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 Pavir.5NG495200.3.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family HB-PHD
Protein Properties Length: 1138aa    MW: 124394 Da    PI: 4.7667
Description HB-PHD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5NG495200.3.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox29.99.4e-10361405852
                          -HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHH CS
             Homeobox   8 tkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrR 52 
                           +  ++ L+ +F +++yps++++e LA++lgLt +qV  WF   R
  Pavir.5NG495200.3.p 361 GPIVTQKLKVHFDEDPYPSRATKENLAQELGLTFNQVCRWFSSTR 405
                          5667899**********************************8776 PP
2Homeobox33.29.2e-115796151349
                          HHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHH CS
             Homeobox  13 eeLeelFeknrypsaeereeLAkklgLterqVkvWFq 49 
                          + L+++Fek++yps++++e LA++lgLt +qV+ WF 
  Pavir.5NG495200.3.p 579 QKLKAHFEKDPYPSRSTKESLAQELGLTFNQVTKWFS 615
                          78**********************************7 PP
3PHD42.21.8e-142781150
                         SBTTTSS..TCTTSSEEEBSS.SSSEEETTTSTSSSSHHSHHSS..TBSSHHHHT CS
                  PHD  1 rCkvCgk..sdeegelvlCdg.CkewfHlkClglkleseekpeg..ewlCeeCke 50
                         +C++Cg+   + +++++lCdg C++ fH++Cl+++l +e++p g   wlC+ C +
  Pavir.5NG495200.3.p 27 FCAICGSkdVTLQNDIILCDGaCDRGFHQNCLKPPLLTEDIPPGdeGWLCPACVC 81
                         7******64445********66********************9999*******87 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF579039.75E-161784IPR011011Zinc finger, FYVE/PHD-type
Gene3DG3DSA:3.30.40.101.3E-142382IPR013083Zinc finger, RING/FYVE/PHD-type
PROSITE profilePS5001611.1632582IPR019787Zinc finger, PHD-finger
PfamPF006281.1E-112781IPR019787Zinc finger, PHD-finger
SMARTSM002496.5E-122780IPR001965Zinc finger, PHD-type
CDDcd155046.36E-292779No hitNo description
PROSITE patternPS0135902879IPR019786Zinc finger, PHD-type, conserved site
SMARTSM003892.1E-10354415IPR001356Homeobox domain
SuperFamilySSF466891.88E-10357410IPR009057Homeodomain-like
CDDcd000863.26E-11358409No hitNo description
PfamPF000463.5E-7362405IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.606.5E-11365418IPR009057Homeodomain-like
PROSITE profilePS5007112.276368411IPR001356Homeobox domain
SuperFamilySSF466891.67E-10561620IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.603.3E-11561614IPR009057Homeodomain-like
PROSITE profilePS5007112.779564624IPR001356Homeobox domain
SMARTSM003892.7E-11566628IPR001356Homeobox domain
CDDcd000864.84E-12570622No hitNo description
PfamPF000463.2E-8579615IPR001356Homeobox domain
PROSITE patternPS000270599622IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005515Molecular Functionprotein binding
GO:0008270Molecular Functionzinc ion binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 1138 aa     Download sequence    Send to blast
MDAILSEGKL EESLFDSAGE IFSEDIFCAI CGSKDVTLQN DIILCDGACD RGFHQNCLKP  60
PLLTEDIPPG DEGWLCPACV CKANSIDALN ELQGSKLSIH DSWEKVFPEA ASLANGSKQV  120
GSSDLPPDRI DHNDYNPALA EGHMNQDKFS AGDDDKVDDL GLPSEDSEDD DFDPAGPDSS  180
EDQKNELNSE ESDFTSDSDY FCAEIAKSCG QDEVLASPLL DVINHTDRMK TRAVDTHSNE  240
ETSNRTFADM ELDQGMVLPI LSRRQVQRLD YKKLYDEAYG KESSGSSDDE EWSGKELLES  300
SGTDSHGEQL HPEKRCSRRA PARQQNNEHT PQRERLHGSE SVQQTEVLRS NGSSSTGRKF  360
GPIVTQKLKV HFDEDPYPSR ATKENLAQEL GLTFNQVCRW FSSTRHYSRV ASAKKEKHLD  420
NHTSENNDST NVDSMQMREP SAGVMEKLTV DRNAIVPEKP MVQNNLNQCN KKDMPLSGTE  480
IEMDSYGQES SDSSDEEWSA FSTPRKARLH DNETASPAES LHPAKRCSRR APARGQNNEH  540
TPQSEQRHGS ASEQQTDVLC SNSSGSKVSK YHFGPIVNQK LKAHFEKDPY PSRSTKESLA  600
QELGLTFNQV TKWFSAIRHY SRGAAAKNKK HPGKNTTVND NRTTFDGVQI REGSVEKPSA  660
DINDIISEKL MVQINLNEGI EEDIPPSQYA RCEERATMTP TTISREVGPP GYGPGENFLQ  720
IGSRNTCEQN VITTPTPILR VDPPGYVRGE NQGNGAPWNS SCEQNMFMSS ATISREVGPP  780
GYGPEQNQGN GISWSMSCEQ GVSMSYTTIS REAGPPGYGS GENQGSGTSW NTSCERGMFT  840
SPAIISREVG PPGYGPGENQ GNSTSPNTSC ELRMFTSPMA ISREVSLPGC EPGENQNNGT  900
SWNMSYKKGV FMSPTASREV GPPGFGPGEN QSSGTSWNMR CEQRMYRSPT AISTEVGPPG  960
YGGENQGNGG SWSMSYEHGV FASPTAISRE VGPPGYGPGE NQGNTTTWIT SGKQRMFTSP  1020
TTVSSEGGLP GYSIVENHGT GGSRNIDLEQ RVVATPATIS REVFPPGYDL EQRVVATPAT  1080
ISKEVFPPEY GPGENQGSGA SGSVRIPEGR SAEKFGFSDE ARKKAIQREL RRRQKFR*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.80891e-137callus| leaf| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the outer layers of globular embryos. {ECO:0000269|PubMed:15094187}.
UniprotTISSUE SPECIFICITY: Expressed in roots, leaves, stems, panicle and seeds. {ECO:0000269|PubMed:21951842}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.5NG495200.3.p
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025814926.10.0uncharacterized protein LOC112892070 isoform X2
SwissprotQ8H9910.0HAZ1_ORYSJ; Homeobox protein HAZ1
TrEMBLA0A2T7DGV40.0A0A2T7DGV4_9POAL; Uncharacterized protein
STRINGPavir.Eb03127.1.p0.0(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G19510.12e-62Homeodomain-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]