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.5KG538400.1.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: 1488aa    MW: 162414 Da    PI: 6.8056
Description HB-PHD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5KG538400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox29.71.1e-097688101052
                          HHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHH CS
             Homeobox  10 eqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrR 52 
                            ++ L  +Fe+++yps++++e LA++lgLt +qV  WF   R
  Pavir.5KG538400.1.p 768 IVTQKLRVHFEQDPYPSRATKENLAQELGLTFNQVCRWFSSTR 810
                          568999*********************************8776 PP
2Homeobox31.33.6e-1098410201349
                           HHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHH CS
             Homeobox   13 eeLeelFeknrypsaeereeLAkklgLterqVkvWFq 49  
                           + L+++Fek++yps++ +e LA++lgLt +qV+ WF 
  Pavir.5KG538400.1.p  984 QKLKAHFEKDPYPSRSIKESLAQELGLTFNQVSKWFS 1020
                           78**********************************7 PP
3PHD41.82.5e-14432486150
                          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.5KG538400.1.p 432 FCAICGSkdVTLQNDIILCDGaCDRGFHQNCLKPPLLTEDIPPGdeGWLCPACVC 486
                          7******64445********66********************9999*******87 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF579036.2E-16422489IPR011011Zinc finger, FYVE/PHD-type
Gene3DG3DSA:3.30.40.102.6E-14428487IPR013083Zinc finger, RING/FYVE/PHD-type
PROSITE profilePS5001611.163430487IPR019787Zinc finger, PHD-finger
CDDcd155049.85E-29432484No hitNo description
SMARTSM002496.5E-12432485IPR001965Zinc finger, PHD-type
PfamPF006281.5E-11432486IPR019787Zinc finger, PHD-finger
PROSITE patternPS013590433484IPR019786Zinc finger, PHD-type, conserved site
SMARTSM003894.4E-11759820IPR001356Homeobox domain
SuperFamilySSF466891.75E-10763816IPR009057Homeodomain-like
CDDcd000861.37E-10765814No hitNo description
PfamPF000464.5E-7769810IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.606.1E-11770822IPR009057Homeodomain-like
PROSITE profilePS5007112.341773816IPR001356Homeobox domain
SuperFamilySSF466894.71E-109661025IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.604.6E-119661019IPR009057Homeodomain-like
PROSITE profilePS5007112.6819691029IPR001356Homeobox domain
SMARTSM003892.0E-109711033IPR001356Homeobox domain
CDDcd000865.10E-119721027No hitNo description
PfamPF000461.1E-79841020IPR001356Homeobox domain
PROSITE patternPS00027010041027IPR017970Homeobox, 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: 1488 aa     Download sequence    Send to blast
MRRKGSEVSP NKRYPLRSAH SSGRVLRSAS TKDNKASSEP PNDSAAVQSA VRKRRNGSPS  60
VSPNNSVRVL RSAAKNKDDA CSEPLNDQTT AKPAANKRKN ASPSQVGSIT NTVRVLRSAL  120
KSKDEVCSGP ITNRTAGEPA ANKRKNVSPS KLRSPSNSVR VLRSALKYKE TYTEPLNDST  180
GVEPAANRRK IASSSKAGSP NNTVRVLRSA LKNKSEACSE PLNDSTVGQP TVKRRKTGSP  240
LKVASPVSSA RVLRSTSERK NEACSEPLND STTAQPAAGK RKGETLLNTD SPKVDVRVLR  300
SASGKKNEAC SEPVNDSTSA QKAVRKRKAC RPLNDRSPKK EYVKVCQRVR YILNRMNYQQ  360
SFIQAYASEG WKGQSLEKIR PEKELERAKE EILQCKLKIR EAFRNMDAIL SEGKLEESLF  420
DSAGEISSED IFCAICGSKD VTLQNDIILC DGACDRGFHQ NCLKPPLLTE DIPPGDEGWL  480
CPACVCKADS IYALNELQGS KLSIHDSWEK VFPEAASLAN GSKQVGSSDL PPDRIEDNDY  540
KPALAEGHMN QYRSSAEDDD KVDDLALPSE DSEDDDFDPA GPDSSEDQTN ELNSEESDFT  600
SDSDDFCAEI AKSCGQDEVS ASQLLDVINY TDRMKTRAVD NHSNEETSNR TFADMELDQG  660
MVLPILSRRK VERLDYKKLY DEAYGKESSG SSDDEEWSGK ELLEGSGTDS HGERLHPAKR  720
CSRRAPARQQ NNEHAPQREW LHGSESVQQT EVLRSNSSGS TGRQFGPIVT QKLRVHFEQD  780
PYPSRATKEN LAQELGLTFN QVCRWFSSTR HYSRVASAKK EKHPDNHTSE NNDSTNVDSM  840
QTREPSAGVM EKLTMDSSVI VPEEPMVQNN LNQCNKKDMP LSGTEIEMDS YGQESSDSSD  900
EEWSAFSTPR KARLQDKETA SPAESLHPAK RCSRRAPARG QNNEHTPQSE HRHGSASEQQ  960
TDVLCSNSSG SKASKYHFGP IVNQKLKAHF EKDPYPSRSI KESLAQELGL TFNQVSKWFS  1020
AIRHYSRGAA AKNKKHPGSN TTENDNSTTF DGIQIRETLV EKPSADLNDM ISEKLMVQIN  1080
LNEGIEEEDI PPSQYTRCEE RATMTPTTVS REVGPPGYGP GENFLQIGSR NTCEQNVITT  1140
PTPILRVDPP GYVRGENQGN DSPWNLSCEQ SMFMSSATIS REVGPPGYGP EQNQGNGVSW  1200
SMSCEQGVPM SSTAISREAG PPGYGSGENQ GSGTSWNTSC EQGMFTSPAI ISREVGSPGY  1260
GPGENQNNGT SWNMSNKNGV FMSPAAISKE VGPPGFGPGE NQGSGTSWNM RCEQRMYRTP  1320
TAISREVGPP GSGPGENQGN GGSWSISYEH GVFTSPTAIS REVGPPGYGP GENQGNITSL  1380
ITSSKQRMFT SPTTVSSEGG PPGYSIVENQ GTGGSRNIDL QQRVVATPAT IPKEVFPPGY  1440
GPGENQGSGA SGSVRIPEGR SAEKVGFSDE ARKKAIQREL RRRQKFR*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1321327KAVRKRK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.80890.0callus| 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.5KG538400.1.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
TrEMBLA0A2T8IK920.0A0A2T8IK92_9POAL; Uncharacterized protein
STRINGPavir.Eb03127.1.p0.0(Panicum virgatum)
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
AT3G19510.12e-94Homeodomain-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]