RXRBA_DANRE
ID RXRBA_DANRE Reviewed; 471 AA.
AC Q7SYN5; O42556; Q1LV98; Q8AW18; Q90418;
DT 27-SEP-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2003, sequence version 1.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=Retinoic acid receptor RXR-beta-A;
DE AltName: Full=Nuclear receptor subfamily 2 group B member 2-A;
DE AltName: Full=Retinoid X receptor beta-A;
GN Name=rxrba;
GN Synonyms=nr2b2a, rxrb, rxre {ECO:0000312|ZFIN:ZDB-GENE-980526-436};
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]
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 [2] {ECO:0000305, ECO:0000312|EMBL:AAH54649.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=SJD;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (JUL-2003) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000305, ECO:0000312|EMBL:AAC59722.1}
RP NUCLEOTIDE SEQUENCE [MRNA] OF 6-471, FUNCTION, HETERODIMERIZATION WITH
RP RARGA, AND DEVELOPMENTAL STAGE.
RX PubMed=7565671; DOI=10.1128/mcb.15.10.5226;
RA Jones B.B., Ohno C.K., Allenby G., Boffa M.B., Levin A.A., Grippo J.F.,
RA Petkovich M.;
RT "New retinoid X receptor subtypes in zebra fish (Danio rerio)
RT differentially modulate transcription and do not bind 9-cis retinoic
RT acid.";
RL Mol. Cell. Biol. 15:5226-5234(1995).
RN [4] {ECO:0000305, ECO:0000312|EMBL:AAB68760.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 142-181.
RX PubMed=9192646; DOI=10.1073/pnas.94.13.6803;
RA Escriva H., Safi R., Haenni C., Langlois M.-C., Saumitou-Laprade P.,
RA Stehelin D., Capron A., Pierce R., Laudet V.;
RT "Ligand binding was acquired during evolution of nuclear receptors.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:6803-6808(1997).
RN [5]
RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=16448862; DOI=10.1016/j.modgep.2005.10.005;
RA Tallafuss A., Hale L.A., Yan Y.-L., Dudley L., Eisen J.S.,
RA Postlethwait J.H.;
RT "Characterization of retinoid-X receptor genes rxra, rxrba, rxrbb and rxrg
RT during zebrafish development.";
RL Gene Expr. Patterns 6:556-565(2006).
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 ECO:0000269|PubMed:7565671}.
CC -!- SUBUNIT: Homodimer (By similarity). Heterodimer; with a rar molecule
CC (By similarity). Binds DNA preferentially as a rar/rxr heterodimer (By
CC similarity). Heterodimerizes with rarga. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- TISSUE SPECIFICITY: Shows uniform expression from the blastula to mid-
CC gastrula stages. At 12 hours post-fertilization (hpf), expressed
CC ubiquitously but more weakly. At 24 hpf, restricted to the ventral
CC diencephalon, pharangeal endoderm and trunk and tail mesoderm; mesoderm
CC expression is in medial cells of each somite along the dorsoventral
CC axis, forming stripes. At 48 hpf, expressed in forebrain, eye, midbrain
CC and anterior hindbrain. {ECO:0000269|PubMed:16448862}.
CC -!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically.
CC {ECO:0000269|PubMed:16448862, ECO:0000269|PubMed:7565671}.
CC -!- DOMAIN: Composed of three domains: a modulating N-terminal domain, a
CC DNA-binding domain and a C-terminal ligand-binding domain.
CC -!- SIMILARITY: Belongs to the nuclear hormone receptor family. NR2
CC subfamily. {ECO:0000255}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC59722.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAK11469.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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; AL672176; CAD54660.1; -; Genomic_DNA.
DR EMBL; BX890617; CAK11469.1; ALT_SEQ; Genomic_DNA.
DR EMBL; BC054649; AAH54649.1; -; mRNA.
DR EMBL; U29942; AAC59722.1; ALT_INIT; mRNA.
