RARAA_DANRE
ID RARAA_DANRE Reviewed; 444 AA.
AC Q90271; Q91391;
DT 28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
DT 28-NOV-2006, sequence version 2.
DT 03-AUG-2022, entry version 149.
DE RecName: Full=Retinoic acid receptor alpha-A;
DE Short=RAR-alpha-A;
DE AltName: Full=Nuclear receptor subfamily 1 group B member 1-A;
DE AltName: Full=Retinoic acid receptor alpha;
DE Short=zRAR alpha;
DE AltName: Full=Retinoic acid receptor alpha-2.A;
DE Short=RAR-alpha-2.A;
GN Name=raraa {ECO:0000312|ZFIN:ZDB-GENE-980526-284};
GN Synonyms=nr1b1a, rara2a {ECO:0000312|ZFIN:ZDB-GENE-980526-284};
GN ORFNames=zgc:109797;
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:AAB32276.1}
RP NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND
RP INDUCTION.
RC TISSUE=Embryo {ECO:0000269|PubMed:7918098};
RX PubMed=7918098; DOI=10.1016/0925-4773(94)90082-5;
RA Joore J., van der Lans G.B.L.J., Lanser P.H., Vervaart J.M.A., Zivkovic D.,
RA Speksnijder J.E., Kruijer W.;
RT "Effects of retinoic acid on the expression of retinoic acid receptors
RT during zebrafish embryogenesis.";
RL Mech. Dev. 46:137-150(1994).
RN [2] {ECO:0000305, ECO:0000312|EMBL:AAA50049.1}
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Gastrula {ECO:0000312|EMBL:AAA50049.1};
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 [3] {ECO:0000305, ECO:0000312|EMBL:AAA50049.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain {ECO:0000312|EMBL:AAH92692.1};
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases.
RN [4] {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 [5]
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 patterning. {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 rarab, with high levels in hindbrain, lateral mesoderm and tail
CC bud. In the adult, strong expression in brain and muscle, weaker
CC expression in ovary, liver and digestive tract.
CC {ECO:0000269|PubMed:16455309, ECO:0000269|PubMed:7918098}.
CC -!- DEVELOPMENTAL STAGE: Not expressed maternally. First detected at 8
CC hours post-fertilization (hpf) during gastrulation, with expression
CC being restricted to the posterior epiblast. Expression then increases,
CC reaching a peak at 24 hpf and decreasing from 30-48 hpf. At 9 hpf,
CC expressed throughout the dorsal epiblast except at the dorsal midline,
CC and ventrally in prospective tail and head regions. At 10-11 hpf,
CC expressed in presumptive hindbrain, posterior neural plate, lateral
CC mesoderm and tail bud. At 12 hpf, strongly expressed in the neural
CC epithelium and tail bud and expressed at low levels elsewhere including
CC the eye. At 24 hpf, restricted to the hindbrain with an anterior border
CC at rhombomere 6-7, to anterior spinal cord and to head mesenchyme just
CC posterior to the otic vesicle. At 48 hpf, hindbrain expression remains
CC and there is diffuse expression in non-neural tissue in the pharyngeal
CC region. {ECO:0000269|PubMed:16455309, ECO:0000269|PubMed:18929555,
CC ECO:0000269|PubMed:7918098}.
CC -!- INDUCTION: By retinoic acid in embryos. {ECO:0000269|PubMed:18929555,
CC ECO:0000269|PubMed:7918098}.
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; S74155; AAB32276.1; -; mRNA.
DR EMBL; L03398; AAA50049.1; -; mRNA.
DR EMBL; BC092692; AAH92692.1; -; mRNA.
DR PIR; I51256; I51256.
DR RefSeq; NP_571481.2; NM_131406.2.
DR AlphaFoldDB; Q90271; -.
DR SMR; Q90271; -.
DR STRING; 7955.ENSDARP00000073792; -.
DR PaxDb; Q90271; -.
DR Ensembl; ENSDART00000079336; ENSDARP00000073792; ENSDARG00000056783.
DR GeneID; 30680; -.
DR KEGG; dre:30680; -.
DR CTD; 30680; -.
DR ZFIN; ZDB-GENE-980526-284; raraa.
DR eggNOG; KOG3575; Eukaryota.
DR GeneTree; ENSGT00940000165576; -.
DR InParanoid; Q90271; -.
DR PhylomeDB; Q90271; -.
DR TreeFam; TF328382; -.
DR Reactome; R-DRE-383280; Nuclear Receptor transcription pathway.
DR Reactome; R-DRE-4090294; SUMOylation of intracellular receptors.
DR Reactome; R-DRE-5362517; Signaling by Retinoic Acid.
DR Reactome; R-DRE-9616222; Transcriptional regulation of granulopoiesis.
DR SignaLink; Q90271; -.
DR PRO; PR:Q90271; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 12.
DR Bgee; ENSDARG00000056783; Expressed in retinal neural layer and 55 other tissues.
DR ExpressionAtlas; Q90271; baseline and differential.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0004879; F:nuclear receptor activity; IDA:UniProtKB.
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:0030154; P:cell differentiation; IBA:GO_Central.
DR GO; GO:0021575; P:hindbrain morphogenesis; IDA:UniProtKB.
DR GO; GO:0009755; P:hormone-mediated signaling pathway; IBA:GO_Central.
DR GO; GO:0001889; P:liver development; IMP:ZFIN.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0032526; P:response to retinoic acid; IDA:UniProtKB.
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; 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..444
FT /note="Retinoic acid receptor alpha-A"
FT /id="PRO_0000262962"
FT DOMAIN 170..404
FT /note="NR LBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01189"
FT DNA_BIND 72..147
FT /note="Nuclear receptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 75..95
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 111..130
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT REGION 1..71
FT /note="Modulating"
FT /evidence="ECO:0000255"
FT REGION 35..67
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 148..169
FT /note="Hinge"
FT /evidence="ECO:0000255"
FT REGION 402..444
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 395..403
FT /note="9aaTAD"
FT /evidence="ECO:0000250|UniProtKB:P10276"
FT COMPBIAS 35..58
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 403..444
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 381..382
FT /note="RV -> LL (in Ref. 2; AAA50049)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 444 AA; 49924 MW; 7B0DED7B660D5E7F CRC64;
MYESVDVNPF LMMDYYNQSR GCLIPDKMPH PFSSSIRHQH WSGSNHSIET QSTSSEEIVP
SPPSPPPPPR IYKPCFVCQD KSSGYHYGVS ACEGCKGFFR RSIQKNMVYT CHREKNCIIN
KVTRNRCQYC RLQKCLEVGM SKESVRNDRN KKKKEEKKPE CTENYTLSPD TEQMIDRVRK
AHQETFPSLC QLGKYTTSNS SERRVALDVD LWDKFSELST KCIIKTVEFA KQLPGFTTLT
IADQITLLKA ACLDILILRI CTRYTPEQDT MTFSDGLTLN RTQMHNAGFG PLTDLVFAFA
NQLLPLEMDD AETGLLSAIC LLCGDRQDLE QADKVDVLQE PLLEALKIYV RNRRPHKPHM
FPKMLMKITD LRSISAKGAE RVITLKMEIP GSMPPLIQEM LENSEGLESS SGAQGSRASA
TTPGSCSPSL SPNSAQSSPP TQSP
