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Q9PVE4

- THB_DANRE

UniProt

Q9PVE4 - THB_DANRE

Protein

Thyroid hormone receptor beta

Gene

thrb

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 117 (01 Oct 2014)
      Sequence version 2 (25 Nov 2008)
      Previous versions | rss
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    Functioni

    Nuclear hormone receptor that can act as a repressor or activator of transcription. High affinity receptor for the thyroid gland hormone triiodothyronine (T3). Transactivating activity is ligand-dependent, and is repressed in the absence of T3.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei216 – 2161Thyroid hormoneBy similarity
    Binding sitei254 – 2541Thyroid hormoneBy similarity
    Binding sitei265 – 2651Thyroid hormone; via amide nitrogenBy similarity
    Binding sitei369 – 3691Thyroid hormoneBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi29 – 10678Nuclear receptorPROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri32 – 5221NR C4-typePROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri70 – 8920NR C4-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. protein binding Source: UniProtKB
    2. sequence-specific DNA binding Source: InterPro
    3. steroid hormone receptor activity Source: InterPro
    4. thyroid hormone binding Source: UniProtKB
    5. thyroid hormone receptor activity Source: UniProtKB
    6. zinc ion binding Source: InterPro

    GO - Biological processi

    1. intracellular receptor signaling pathway Source: GOC

    Keywords - Molecular functioni

    Receptor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Thyroid hormone receptor beta
    Short name:
    TR-beta
    Short name:
    TRb
    Alternative name(s):
    Nuclear receptor subfamily 1 group A member 2
    Thyroid hormone receptor beta-1
    Short name:
    TRbeta1
    Gene namesi
    Name:thrb
    Synonyms:nr1a2, trb
    ORF Names:si:ch211-264a6.2
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Chromosome 19

    Organism-specific databases

    ZFINiZDB-GENE-990415-268. thrb.

    Subcellular locationi

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 395395Thyroid hormone receptor betaPRO_0000053455Add
    BLAST

    Expressioni

    Tissue specificityi

    Widely expressed in a range of adult tissues including the brain, eye, fin, gill, intestine, liver, swim bladder and ovary. In the eye, expressed in the outer nuclear layer of the retina.2 Publications

    Developmental stagei

    Expressed both maternally and zygotically. Expressed at the 1 cell stage (0 hpf) but disappears by the 2 cell stage. Expressed again from the 16 cell stage onwards. Embryonic expression increases dramatically around the hatching period. High expression then continues until 6 dpf, before declining.3 Publications

    Inductioni

    By triiodothyronine (T3) and L-thyroxine (T4).2 Publications

    Gene expression databases

    BgeeiQ9PVE4.

    Interactioni

    Subunit structurei

    Interacts (via the ligand-binding domain) with ncoa2.1 Publication

    Structurei

    3D structure databases

    ProteinModelPortaliQ9PVE4.
    SMRiQ9PVE4. Positions 29-117, 136-394.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 3131ModulatingSequence AnalysisAdd
    BLAST
    Regioni149 – 395247Ligand-bindingAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi121 – 1266Poly-Arg

    Domaini

    Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.

    Sequence similaritiesi

    Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri32 – 5221NR C4-typePROSITE-ProRule annotationAdd
    BLAST
    Zinc fingeri70 – 8920NR C4-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG272726.
    GeneTreeiENSGT00740000114969.
    HOGENOMiHOG000010313.
    HOVERGENiHBG005606.
    KOiK08362.
    OMAiLYEVHPA.
    OrthoDBiEOG7TBC2V.
    PhylomeDBiQ9PVE4.

    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.
    IPR001723. Str_hrmn_rcpt.
    IPR001728. ThyrH_rcpt.
    IPR001628. Znf_hrmn_rcpt.
    IPR013088. Znf_NHR/GATA.
    [Graphical view]
    PfamiPF00104. Hormone_recep. 1 hit.
    PF00105. zf-C4. 1 hit.
    [Graphical view]
    PRINTSiPR00398. STRDHORMONER.
    PR00047. STROIDFINGER.
    PR00546. THYROIDHORMR.
    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]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9PVE4-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MSEQADKCNS RWKDEAMQNG YIPSYLDKDE LCVVCGDKAT GYHYRCITCE    50
    GCKGFFRRTI QKNLNPTYAC KYEGKCVIDK VTRNQCQECR FKKCIAVGMA 100
    TDLVLDDSKR LAKRKLIEEN RERRRREELQ KTVWDRPEPT QEEWEMIRVV 150
    TEAHMATNAQ GNHWKQKRKF LSAVGVKEAK PEDIGSAPIV NAPEGNKVDI 200
    EAFSQFTKII TPAITRVVDF AKKLPMFCEL PCEDQIILLK GCCMEIMSLR 250
    AAVRYDPESD TLTLNGEMAV TRGQLKNGGL GVVSDAIFDL GVSLSSFNLD 300
    DSEVALLQAV ILLSSDRPGL TSVERIERCQ EEFLLAFEHY INYRKHKVAH 350
    FWPKLLMKVT DLRMIGACHA SRFLHMKVEC PTELFPPLFL EVFED 395
    Length:395
    Mass (Da):45,155
    Last modified:November 25, 2008 - v2
    Checksum:i1E18666BCCACFE8A
    GO
    Isoform 2 (identifier: Q9PVE4-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         172-180: Missing.

