RARAB_DANRE
ID RARAB_DANRE Reviewed; 458 AA.
AC Q7ZTI3; Q90272;
DT 28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Retinoic acid receptor alpha-B;
DE Short=RAR-alpha-B;
DE AltName: Full=Nuclear receptor subfamily 1 group B member 1-B;
DE AltName: Full=Retinoic acid receptor alpha-2.B;
DE Short=RAR-alpha-2.B;
GN Name=rarab {ECO:0000312|ZFIN:ZDB-GENE-980526-72};
GN Synonyms=nr1b1b, rara2b {ECO:0000312|ZFIN:ZDB-GENE-980526-72};
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:AAA50050.1}
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Gastrula {ECO:0000312|EMBL:AAA50050.1};
RA Stachel S.E., Kushner P.;
RT "The molecular characterization of three zebrafish retinoic acid receptor
RT genes suggests the retinoic acid pathway functions in embryonic hindbrain
RT development.";
RL Submitted (DEC-1992) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000305, ECO:0000312|EMBL:AAA50050.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=SJD;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (MAR-2003) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000305}
RP DEVELOPMENTAL STAGE, AND TISSUE SPECIFICITY.
RX PubMed=16455309; DOI=10.1016/j.modgep.2005.10.007;
RA Hale L.A., Tallafuss A., Yan Y.-L., Dudley L., Eisen J.S.,
RA Postlethwait J.H.;
RT "Characterization of the retinoic acid receptor genes raraa, rarab and rarg
RT during zebrafish development.";
RL Gene Expr. Patterns 6:546-555(2006).
RN [4]
RP DEVELOPMENTAL STAGE, INDUCTION, AND FUNCTION.
RX PubMed=18929555; DOI=10.1016/j.ydbio.2008.09.022;
RA Linville A., Radtke K., Waxman J.S., Yelon D., Schilling T.F.;
RT "Combinatorial roles for zebrafish retinoic acid receptors in the
RT hindbrain, limbs and pharyngeal arches.";
RL Dev. Biol. 325:60-70(2009).
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 (By similarity). Required for hindbrain
CC development and, in lateral plate mesoderm, for specification of the
CC pectoral fins. {ECO:0000250, ECO:0000269|PubMed:18929555}.
CC -!- SUBUNIT: Heterodimer; with an rxr molecule. Binds DNA preferentially as
CC a rar/rxr heterodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00407}.
CC -!- TISSUE SPECIFICITY: In the embryo, zygotic expression largely overlaps
CC that of raraa, with high levels in hindbrain, lateral plate mesoderm
CC (LPM) and tail bud, but in later stages rarab is expressed more broadly
CC in the brain, pectoral fin bud and pharyngeal arches.
CC {ECO:0000269|PubMed:16455309}.
CC -!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically. At 9
CC hpf, expressed in the dorsal epiblast and prospective tail regions, but
CC absent from the ventral epiblast. At 10 hpf, expressed in presumptive
CC diencephalon and hindbrain, in tissue lateral to the head, the
CC posterior neural plate, tail bud and adjacent mesoderm. At 11-15 hpf,
CC restricted expression along the A-P axis of the neural plate up to the
CC rhobomere 1/2 boundary. During somitogenesis, head and tail expression
CC remains. At 18 hpf, retained expression in the neural tube. At 24 hpf,
CC low levels of ubiquitous expression with stronger expression in eyes,
CC hindbrain and spinal cord; in hindbrain the anterior border is at
CC rhombomeres 3-4. Also expressed in non-neural tissues including
CC pharyngeal endoderm, mesenchyme and tail bud. At 48 hpf, expression is
CC maintained in hindbrain, eyes, diencephalon and the pharyngeal region,
CC and is also observed in forebrain, midbrain and pectoral fin bud.
CC {ECO:0000269|PubMed:16455309, ECO:0000269|PubMed:18929555}.
CC -!- INDUCTION: Induced by retinoic acid. {ECO:0000269|PubMed:18929555}.
CC -!- DOMAIN: Composed of three domains: a modulating N-terminal domain, a
CC DNA-binding domain and a C-terminal ligand-binding domain.
CC -!- DOMAIN: The 9aaTAD motif is a transactivation domain present in a large
CC number of yeast and animal transcription factors.
CC {ECO:0000250|UniProtKB:P10276}.
CC -!- SIMILARITY: Belongs to the nuclear hormone receptor family. NR1
CC subfamily. {ECO:0000255}.
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DR EMBL; L03399; AAA50050.1; -; mRNA.
DR EMBL; BC049301; AAH49301.1; -; mRNA.
DR RefSeq; NP_571474.1; NM_131399.1.
DR AlphaFoldDB; Q7ZTI3; -.
DR SMR; Q7ZTI3; -.
DR STRING; 7955.ENSDARP00000111644; -.