DR EMBL; U93483; AAB68760.1; -; Genomic_DNA.
DR PIR; I50517; I50517.
DR RefSeq; NP_571350.1; NM_131275.1.
DR RefSeq; XP_005159467.1; XM_005159410.3.
DR RefSeq; XP_009292301.1; XM_009294026.2.
DR AlphaFoldDB; Q7SYN5; -.
DR SMR; Q7SYN5; -.
DR STRING; 7955.ENSDARP00000015784; -.
DR PaxDb; Q7SYN5; -.
DR PRIDE; Q7SYN5; -.
DR Ensembl; ENSDART00000102075; ENSDARP00000125725; ENSDARG00000078954.
DR GeneID; 30530; -.
DR KEGG; dre:30530; -.
DR CTD; 30530; -.
DR ZFIN; ZDB-GENE-980526-436; rxrba.
DR eggNOG; KOG3575; Eukaryota.
DR GeneTree; ENSGT00940000159208; -.
DR InParanoid; Q7SYN5; -.
DR OrthoDB; 912470at2759; -.
DR PhylomeDB; Q7SYN5; -.
DR TreeFam; TF352097; -.
DR Reactome; R-DRE-383280; Nuclear Receptor transcription pathway.
DR Reactome; R-DRE-5362517; Signaling by Retinoic Acid.
DR Reactome; R-DRE-9029569; NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux.
DR Reactome; R-DRE-9623433; NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis.
DR SignaLink; Q7SYN5; -.
DR PRO; PR:Q7SYN5; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 19.
DR Bgee; ENSDARG00000078954; Expressed in pharyngeal gill and 28 other tissues.
DR ExpressionAtlas; Q7SYN5; 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:0045892; P:negative regulation of transcription, DNA-templated; IDA:ZFIN.
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:0006355; P:regulation of transcription, DNA-templated; IDA:UniProtKB.
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 Activator; DNA-binding; Metal-binding; Nucleus; Receptor;
KW Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..471
FT /note="Retinoic acid receptor RXR-beta-A"
FT /id="PRO_0000053575"
FT DOMAIN 224..467
FT /note="NR LBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01189"
FT DNA_BIND 122..197
FT /note="Nuclear receptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 125..145
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 161..185
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT REGION 1..102
FT /note="Modulating"
FT /evidence="ECO:0000250"
FT REGION 1..34
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 196..226
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 198..221
FT /note="Hinge"
FT /evidence="ECO:0000250"
FT COMPBIAS 7..21
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 196..220
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 158
FT /note="S -> N (in Ref. 4; AAB68760)"
FT /evidence="ECO:0000305"
FT CONFLICT 181
FT /note="R -> S (in Ref. 4; AAB68760)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 471 AA; 51597 MW; 522D77766400A089 CRC64;
MGDSRDSRSP DSSSVSSPPS GQRSPPLAPS AAAMTSLPPI TSAVNSPISS MGSPFSVISS
SLGSPCLPGT PSVGYGPISS PQINSTVSMS GLHAVSSSDD VKPPFGLKPL SSHSPGPMVS
QKRLCAICGD RSSGKHYGVY SCEGCKGFFK RTVRKDLSYT CRDNKDCLVD KRQRNRCQYC
RYQKCLAMGM KREVVQDERQ RSVQEERQRN KERDGEVESS SAANEEMPVE KILEAEMAVE
QKTELHADGS SGGSSPNDPV TNICQAADKQ LFTLVEWAKR IPHFSELSLD DQVILLRAGW
NELLIASFSH RSITVKDGIL LATGLHVHRN SAHSAGVGAI FDRESAHNAE VGAIFDRVLT
ELVSKMRDMQ MDKTELGCLR AIILFNPDAK GLSSPSEVEL LREKVYASLE AYCKQRYPDQ
QGRFAKLLLR LPALRSIGLK CLEHLFFFKL IGDTPIDTFL MEMLEAPHQL T
