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Protein

Retinoic acid receptor RXR-beta-B

Gene

rxrbb

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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. The high affinity ligand for rxrs is 9-cis retinoic acid (By similarity).By similarity1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi90 – 15566Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri90 – 11021NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri126 – 15025NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Receptor, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Retinoic acid receptor RXR-beta-B
Alternative name(s):
Nuclear receptor subfamily 2 group B member 2-B
Retinoic acid receptor RXR-delta
Retinoid X receptor beta-B
Retinoid X receptor delta
Gene namesi
Name:rxrbb
Synonyms:nr2b2b, rxrd
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-990415-242. rxrbb.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 422422Retinoic acid receptor RXR-beta-BPRO_0000053581Add
BLAST

Proteomic databases

PaxDbiQ90417.

Expressioni

Tissue specificityi

Shows uniform expression from the blastula to mid-gastrula stages. At 12 hours post-fertilization (hpf), expressed ubiquitously but more weakly. At 24 hpf, restricted to the ventral diencephalon, pharangeal endoderm and trunk and tail mesoderm; mesoderm expression is in medial cells of each somite along the dorsoventral axis, forming stripes. At 48 hpf, expressed in forebrain, eye, midbrain and anterior hindbrain.1 Publication

Developmental stagei

Expressed both maternally and zygotically.2 Publications

Interactioni

Subunit structurei

Homodimer (By similarity). Heterodimer; with a rar molecule (By similarity). Binds DNA preferentially as a rar/rxr heterodimer (By similarity). Heterodimerizes with rarga.By similarity

Protein-protein interaction databases

STRINGi7955.ENSDARP00000022973.

Structurei

3D structure databases

ProteinModelPortaliQ90417.
SMRiQ90417. Positions 87-166, 179-422.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 8989ModulatingBy similarityAdd
BLAST
Regioni156 – 17823HingeBy similarityAdd
BLAST
Regioni179 – 422244Ligand-bindingBy similarityAdd
BLAST

Domaini

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

Sequence similaritiesi

Belongs to the nuclear hormone receptor family. NR2 subfamily.Sequence analysis
Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri90 – 11021NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri126 – 15025NR C4-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
HOGENOMiHOG000260821.
HOVERGENiHBG005606.
InParanoidiQ90417.
PhylomeDBiQ90417.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR021780. Nuc_recep-AF1.
IPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR000003. Retinoid-X_rcpt/HNF4.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF11825. Nuc_recep-AF1. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR00545. RETINOIDXR.
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]

Sequencei

Sequence statusi: Complete.

Q90417-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNSLPPSTSA VSSPVSSVDS PLSAVSSSIG SPGVPGTPSI GYGPISNSQI
60 70 80 90 100
NSSMSVSRLH AVSSSDDVKP PFGLKSVSGS GPMLSQKRMC AICGDRSSGK
110 120 130 140 150
HYGVYSCEGC KGFFKRTVRK DLSYTCRDNK ECLVDKRQRN RCQYCRYQKC
160 170 180 190 200
LAMGMKREAV QEERQKNKER DGDYECSSSA NEEMPVEKIL EAETAVEHRT
210 220 230 240 250
DLHSDATGSP NDPVTNICQA ADKQLFTLVE WAKRVPHFSD VPLDDQVILL
260 270 280 290 300
RAGWNELLIA AFSHRSISVK DEILLATGLH VPKESTHNLG VEAFFDRESS
310 320 330 340 350
HSAEVGALFD RVLTELVCKM RDMQMDKTEL GCLRAIVLFN PDAKGLTSSS
360 370 380 390 400
EVELLREKVY ASLESYCKQK YPDQQGRFAK LLLRLPALRS IGLKCLEHLF
410 420
FFKLIGNTPI DTFLMEMLES PH
Length:422
Mass (Da):46,732
Last modified:November 1, 1996 - v1
Checksum:i6CCDBA3CE29C7238
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29941 mRNA. Translation: AAC59721.1.
PIRiI50516.
RefSeqiNP_571313.1. NM_131238.1.
UniGeneiDr.350.

Genome annotation databases

GeneIDi30486.
KEGGidre:30486.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29941 mRNA. Translation: AAC59721.1.
PIRiI50516.
RefSeqiNP_571313.1. NM_131238.1.
UniGeneiDr.350.

3D structure databases

ProteinModelPortaliQ90417.
SMRiQ90417. Positions 87-166, 179-422.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000022973.

Proteomic databases

PaxDbiQ90417.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi30486.
KEGGidre:30486.

Organism-specific databases

CTDi30486.
ZFINiZDB-GENE-990415-242. rxrbb.

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
HOGENOMiHOG000260821.
HOVERGENiHBG005606.
InParanoidiQ90417.
PhylomeDBiQ90417.

Miscellaneous databases

PROiQ90417.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR021780. Nuc_recep-AF1.
IPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR000003. Retinoid-X_rcpt/HNF4.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF11825. Nuc_recep-AF1. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR00545. RETINOIDXR.
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...

Publicationsi

  1. "New retinoid X receptor subtypes in zebra fish (Danio rerio) differentially modulate transcription and do not bind 9-cis retinoic acid."
    Jones B.B., Ohno C.K., Allenby G., Boffa M.B., Levin A.A., Grippo J.F., Petkovich M.
    Mol. Cell. Biol. 15:5226-5234(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, HETERODIMERIZATION WITH RARGA, DEVELOPMENTAL STAGE.
  2. "Characterization of retinoid-X receptor genes rxra, rxrba, rxrbb and rxrg during zebrafish development."
    Tallafuss A., Hale L.A., Yan Y.-L., Dudley L., Eisen J.S., Postlethwait J.H.
    Gene Expr. Patterns 6:556-565(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.

Entry informationi

Entry nameiRXRBB_DANRE
AccessioniPrimary (citable) accession number: Q90417
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 27, 2004
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 110 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

Complete proteome, Reference proteome

Documents

  1. 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.