DR PaxDb; Q7ZTI3; -.
DR PRIDE; Q7ZTI3; -.
DR Ensembl; ENSDART00000044677; ENSDARP00000044676; ENSDARG00000034893.
DR Ensembl; ENSDART00000189058; ENSDARP00000146437; ENSDARG00000111757.
DR GeneID; 555364; -.
DR KEGG; dre:555364; -.
DR CTD; 555364; -.
DR ZFIN; ZDB-GENE-980526-72; rarab.
DR eggNOG; KOG3575; Eukaryota.
DR GeneTree; ENSGT00940000165576; -.
DR InParanoid; Q7ZTI3; -.
DR OrthoDB; 1165737at2759; -.
DR PhylomeDB; Q7ZTI3; -.
DR TreeFam; TF328382; -.
DR Reactome; R-DRE-383280; Nuclear Receptor transcription pathway.
DR Reactome; R-DRE-5362517; Signaling by Retinoic Acid.
DR SignaLink; Q7ZTI3; -.
DR PRO; PR:Q7ZTI3; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 3.
DR Bgee; ENSDARG00000034893; Expressed in ovary and 27 other tissues.
DR ExpressionAtlas; Q7ZTI3; baseline.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0001227; F:DNA-binding transcription repressor activity, RNA polymerase II-specific; IDA:ZFIN.
DR GO; GO:0004879; F:nuclear receptor activity; IBA:GO_Central.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IDA:ZFIN.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
DR GO; GO:0007507; P:heart development; IMP:ZFIN.
DR GO; GO:0009755; P:hormone-mediated signaling pathway; IBA:GO_Central.
DR GO; GO:0001889; P:liver development; IMP:ZFIN.
DR GO; GO:0030917; P:midbrain-hindbrain boundary development; IGI:ZFIN.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:ZFIN.
DR GO; GO:0033339; P:pectoral fin development; IDA:UniProtKB.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0048384; P:retinoic acid receptor signaling pathway; IBA:GO_Central.
DR GO; GO:0003139; P:secondary heart field specification; IMP:ZFIN.
DR Gene3D; 1.10.565.10; -; 1.
DR Gene3D; 3.30.50.10; -; 1.
DR InterPro; IPR035500; NHR-like_dom_sf.
DR InterPro; IPR000536; Nucl_hrmn_rcpt_lig-bd.
DR InterPro; IPR001723; Nuclear_hrmn_rcpt.
DR InterPro; IPR003078; Retinoic_acid_rcpt.
DR InterPro; IPR001628; Znf_hrmn_rcpt.
DR InterPro; IPR013088; Znf_NHR/GATA.
DR Pfam; PF00104; Hormone_recep; 1.
DR Pfam; PF00105; zf-C4; 1.
DR PRINTS; PR01292; RETNOICACIDR.
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..458
FT /note="Retinoic acid receptor alpha-B"
FT /id="PRO_0000262963"
FT DOMAIN 178..412
FT /note="NR LBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01189"
FT DNA_BIND 80..155
FT /note="Nuclear receptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 83..103
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 119..138
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT REGION 1..79
FT /note="Modulating"
FT /evidence="ECO:0000255"
FT REGION 48..75
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 156..177
FT /note="Hinge"
FT /evidence="ECO:0000255"
FT REGION 411..458
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 403..411
FT /note="9aaTAD"
FT /evidence="ECO:0000250|UniProtKB:P10276"
FT COMPBIAS 48..66
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 440..458
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 110
FT /note="S -> T (in Ref. 1; AAA50050)"
FT /evidence="ECO:0000305"
FT CONFLICT 424
FT /note="Missing (in Ref. 1; AAA50050)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 458 AA; 50525 MW; 05328DF20E040D3C CRC64;
MYESVDVVGL TPSPNPFLSM DYYHQNRGCL IPDKGLVSGA ARGFRNPHWS GSNHSVETQS
TSSEEIVPSP PSPPPPPRVY KPCFVCQDKS SGYHYGVSAC EGCKGFFRRS IQKNMVYTCH
REKSCIINKV TRNRCQYCRL QKCLEVGMSK ESVRNDRNKR KKDDKKQECL ENYVLSPDTE
KMIEQVRKAH QETFPSLCQL GKYTTNNSAD HRVALDVDLW DKFSELSTKC IIKTVEFAKQ
LPGFTTLTIA DQITLLKAAC LDILILRICT RYTPDQDTMT FSDGLTLNRT QMHNAGFGPL
TDLVFAFANQ LLPLEMDDAE TGLLSAICLL CGDRQDLEQS DKVDELQEPL LEALKIYVRN
RRPHKPHMFP KMLMKITDLR SISAKGAERV ITLKMEIPGS MPPLIQEMLE NSEGLEGGGS
KGAGGGGGGG GGKGAPPGSC SPSLSPSSAH SSPSAHSP
