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A2T928

- RARGB_DANRE

UniProt

A2T928 - RARGB_DANRE

Protein

Retinoic acid receptor gamma-B

Gene

rargb

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 48 (01 Oct 2014)
      Sequence version 1 (06 Mar 2007)
      Previous versions | rss
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    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 By similarity. Required for hindbrain development.By similarity1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi62 – 13776Nuclear receptorPROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri65 – 8521NR C4-typePROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri101 – 12020NR C4-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. retinoic acid receptor activity Source: InterPro
    2. sequence-specific DNA binding Source: InterPro
    3. steroid hormone receptor activity Source: InterPro
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. determination of digestive tract left/right asymmetry Source: ZFIN
    2. determination of heart left/right asymmetry Source: ZFIN
    3. determination of left/right asymmetry in lateral mesoderm Source: ZFIN
    4. determination of liver left/right asymmetry Source: ZFIN
    5. determination of pancreatic left/right asymmetry Source: ZFIN
    6. intrahepatic bile duct development Source: ZFIN
    7. negative regulation of BMP signaling pathway Source: ZFIN

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Retinoic acid receptor gamma-B
    Short name:
    RAR-gamma-B
    Alternative name(s):
    Nuclear receptor subfamily 1 group B member 3-B
    Gene namesi
    Name:rargbImported
    Synonyms:nr1b3b
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Unplaced

    Organism-specific databases

    ZFINiZDB-GENE-070314-1. rargb.

    Subcellular locationi

    Nucleus PROSITE-ProRule annotation

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 489489Retinoic acid receptor gamma-BPRO_0000299171Add
    BLAST

    Expressioni

    Developmental stagei

    Expressed both maternally and zygotically. Expressed ubiquitously throughout gastrulation. At the tailbud stage, expressed at higher levels in the anterior and tailbud. Also expressed in migrating cranial neural crest cells.2 Publications

    Interactioni

    Subunit structurei

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

    Protein-protein interaction databases

    STRINGi7955.ENSDARP00000052545.

    Structurei

    3D structure databases

    ProteinModelPortaliA2T928.
    SMRiA2T928. Positions 59-137, 158-395.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi53 – 597Poly-ProSequence Analysis
    Compositional biasi141 – 1444Poly-LysSequence Analysis
    Compositional biasi342 – 3454Poly-Arg

    Sequence similaritiesi

    Belongs to the nuclear hormone receptor family. NR1 subfamily.Sequence Analysis
    Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri65 – 8521NR C4-typePROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri101 – 12020NR C4-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG297448.
    HOVERGENiHBG005606.
    PhylomeDBiA2T928.

    Family and domain databases

    Gene3Di1.10.565.10. 1 hit.
    3.30.50.10. 1 hit.
    InterProiIPR008946. Nucl_hormone_rcpt_ligand-bd.
    IPR000536. Nucl_hrmn_rcpt_lig-bd_core.
    IPR003078. Retinoic_acid_rcpt.
    IPR001723. Str_hrmn_rcpt.
    IPR001628. Znf_hrmn_rcpt.
    IPR013088. Znf_NHR/GATA.
    [Graphical view]
    PfamiPF00104. Hormone_recep. 1 hit.
    PF00105. zf-C4. 1 hit.
    [Graphical view]
    PRINTSiPR01292. RETNOICACIDR.
    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.

    A2T928-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRDVFREATP MTCRSPLPDL RDMMEKLTVF EPTIDSTVET QSTSSEEMIP    50
    SSPSPPPPPR VYKPCFVCQD KSSGYHYGVS SCEGCKGFFR RSIQKNMVYT 100
    CHRDKNCQIN KVTRNRCQYC RLRKCFEVGM SKEAVRNDRN KKKKDVKEEV 150
    VLPESYELSG ELEELVNKVS KAHRETFPSL CQLGKYTTNS SADHRVQLDL 200
    GLWDKFSELS TKCIIKIVEF AKRLPGFTSL TIADQITLLK SACLDILMLR 250
    ICTRYTPEQD TMTFSDGLTL NRTQMHNAGF GPLTDLVFAF AGQLLPLEMD 300
    DTETGLLSAI CLICGDRMDL EEPHRVDQLQ EPLLEALKIY ARRRRPNKPH 350
    MFPRMLMKVT DLRGISTKGA ERAITLKMEI PGPMPPLIRE MLENPEIFED 400
    SSDSNDSGAA AVVPAPNIKR MGQRQAAWVK GERPEWVRGR RRGSKSRYKA 450
    GFKAGKARSR DSPDNNGEIR QGDERSEMSV RAEQDFALE 489
    Length:489
    Mass (Da):55,571
    Last modified:March 6, 2007 - v1
    Checksum:iF181AE31C836F2C8
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    EF028131 mRNA. Translation: ABM89228.1.
    RefSeqiNP_001076779.1. NM_001083310.1.
    UniGeneiDr.135572.

    Genome annotation databases

    GeneIDi100034753.
    KEGGidre:100034753.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    EF028131 mRNA. Translation: ABM89228.1 .
    RefSeqi NP_001076779.1. NM_001083310.1.
    UniGenei Dr.135572.

    3D structure databases

    ProteinModelPortali A2T928.
    SMRi A2T928. Positions 59-137, 158-395.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 7955.ENSDARP00000052545.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 100034753.
    KEGGi dre:100034753.

    Organism-specific databases

    CTDi 100034753.
    ZFINi ZDB-GENE-070314-1. rargb.

    Phylogenomic databases

    eggNOGi NOG297448.
    HOVERGENi HBG005606.
    PhylomeDBi A2T928.

    Miscellaneous databases

    NextBioi 20788475.

    Family and domain databases

    Gene3Di 1.10.565.10. 1 hit.
    3.30.50.10. 1 hit.
    InterProi IPR008946. Nucl_hormone_rcpt_ligand-bd.
    IPR000536. Nucl_hrmn_rcpt_lig-bd_core.
    IPR003078. Retinoic_acid_rcpt.
    IPR001723. Str_hrmn_rcpt.
    IPR001628. Znf_hrmn_rcpt.
    IPR013088. Znf_NHR/GATA.
    [Graphical view ]
    Pfami PF00104. Hormone_recep. 1 hit.
    PF00105. zf-C4. 1 hit.
    [Graphical view ]
    PRINTSi PR01292. RETNOICACIDR.
    PR00398. STRDHORMONER.
    PR00047. STROIDFINGER.
    SMARTi SM00430. HOLI. 1 hit.
    SM00399. ZnF_C4. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48508. SSF48508. 1 hit.
    PROSITEi PS00031. NUCLEAR_REC_DBD_1. 1 hit.
    PS51030. NUCLEAR_REC_DBD_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "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: NUCLEOTIDE SEQUENCE [MRNA], DEVELOPMENTAL STAGE.
      Tissue: Embryo1 Publication.
    2. "Combinatorial roles for zebrafish retinoic acid receptors in the hindbrain, limbs and pharyngeal arches."
      Linville A., Radtke K., Waxman J.S., Yelon D., Schilling T.F.
      Dev. Biol. 325:60-70(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: DEVELOPMENTAL STAGE, INDUCTION, FUNCTION.

    Entry informationi

    Entry nameiRARGB_DANRE
    AccessioniPrimary (citable) accession number: A2T928
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 21, 2007
    Last sequence update: March 6, 2007
    Last modified: October 1, 2014
    This is version 48 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

    External Data

    Dasty 3