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Q8R1B8

- RORB_MOUSE

UniProt

Q8R1B8 - RORB_MOUSE

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Protein
Nuclear receptor ROR-beta
Gene
Rorb, Nr1f2
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.7 Publications
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 FOXN4.7 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi18 – 9376Nuclear receptor1 Publication
Add
BLAST
Zinc fingeri21 – 4121NR C4-type
Add
BLAST
Zinc fingeri57 – 8125NR C4-type
Add
BLAST

GO - Molecular functioni

  1. ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity Source: InterPro
  2. protein binding Source: MGI
  3. sequence-specific DNA binding Source: UniProtKB
  4. sequence-specific DNA binding transcription factor activity Source: UniProtKB
  5. steroid hormone receptor activity Source: InterPro
  6. transcription factor binding Source: UniProtKB
  7. zinc ion binding Source: InterPro

GO - Biological processi

  1. amacrine cell differentiation Source: UniProtKB
  2. cellular response to retinoic acid Source: UniProtKB
  3. eye photoreceptor cell development Source: UniProtKB
  4. negative regulation of osteoblast differentiation Source: UniProtKB
  5. negative regulation of transcription, DNA-templated Source: UniProtKB
  6. positive regulation of transcription, DNA-templated Source: UniProtKB
  7. regulation of circadian rhythm Source: UniProtKB
  8. retina development in camera-type eye Source: UniProtKB
  9. retinal cone cell development Source: UniProtKB
  10. retinal rod cell development Source: UniProtKB
  11. rhythmic process Source: UniProtKB-KW
  12. visual perception Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Developmental protein, Receptor

Keywords - Biological processi

Biological rhythms, Sensory transduction, Transcription, Transcription regulation, Vision

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:Rorb
Synonyms:Nr1f2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 19

Organism-specific databases

MGIiMGI:1343464. Rorb.

Subcellular locationi

Nucleus 1 Publication

GO - Cellular componenti

  1. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

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.5 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 470470Nuclear receptor ROR-beta
PRO_0000053515Add
BLAST

Proteomic databases

PRIDEiQ8R1B8.

PTM databases

PhosphoSiteiQ8R1B8.

Expressioni

Tissue specificityi

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.5 Publications

Developmental stagei

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.3 Publications

Inductioni

Induced by aging in bone marrow.1 Publication

Gene expression databases

BgeeiQ8R1B8.
CleanExiMM_RORB.
GenevestigatoriQ8R1B8.

Interactioni

Subunit structurei

Monomer. Interacts with CRX.

Protein-protein interaction databases

BioGridi230457. 6 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ8R1B8.
SMRiQ8R1B8. Positions 10-463.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni94 – 221128Hinge Reviewed prediction
Add
BLAST
Regioni222 – 470249Ligand-binding Reviewed prediction
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi456 – 4616AF-2

Domaini

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.

Sequence similaritiesi

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG324222.
GeneTreeiENSGT00740000114909.
HOGENOMiHOG000010200.
HOVERGENiHBG106848.
KOiK08533.
OMAiWEQLHDY.
OrthoDBiEOG79PJNW.
PhylomeDBiQ8R1B8.
TreeFamiTF319910.

Family and domain databases

Gene3Di1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProiIPR008946. 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]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR01293. RORNUCRECPTR.
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 (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative promoter usage. Align

Isoform 2 (identifier: Q8R1B8-2) [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

MCENQPKTKA DGTAQIEVIP CKICGDKSSG IHYGVITCEG CKGFFRRSQQ    50
NNASYSCPRQ RNCLIDRTNR NRCQHCRLQK CLALGMSRDA VKFGRMSKKQ 100
RDSLYAEVQK HQQRLQEQRQ QQSGEAEALA RVYSSSISNG LSNLNTETGG 150
TYANGHVIDL PKSEGYYSID SGQPSPDQSG LDMTGIKQIK QEPIYDLTSV 200
PNLFTYSSFN NGQLAPGITM SEIDRIAQNI IKSHLETCQY TMEELHQLAW 250
QTHTYEEIKA YQSKSREALW QQCAIQITHA IQYVVEFAKR ITGFMELCQN 300
DQILLLKSGC LEVVLVRMCR AFNPLNNTVL FEGKYGGMQM FKALGSDDLV 350
NEAFDFAKNL CSLQLTEEEI ALFSSAVLIS PDRAWLIEPR KVQKLQEKIY 400
FALQHVIQKN HLDDETLAKL IAKIPTITAV CNLHGEKLQV FKQSHPDIVN 450
TLFPPLYKEL FNPDCAAVCK 470
Length:470
Mass (Da):53,118
Last modified:January 23, 2007 - v3
Checksum:i6E2F30DB56E94B86
GO
Isoform 1 (identifier: Q8R1B8-1) [UniParc]FASTAAdd to Basket

