RXRGB_DANRE
ID RXRGB_DANRE Reviewed; 452 AA.
AC Q6DHP9;
DT 21-AUG-2007, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Retinoic acid receptor RXR-gamma-B;
DE AltName: Full=Nuclear receptor subfamily 2 group B member 3-B;
DE AltName: Full=Retinoid X receptor gamma-B;
GN Name=rxrgb {ECO:0000312|ZFIN:ZDB-GENE-040718-34}; Synonyms=nr3b3b;
GN ORFNames=si:ch211-260g14.2, zgc:92183;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1] {ECO:0000305, ECO:0000312|EMBL:ABM89230.1}
RP NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=17195188; DOI=10.1002/dvdy.21049;
RA Waxman J.S., Yelon D.;
RT "Comparison of the expression patterns of newly identified zebrafish
RT retinoic acid and retinoid X receptors.";
RL Dev. Dyn. 236:587-595(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [3] {ECO:0000312|EMBL:CAI11930.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Receptor for retinoic acid. Retinoic acid receptors bind as
CC heterodimers to their target response elements in response to their
CC ligands, all-trans or 9-cis retinoic acid, and regulate gene expression
CC in various biological processes. The rar/rxr heterodimers bind to the
CC retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3'
CC sites known as DR1-DR5. The high affinity ligand for rxrs is 9-cis
CC retinoic acid (By similarity). {ECO:0000250}.
CC -!- SUBUNIT: Homodimer. Heterodimer; with a rar molecule. Binds DNA
CC preferentially as a rar/rxr heterodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00407}.
CC -!- TISSUE SPECIFICITY: By the 5-somite stage, expressed in the anterior
CC spinal cord. Expression becomes restricted to the ventral spinal cord
CC and by 24 hpf, expression is low and restricted to the medial ventral
CC spinal cord. {ECO:0000269|PubMed:17195188}.
CC -!- DEVELOPMENTAL STAGE: Expressed zygotically.
CC {ECO:0000269|PubMed:17195188}.
CC -!- DOMAIN: Composed of three domains: a modulating N-terminal domain, a
CC DNA-binding domain and a C-terminal ligand-binding domain.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the nuclear hormone receptor family. NR2
CC subfamily. {ECO:0000255}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; EF028133; ABM89230.1; -; mRNA.
DR EMBL; BX296562; CAI11930.1; -; Genomic_DNA.
DR EMBL; BC075918; AAH75918.1; -; mRNA.
DR RefSeq; NP_001002345.1; NM_001002345.1.
DR AlphaFoldDB; Q6DHP9; -.
DR SMR; Q6DHP9; -.
DR STRING; 7955.ENSDARP00000003080; -.
DR PaxDb; Q6DHP9; -.
DR Ensembl; ENSDART00000002554; ENSDARP00000003080; ENSDARG00000004697.
DR GeneID; 436617; -.
DR KEGG; dre:436617; -.
DR CTD; 436617; -.
DR ZFIN; ZDB-GENE-040718-34; rxrgb.
DR eggNOG; KOG3575; Eukaryota.
DR GeneTree; ENSGT00940000166019; -.
DR HOGENOM; CLU_007368_5_4_1; -.
DR InParanoid; Q6DHP9; -.
DR OrthoDB; 912470at2759; -.
DR PhylomeDB; Q6DHP9; -.
DR TreeFam; TF352097; -.
DR Reactome; R-DRE-383280; Nuclear Receptor transcription pathway.
DR Reactome; R-DRE-5362517; Signaling by Retinoic Acid.
DR PRO; PR:Q6DHP9; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 20.
DR Bgee; ENSDARG00000004697; Expressed in Kupffer's vesicle and 25 other tissues.
DR ExpressionAtlas; Q6DHP9; baseline.
DR GO; GO:0090575; C:RNA polymerase II transcription regulator complex; IBA:GO_Central.
DR GO; GO:0004879; F:nuclear receptor activity; IBA:GO_Central.
DR GO; GO:0003707; F:nuclear steroid receptor activity; IEA:InterPro.
DR GO; GO:0044323; F:retinoic acid-responsive element binding; IBA:GO_Central.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0048856; P:anatomical structure development; IBA:GO_Central.
DR GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0032526; P:response to retinoic acid; IBA:GO_Central.
DR GO; GO:0048384; P:retinoic acid receptor signaling pathway; IBA:GO_Central.
DR Gene3D; 1.10.565.10; -; 1.
DR Gene3D; 3.30.50.10; -; 1.
DR InterPro; IPR035500; NHR-like_dom_sf.
DR InterPro; IPR021780; Nuc_recep-AF1.
DR InterPro; IPR000536; Nucl_hrmn_rcpt_lig-bd.
DR InterPro; IPR001723; Nuclear_hrmn_rcpt.
DR InterPro; IPR000003; Retinoid-X_rcpt/HNF4.
DR InterPro; IPR001628; Znf_hrmn_rcpt.
DR InterPro; IPR013088; Znf_NHR/GATA.
DR Pfam; PF00104; Hormone_recep; 1.
DR Pfam; PF11825; Nuc_recep-AF1; 1.
DR Pfam; PF00105; zf-C4; 1.
DR PRINTS; PR00545; RETINOIDXR.
DR PRINTS; PR00398; STRDHORMONER.
DR PRINTS; PR00047; STROIDFINGER.
DR SMART; SM00430; HOLI; 1.
DR SMART; SM00399; ZnF_C4; 1.
DR SUPFAM; SSF48508; SSF48508; 1.
DR PROSITE; PS51843; NR_LBD; 1.
DR PROSITE; PS00031; NUCLEAR_REC_DBD_1; 1.
DR PROSITE; PS51030; NUCLEAR_REC_DBD_2; 1.
PE 2: Evidence at transcript level;
KW DNA-binding; Metal-binding; Nucleus; Receptor; Reference proteome;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..452
FT /note="Retinoic acid receptor RXR-gamma-B"
FT /id="PRO_0000299072"
FT DOMAIN 220..448
FT /note="NR LBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01189"
FT DNA_BIND 125..200
FT /note="Nuclear receptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 128..148
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 164..183
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT REGION 1..127
FT /note="Modulating"
FT /evidence="ECO:0000250|UniProtKB:P10826"
FT REGION 1..46
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 194..217
FT /note="Hinge"
FT /evidence="ECO:0000250|UniProtKB:P10826"
FT COMPBIAS 9..46
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 452 AA; 50140 MW; 2AB615B129B47626 CRC64;
MDTHDTYLHL HSSPLNSSPS QPPVMSSMVG HPSVISSSRP LPSPMSTLGS SMNGLPSPYS
VITPSLSSPS ISLPSTPSMG FNTLNSPQMN SLSMNGNEDI KPPPGLAPLG NMSSYQCTSP
GSLSKHICAI CGDRSSGKHY GVYSCEGCKG FFKRTIRKDL TYTCRDIKEC LIDKRQRNRC
QYCRYQKCLA MGMKREAVQE ERQRGKEKSD TEVETTSRFN EDMPVDKILD AELSVEPKTE
TYTESSPSNS TNDPVTNICH AADKQLFTLV EWAKRIPHFS DLPLDDQVIL LRAGWNELLI
ASFSHRSITV KDGILLGTGL HVHRSSAHSA GVGSIFNRVL TELVSKMKDM QMDKTELGCL
RAIVLFNPDA KGLSNSLEVE ALREKVYASL ETYTKQKYPD QPGRFAKLLL RLPALRSIGL
KCLEHLFFFK LIGDTPIDTF LMEMLEAPHQ IT