    Show »
    Length:386
    Mass (Da):44,285
    Checksum:iAAFA044D31425D92
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti95 – 962IA → NP in AAB68764. (PubMed:9192646)Curated
    Sequence conflicti347 – 3471K → Q in AAL06722. (PubMed:11174854)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei172 – 1809Missing in isoform 2. 2 PublicationsVSP_035801

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF109732 mRNA. Translation: AAF14239.1.
    BX927163, CR382334 Genomic DNA. Translation: CAN87984.1.
    CR382334, BX927163 Genomic DNA. Translation: CAM56478.2.
    BC163106 mRNA. Translation: AAI63106.1.
    BC163114 mRNA. Translation: AAI63114.1.
    U93487 Genomic DNA. Translation: AAB68764.1.
    AF302242 mRNA. Translation: AAL06722.1.
    RefSeqiNP_571415.1. NM_131340.1. [Q9PVE4-2]
    XP_005159560.1. XM_005159503.1. [Q9PVE4-2]
    XP_005159561.1. XM_005159504.1. [Q9PVE4-2]
    UniGeneiDr.80868.

    Genome annotation databases

    EnsembliENSDART00000151766; ENSDARP00000126275; ENSDARG00000021163. [Q9PVE4-1]
    GeneIDi30607.
    KEGGidre:30607.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF109732 mRNA. Translation: AAF14239.1 .
    BX927163 , CR382334 Genomic DNA. Translation: CAN87984.1 .
    CR382334 , BX927163 Genomic DNA. Translation: CAM56478.2 .
    BC163106 mRNA. Translation: AAI63106.1 .
    BC163114 mRNA. Translation: AAI63114.1 .
    U93487 Genomic DNA. Translation: AAB68764.1 .
    AF302242 mRNA. Translation: AAL06722.1 .
    RefSeqi NP_571415.1. NM_131340.1. [Q9PVE4-2 ]
    XP_005159560.1. XM_005159503.1. [Q9PVE4-2 ]
    XP_005159561.1. XM_005159504.1. [Q9PVE4-2 ]
    UniGenei Dr.80868.

    3D structure databases

    ProteinModelPortali Q9PVE4.
    SMRi Q9PVE4. Positions 29-117, 136-394.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSDART00000151766 ; ENSDARP00000126275 ; ENSDARG00000021163 . [Q9PVE4-1 ]
    GeneIDi 30607.
    KEGGi dre:30607.

    Organism-specific databases

    CTDi 7068.
    ZFINi ZDB-GENE-990415-268. thrb.

    Phylogenomic databases

    eggNOGi NOG272726.
    GeneTreei ENSGT00740000114969.
    HOGENOMi HOG000010313.
    HOVERGENi HBG005606.
    KOi K08362.
    OMAi LYEVHPA.
    OrthoDBi EOG7TBC2V.
    PhylomeDBi Q9PVE4.

    Miscellaneous databases

    NextBioi 20806972.
    PROi Q9PVE4.

    Gene expression databases

    Bgeei Q9PVE4.

    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.
    IPR001723. Str_hrmn_rcpt.
    IPR001728. ThyrH_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 PR00398. STRDHORMONER.
    PR00047. STROIDFINGER.
    PR00546. THYROIDHORMR.
    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. "Temporal expression and T3 induction of thyroid hormone receptors alpha1 and beta1 during early embryonic and larval development in zebrafish, Danio rerio."
      Liu Y.-W., Lo L.-J., Chan W.-K.
      Mol. Cell. Endocrinol. 159:187-195(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION.
    2. "The zebrafish reference genome sequence and its relationship to the human genome."
      Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
      , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
      Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Tuebingen.
    3. NIH - Zebrafish Gene Collection (ZGC) project
      Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 56-97.
    5. "Molecular cloning and characterization of thyroid hormone receptors in teleost fish."
      Marchand O., Safi R., Escriva H., Van Rompaey E., Prunet P., Laudet V.
      J. Mol. Endocrinol. 26:51-65(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 70-347 (ISOFORM 1).
    6. Cited for: REVIEW.
    7. "Thyroid hormones are important for embryonic to larval transitory phase in zebrafish."
      Liu Y.-W., Chan W.-K.
      Differentiation 70:36-45(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: DEVELOPMENTAL STAGE, INDUCTION.
    8. "Cloning, genomic organization, and expression analysis of zebrafish nuclear receptor coactivator, TIF2."
      Tan J.-H., Quek S.-I., Chan W.-K.
      Zebrafish 2:33-46(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH NCOA2.
    9. "The effect of 3,5,3'-triiodothyronine supplementation on zebrafish (Danio rerio) embryonic development and expression of iodothyronine deiodinases and thyroid hormone receptors."
      Walpita C.N., Van der Geyten S., Rurangwa E., Darras V.M.
      Gen. Comp. Endocrinol. 152:206-214(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: DEVELOPMENTAL STAGE.
    10. "Unexpected novel relational links uncovered by extensive developmental profiling of nuclear receptor expression."
      Bertrand S., Thisse B., Tavares R., Sachs L., Chaumot A., Bardet P.-L., Escriva H., Duffraisse M., Marchand O., Safi R., Thisse C., Laudet V.
      PLoS Genet. 3:E188-E188(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY.

    Entry informationi

    Entry nameiTHB_DANRE
    AccessioniPrimary (citable) accession number: Q9PVE4
    Secondary accession number(s): A3QJW1
    , B3DIF2, O42560, Q90Y31
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 27, 2001
    Last sequence update: November 25, 2008
    Last modified: October 1, 2014
    This is version 117 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Caution

    In contrast to PubMed:10687864 and PubMed:11963654, PubMed:17418841 found that triiodothyronine (T3) did not induce expression in the embryo.Curated

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3