PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID ONIVA06G09490.1
Organism
Oryza nivara
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
Family HB-PHD
Protein Properties Length: 792aa    MW: 87264.3 Da    PI: 4.9016
Description HB-PHD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA06G09490.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox35.32e-116226621252
                      HHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHH CS
         Homeobox  12 leeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrR 52 
                       + L+++F++++yps++++e LA++lgLt +qV+ WF   R
  ONIVA06G09490.1 622 NQKLKAHFKEDPYPSRATKENLAQELGLTFNQVTKWFSSTR 662
                      589**********************************8776 PP
2PHD42.81.2e-14246301151
                      SBTTTSS..TCTTSSEEEBSS.SSSEEETTTSTSSSSHHSHHSS..TBSSHHHHTT CS
              PHD   1 rCkvCgk..sdeegelvlCdg.CkewfHlkClglkleseekpeg..ewlCeeCkek 51 
                      +C++Cg+   + +++++lCdg C++ fH++Cl+++l  e++p+g   wlC+ C++k
  ONIVA06G09490.1 246 FCAACGSkdVTLKNDIILCDGiCDRGFHQYCLNPPLLAEDIPQGdeGWLCPACDCK 301
                      7******64445********88*********************999*******985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF579031.37E-14236304IPR011011Zinc finger, FYVE/PHD-type
Gene3DG3DSA:3.30.40.109.3E-14242300IPR013083Zinc finger, RING/FYVE/PHD-type
PROSITE profilePS5001610.941244301IPR019787Zinc finger, PHD-finger
SMARTSM002492.4E-10246299IPR001965Zinc finger, PHD-type
PfamPF006286.5E-12246301IPR019787Zinc finger, PHD-finger
CDDcd155043.38E-26246298No hitNo description
PROSITE patternPS013590247298IPR019786Zinc finger, PHD-type, conserved site
PROSITE profilePS5007113.183608668IPR001356Homeobox domain
SMARTSM003897.1E-12611672IPR001356Homeobox domain
CDDcd000862.12E-12613666No hitNo description
SuperFamilySSF466892.01E-11613675IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.603.3E-12622677IPR009057Homeodomain-like
PfamPF000466.7E-9622662IPR001356Homeobox domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005515Molecular Functionprotein binding
GO:0008270Molecular Functionzinc ion binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 792 aa     Download sequence    Send to blast
MDKTTTSDLV LDNDNIGSNA GSAQEPLTTN GKTSGVRNRY KQTVKRGRKG SQISPSKTYP  60
LRSSHSNVRV LRSASKKKNE TPIVPTNDNT AVQRVAKKRK RSKPLRPAPS RVLRSTSEKK  120
NKAHNELLND GAGVQPAEKK RKVGRPPKGG TPKDDYLMIR KRVRYVLNRM NYEQSLIQAY  180
ASEGWKGQSL EKIRPEKELE RAKVEILRCK SRIREAFRNL DSLLSEGKLD ESMFDSAGEI  240
SSEDIFCAAC GSKDVTLKND IILCDGICDR GFHQYCLNPP LLAEDIPQGD EGWLCPACDC  300
KIDCIDVLNE LQGVKLSIHD SWEKVFPEAA SFLNGSKQID ASDLPSDDSA DNDYDPTLAQ  360
GHKVDEEKSS GEDGGEGLDS DDSSSEDSES SEKEKSKTSQ NGRTVDDLGL PSEDSEDGDF  420
DPAGPDSDKE QNDESNSDQS DESDFTSDSD DFCAEIAKSC GQDEISGPSS SQIRTVNRTD  480
GSSFDGEPNA ENSNLAFMET ELEQDMVVPI SSKRQVERLD YKKLYNEAYG KASSDSSDDE  540
EWYGNSTPEK GNLEDSETDS LAESPQGGKG FSRRAPVRYH NNEHTPQNVS PGGSVSDQQT  600
EVLCSNSNGS TAKNRHFGPA INQKLKAHFK EDPYPSRATK ENLAQELGLT FNQVTKWFSS  660
TRHYARVAAT KKENNIENHT AENNNNTNTV DSIQLRGSND IVSVDRNDMV SEERTGQSNL  720
NEGTPLRSDT SCGLSVAVTP MVHPENQGND SSSNVRTPNA KNAEKLIPGL ENSDEARRKA  780
VQRELRKMKT GR
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
196101KKRKRS
296103KKRKRSKP
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor involved in the regulation of gibberrelin (GA) signaling. Binds to the 5'-GATC-3' motif of HD16/EL1 promoter. Functions as a positive regulator of GA signaling by suppressing the expression of HD16/EL1, a negative regulator of GA signaling. {ECO:0000269|PubMed:21951842}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by gibberellin. {ECO:0000269|PubMed:21951842}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0813400.0AB081340.1 Oryza sativa Japonica Group HAZ1 mRNA for PHD-finger family homeodomain protein, complete cds.
GenBankAK1213140.0AK121314.1 Oryza sativa Japonica Group cDNA clone:J023113A13, full insert sequence.
GenBankFJ9401970.0FJ940197.1 Oryza sativa Japonica Group clone KCS150D11 PHD-finger family homeodomain protein mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015644127.10.0homeobox protein HAZ1 isoform X1
SwissprotQ8H9910.0HAZ1_ORYSJ; Homeobox protein HAZ1
TrEMBLA0A0E0HN040.0A0A0E0HN04_ORYNI; Uncharacterized protein
STRINGONIVA06G09490.20.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP43933768
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G19510.14e-87Homeodomain-like protein with RING/FYVE/PHD-type zinc finger domain
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Wen BQ,Xing MQ,Zhang H,Dai C,Xue HW
    Rice homeobox transcription factor HOX1a positively regulates gibberellin responses by directly suppressing EL1.
    J Integr Plant Biol, 2011. 53(11): p. 869-78
    [PMID:21951842]