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Protein

Retinoic acid receptor RXR-alpha-B

Gene

rxrab

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 this rxr is 9-cis retinoic acid (By similarity).By similarity1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi54 – 11966Nuclear receptorPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri54 – 7421NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri90 – 11425NR C4-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Retinoic acid receptor RXR-alpha-B
Alternative name(s):
Nuclear receptor subfamily 2 group B member 1-B
Retinoid X receptor alpha-B
Gene namesi
Name:rxrab
Synonyms:nr2b1b, rxra, rxrg
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-990415-243. rxrab.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 379379Retinoic acid receptor RXR-alpha-BPRO_0000053579Add
BLAST

Proteomic databases

PaxDbiQ90415.

Expressioni

Tissue specificityi

Uniform expression from the blastula to mid-gastrula stages. At 12 hours post-fertilization (hpf), expressed strongly in the tail and weakly elsewhere. At 24 hpf, weak expression in the forebrain, eyes and pharyngeal endoderm and continued expression in the tail mesoderm. At 48 hpf, anterior expression limited to ventral cells underlying the head, medial expression in the pectoral fin bud mesoderm and continued tail expression.2 Publications

Developmental stagei

Expressed both maternally and zygotically.4 Publications

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi7955.ENSDARP00000004918.

Structurei

3D structure databases

ProteinModelPortaliQ90415.
SMRiQ90415. Positions 48-130, 143-379.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 5353ModulatingBy similarityAdd
BLAST
Regioni120 – 14122HingeBy similarityAdd
BLAST
Regioni142 – 379238Ligand-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 fingeri54 – 7421NR C4-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri90 – 11425NR C4-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
HOGENOMiHOG000260821.
HOVERGENiHBG005606.
InParanoidiQ90415.
PhylomeDBiQ90415.

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.

Q90415-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPVPEQKQTV QLSSPMNAVS SSEDIKPPLG LNGVMKVPAH RIGTLSLSLT
60 70 80 90 100
KHICAICGDR SSGKHYGVYS CEGCKGFFKR TVRKDLTYTC RDNKDCMIDK
110 120 130 140 150
RQRNRCQYCR YQKCLAMGMK REAVQEERQR AKERSEAEFG GCANEDMPVE
160 170 180 190 200
KILEAELAVE PKTETYVEAN LSPSANSPND PVTNICQAAD KQLFTLVEWA
210 220 230 240 250
KRIPHFSDLP LDDQVILLRA GWNELLIASF SHRSIAVKDG ILLATGLHVH
260 270 280 290 300
RNSAHTAGVG AIFDRVLTEL VSKMRDMQMD KTELGCLRAI VLFNPDSKGL
310 320 330 340 350
SNPSEVEALR ERVYASLEAY CKHKYPDQPG RFAKLLLRLP ALRSIGLKCL
360 370
EHLFFFKLIG DTPIDTFLME MLEAPHQIT
Length:379
Mass (Da):42,556
Last modified:November 1, 1996 - v1
Checksum:i317EA9E9DE455D16
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29894 mRNA. Translation: AAC59719.1.
PIRiI50514.
RefSeqiNP_571228.1. NM_131153.1.
UniGeneiDr.624.

Genome annotation databases

GeneIDi793011.
KEGGidre:793011.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29894 mRNA. Translation: AAC59719.1.
PIRiI50514.
RefSeqiNP_571228.1. NM_131153.1.
UniGeneiDr.624.

3D structure databases

ProteinModelPortaliQ90415.
SMRiQ90415. Positions 48-130, 143-379.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000004918.

Proteomic databases

PaxDbiQ90415.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi793011.
KEGGidre:793011.

Organism-specific databases

CTDi793011.
ZFINiZDB-GENE-990415-243. rxrab.

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
HOGENOMiHOG000260821.
HOVERGENiHBG005606.
InParanoidiQ90415.
PhylomeDBiQ90415.

Miscellaneous databases

PROiQ90415.

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, 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.
  3. "Comparison of the expression patterns of newly identified zebrafish retinoic acid and retinoid X receptors."
    Waxman J.S., Yelon D.
    Dev. Dyn. 236:587-595(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
  4. "Unexpected novel relational links uncovered by extensive developmental profiling of nuclear receptor expression."
    Bertrand S., Thisse B., Tavares R., Sachs L., Chaumot A., Bardet P.-L., Escriva H., Duffraisse M., Marchand O., Safi R., Thisse C., Laudet V.
    PLoS Genet. 3:E188-E188(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE.

Entry informationi

Entry nameiRXRAB_DANRE
AccessioniPrimary (citable) accession number: Q90415
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 27, 2004
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 114 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.