

Belongs to the nuclear hormone receptor family. NR1 subfamily.

Contains 1 nuclear receptor DNA-binding domain.

Sequence caution

The sequence AAH24842.2 differs from that shown. Reason: Intron retention.

The sequence AAH58269.1 differs from that shown. Reason: Intron retention.

Ontologies

Keywords
   Biological processBiological rhythms
Sensory transduction
Transcription
Transcription regulation
Vision
   Cellular componentNucleus
   Coding sequence diversityAlternative promoter usage
   DomainZinc-finger
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionActivator
Developmental protein
Receptor
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processamacrine cell differentiation

Inferred from mutant phenotype Ref.9. Source: UniProtKB

cellular response to retinoic acid

Inferred from sequence or structural similarity. Source: UniProtKB

eye photoreceptor cell development

Inferred from mutant phenotype Ref.1. Source: UniProtKB

negative regulation of osteoblast differentiation

Inferred from direct assay Ref.8. Source: UniProtKB

negative regulation of transcription, DNA-templated

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of transcription, DNA-templated

Inferred from direct assay Ref.1Ref.9. Source: UniProtKB

regulation of circadian rhythm

Inferred from mutant phenotype Ref.5. Source: UniProtKB

retina development in camera-type eye

Inferred from mutant phenotype Ref.9. Source: UniProtKB

retinal cone cell development

Inferred from direct assay Ref.1. Source: UniProtKB

retinal rod cell development

Inferred from mutant phenotype Ref.1Ref.6. Source: UniProtKB

rhythmic process

Inferred from electronic annotation. Source: UniProtKB-KW

visual perception

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from direct assay Ref.1. Source: UniProtKB

   Molecular_functionligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity

Inferred from electronic annotation. Source: InterPro

protein binding

Inferred from physical interaction PubMed 10860982. Source: MGI

sequence-specific DNA binding

Inferred from direct assay Ref.1. Source: UniProtKB

sequence-specific DNA binding transcription factor activity

Inferred from direct assay Ref.1Ref.9. Source: UniProtKB

steroid hormone receptor activity

Inferred from electronic annotation. Source: InterPro

transcription factor binding

Inferred from physical interaction Ref.1. Source: UniProtKB

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative promoter usage. [Align] [Select]
Isoform 2 (identifier: Q8R1B8-2)

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.
Isoform 1 (identifier: Q8R1B8-1)

The sequence of this isoform differs from the canonical sequence as follows:
     1-13: MCENQPKTKADGT → MR

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 470470Nuclear receptor ROR-beta
PRO_0000053515

Regions

DNA binding18 – 9376Nuclear receptor Ref.1
Zinc finger21 – 4121NR C4-type
Zinc finger57 – 8125NR C4-type
Region94 – 221128Hinge Potential
Region222 – 470249Ligand-binding Potential
Motif456 – 4616AF-2

Natural variations

Alternative sequence1 – 1313MCENQ…KADGT → MR in isoform 1.
VSP_022576

Experimental info

Sequence conflict1071E → G in BAE93688. Ref.2
Sequence conflict2201M → L in BAE93688. Ref.2
Sequence conflict2471Q → H in BAE93688. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 2 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 6E2F30DB56E94B86

FASTA47053,118
        10         20         30         40         50         60 
MCENQPKTKA DGTAQIEVIP CKICGDKSSG IHYGVITCEG CKGFFRRSQQ NNASYSCPRQ 

        70         80         90        100        110        120 
RNCLIDRTNR NRCQHCRLQK CLALGMSRDA VKFGRMSKKQ RDSLYAEVQK HQQRLQEQRQ 

       130        140        150        160        170        180 
QQSGEAEALA RVYSSSISNG LSNLNTETGG TYANGHVIDL PKSEGYYSID SGQPSPDQSG 

       190        200        210        220        230        240 
LDMTGIKQIK QEPIYDLTSV PNLFTYSSFN NGQLAPGITM SEIDRIAQNI IKSHLETCQY 

       250        260        270        280        290        300 
TMEELHQLAW QTHTYEEIKA YQSKSREALW QQCAIQITHA IQYVVEFAKR ITGFMELCQN 

       310        320        330        340        350        360 
DQILLLKSGC LEVVLVRMCR AFNPLNNTVL FEGKYGGMQM FKALGSDDLV NEAFDFAKNL 

       370        380        390        400        410        420 
CSLQLTEEEI ALFSSAVLIS PDRAWLIEPR KVQKLQEKIY FALQHVIQKN HLDDETLAKL 

       430        440        450        460        470 
IAKIPTITAV CNLHGEKLQV FKQSHPDIVN TLFPPLYKEL FNPDCAAVCK 

« Hide

Isoform 1 [UniParc].