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

Show »
Length:459
Mass (Da):52,000
Checksum:i8A22F5C8D104B269
GO

Sequence cautioni

The sequence AAH24842.2 differs from that shown. Reason: Intron retention.
The sequence AAH58269.1 differs from that shown. Reason: Intron retention.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 1313MCENQ…KADGT → MR in isoform 1.
VSP_022576Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti107 – 1071E → G in BAE93688. 1 Publication
Sequence conflicti220 – 2201M → L in BAE93688. 1 Publication
Sequence conflicti247 – 2471Q → H in BAE93688. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
CCDSiCCDS37932.1. [Q8R1B8-1]
CCDS37933.1. [Q8R1B8-2]
RefSeqiNP_001036819.1. NM_001043354.2. [Q8R1B8-1]
NP_001276850.1. NM_001289921.1.
NP_666207.3. NM_146095.4. [Q8R1B8-2]
UniGeneiMm.234641.

Genome annotation databases

EnsembliENSMUST00000040153; ENSMUSP00000047597; ENSMUSG00000036192. [Q8R1B8-2]
ENSMUST00000112828; ENSMUSP00000108447; ENSMUSG00000036192.
ENSMUST00000112832; ENSMUSP00000108451; ENSMUSG00000036192. [Q8R1B8-1]
GeneIDi225998.
KEGGimmu:225998.
UCSCiuc008gyc.2. mouse. [Q8R1B8-2]
uc008gye.2. mouse. [Q8R1B8-1]

Keywords - Coding sequence diversityi

Alternative promoter usage

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
CCDSi CCDS37932.1. [Q8R1B8-1 ]
CCDS37933.1. [Q8R1B8-2 ]
RefSeqi NP_001036819.1. NM_001043354.2. [Q8R1B8-1 ]
NP_001276850.1. NM_001289921.1.
NP_666207.3. NM_146095.4. [Q8R1B8-2 ]
UniGenei Mm.234641.

3D structure databases

ProteinModelPortali Q8R1B8.
SMRi Q8R1B8. Positions 10-463.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 230457. 6 interactions.

PTM databases

PhosphoSitei Q8R1B8.

Proteomic databases

PRIDEi Q8R1B8.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000040153 ; ENSMUSP00000047597 ; ENSMUSG00000036192 . [Q8R1B8-2 ]
ENSMUST00000112828 ; ENSMUSP00000108447 ; ENSMUSG00000036192 .
ENSMUST00000112832 ; ENSMUSP00000108451 ; ENSMUSG00000036192 . [Q8R1B8-1 ]
GeneIDi 225998.
KEGGi mmu:225998.
UCSCi uc008gyc.2. mouse. [Q8R1B8-2 ]
uc008gye.2. mouse. [Q8R1B8-1 ]

Organism-specific databases

CTDi 6096.
MGIi MGI:1343464. Rorb.

Phylogenomic databases

eggNOGi NOG324222.
GeneTreei ENSGT00740000114909.
HOGENOMi HOG000010200.
HOVERGENi HBG106848.
KOi K08533.
OMAi WEQLHDY.
OrthoDBi EOG79PJNW.
PhylomeDBi Q8R1B8.
TreeFami TF319910.

Miscellaneous databases

NextBioi 377911.
PROi Q8R1B8.
SOURCEi Search...

Gene expression databases

Bgeei Q8R1B8.
CleanExi MM_RORB.
Genevestigatori Q8R1B8.

Family and domain databases

Gene3Di 1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProi IPR008946. 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 ]
Pfami PF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view ]
PRINTSi PR01293. RORNUCRECPTR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTi SM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view ]
SUPFAMi SSF48508. SSF48508. 1 hit.
PROSITEi PS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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).

Entry informationi

Entry nameiRORB_MOUSE
AccessioniPrimary (citable) accession number: Q8R1B8
Secondary accession number(s): Q0PQZ2, Q0PQZ3, Q1MVR9
Entry historyi
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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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

External Data

Dasty 3

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