Checksum: 8A22F5C8D104B269
Show »

FASTA45952,000

References

« Hide 'large scale' references
[1]"Activation of the blue opsin gene in cone photoreceptor development by retinoid-related orphan receptor beta."
Srinivas M., Ng L., Liu H., Jia L., Forrest D.
Mol. Endocrinol. 20:1728-1741(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), FUNCTION IN CONE PHOTORECEPTOR DEVELOPMENT, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, DNA-BINDING.
Strain: C57BL/6.
Tissue: Embryonic eye.
[2]"Mouse ROR beta partial cDNA."
Takano A., Katsuyama Y.
Submitted (APR-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Strain: C57BL/6J.
Tissue: Brain.
[3]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Strain: C57BL/6.
Tissue: Retina.
[4]"Disruption of retinoid-related orphan receptor beta changes circadian behavior, causes retinal degeneration and leads to vacillans phenotype in mice."
Andre E., Conquet F., Steinmayr M., Stratton S.C., Porciatti V., Becker-Andre M.
EMBO J. 17:3867-3877(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN CIRCADIAN RHYTHMS AND DEVELOPMENT, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY.
[5]"Behavioral characterization and modulation of circadian rhythms by light and melatonin in C3H/HeN mice homozygous for the RORbeta knockout."
Masana M.I., Sumaya I.C., Becker-Andre M., Dubocovich M.L.
Am. J. Physiol. 292:R2357-R2367(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN CIRCADIAN RHYTHMS, DISRUPTION PHENOTYPE.
[6]"Retinoid-related orphan nuclear receptor RORbeta is an early-acting factor in rod photoreceptor development."
Jia L., Oh E.C., Ng L., Srinivas M., Brooks M., Swaroop A., Forrest D.
Proc. Natl. Acad. Sci. U.S.A. 106:17534-17539(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN ROD DIFFERENTIATION, DISRUPTION PHENOTYPE.
[7]"RORbeta induces barrel-like neuronal clusters in the developing neocortex."
Jabaudon D., Shnider S.J., Tischfield D.J., Galazo M.J., Macklis J.D.
Cereb. Cortex 22:996-1006(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN NEUROGENESIS, DEVELOPMENTAL STAGE, TISSUE SPECIFICITY.
[8]"Examination of nuclear receptor expression in osteoblasts reveals Rorbeta as an important regulator of osteogenesis."
Roforth M.M., Liu G., Khosla S., Monroe D.G.
J. Bone Miner. Res. 27:891-901(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN OSTEOGENESIS, TISSUE SPECIFICITY, INDUCTION BY AGING.
[9]"An isoform of retinoid-related orphan receptor beta directs differentiation of retinal amacrine and horizontal interneurons."
Liu H., Kim S.Y., Fu Y., Wu X., Ng L., Swaroop A., Forrest D.
Nat. Commun. 4:1813-1813(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN RETINA DEVELOPMENT (ISOFORM 1), DISRUPTION PHENOTYPE (ISOFORM 1), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE (ISOFORMS 1 AND 2).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
BC024842 mRNA. Translation: AAH24842.2. Sequence problems.
BC058269 mRNA. Translation: AAH58269.1. Sequence problems.
DQ779923 mRNA. Translation: ABG77269.1.
DQ779924 mRNA. Translation: ABG77270.1.
AB258405 mRNA. Translation: BAE93688.1.
CCDSCCDS37932.1. [Q8R1B8-1]
CCDS37933.1. [Q8R1B8-2]
RefSeqNP_001036819.1. NM_001043354.2. [Q8R1B8-1]
NP_001276850.1. NM_001289921.1.
NP_666207.3. NM_146095.4. [Q8R1B8-2]
UniGeneMm.234641.

3D structure databases

ProteinModelPortalQ8R1B8.
SMRQ8R1B8. Positions 10-463.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid230457. 6 interactions.

PTM databases

PhosphoSiteQ8R1B8.

Proteomic databases

PRIDEQ8R1B8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000040153; ENSMUSP00000047597; ENSMUSG00000036192. [Q8R1B8-2]
ENSMUST00000112828; ENSMUSP00000108447; ENSMUSG00000036192.
ENSMUST00000112832; ENSMUSP00000108451; ENSMUSG00000036192. [Q8R1B8-1]
GeneID225998.
KEGGmmu:225998.
UCSCuc008gyc.2. mouse. [Q8R1B8-2]
uc008gye.2. mouse. [Q8R1B8-1]

Organism-specific databases

CTD6096.
MGIMGI:1343464. Rorb.

Phylogenomic databases

eggNOGNOG324222.
GeneTreeENSGT00740000114909.
HOGENOMHOG000010200.
HOVERGENHBG106848.
KOK08533.
OMAWEQLHDY.
OrthoDBEOG79PJNW.
PhylomeDBQ8R1B8.
TreeFamTF319910.

Gene expression databases

BgeeQ8R1B8.
CleanExMM_RORB.
GenevestigatorQ8R1B8.

Family and domain databases

Gene3D1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProIPR008946. Nucl_hormone_rcpt_ligand-bd.
IPR000536. Nucl_hrmn_rcpt_lig-bd_core.
IPR003079. ROR_rcpt.
IPR001723. Str_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSPR01293. RORNUCRECPTR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMSSF48508. SSF48508. 1 hit.
PROSITEPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio377911.
PROQ8R1B8.
SOURCESearch...

Entry information

Entry nameRORB_MOUSE
AccessionPrimary (citable) accession number: Q8R1B8
Secondary accession number(s): Q0PQZ2, Q0PQZ3, Q1MVR9
Entry history
Integrated into UniProtKB/Swiss-Prot: June 21, 2004
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 110 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot