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.6KG093100.1.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 HD-ZIP
Protein Properties Length: 667aa    MW: 71517.3 Da    PI: 5.7036
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6KG093100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox49.95.5e-161431557
                         HHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS
             Homeobox 15 LeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57
                         +e++F+++++p+ ++r+eL+++lgL+  qVk+WFqN+R+++k+
  Pavir.6KG093100.1.p  1 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKN 43
                         799*************************************995 PP
2START195.72.1e-611844021206
                          HHHHHHHHHHHHHHHHC-TT-EEEE..EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGG...CT-TT-SEEE CS
                START   1 elaeeaaqelvkkalaeepgWvkss..esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddke...qWdetlakae 80 
                          ela +a++el+++a +++p+W++ +   +++++e+ + f+ + +      + ea+r+ +vv+m+   lve+l+d+++    ++  + +a+
  Pavir.6KG093100.1.p 184 ELAVAAMDELLRMARLDAPLWSTGAagAQLDEEEYGRMFPGGLGprqygLRPEASRDGAVVIMTRDSLVEILMDVNRfaaVFSSIVSRAS 273
                          57899**********************9***********6655599999999************************88888888888*** PP

                          EEEEECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEE CS
                START  81 tlevissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghsk 163
                          t+ev+s+g      galq+m++e+q++splvp R+++f+Ry++  ++g+w++vdvS+ds +++p    v +++++pSg+li++++ng+sk
  Pavir.6KG093100.1.p 274 THEVLSTGvagsynGALQVMSMEFQVPSPLVPtRESYFARYCKNNPDGTWAVVDVSLDSLRPNP----VLKCRRRPSGCLIQEMPNGYSK 359
                          ***************************************************************9....7********************* PP

                          EEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
                START 164 vtwvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206
                          vtwvehv++++r++h+l+r+lv+sgla+gak+wv tl+rqce+
  Pavir.6KG093100.1.p 360 VTWVEHVEVDDRSVHNLYRPLVNSGLAFGAKRWVGTLDRQCER 402
                          *****************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF000461.5E-13142IPR001356Homeobox domain
SMARTSM003894.5E-7148IPR001356Homeobox domain
PROSITE profilePS5007115.467144IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.601.7E-15151IPR009057Homeodomain-like
SuperFamilySSF466891.55E-13148IPR009057Homeodomain-like
CDDcd000866.69E-15145No hitNo description
PROSITE patternPS0002701942IPR017970Homeobox, conserved site
CDDcd146860.00684064No hitNo description
PROSITE profilePS5084838.84175405IPR002913START domain
SuperFamilySSF559614.23E-32176404No hitNo description
CDDcd088753.07E-118179401No hitNo description
SMARTSM002342.6E-56184402IPR002913START domain
PfamPF018522.1E-51185402IPR002913START domain
Gene3DG3DSA:3.30.530.201.7E-5277401IPR023393START-like domain
SuperFamilySSF559611.26E-24424656No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 667 aa     Download sequence    Send to blast
MEAFFKECPH PDDKQRKELS RELGLEPLQV KFWFQNKRTQ MKNQHERQEN AQLRAENDKL  60
RAENMRYKEA LSTASCPSCG GPAALGEMSF DEHHLRLENA RLRDEIDRIS GIAAKHVGKP  120
MVSFPVLSSP LAAAAARSPL DVVGAFGSAG LGPDPLFGVG TGAGELLRSV STGQLDADKP  180
MIVELAVAAM DELLRMARLD APLWSTGAAG AQLDEEEYGR MFPGGLGPRQ YGLRPEASRD  240
GAVVIMTRDS LVEILMDVNR FAAVFSSIVS RASTHEVLST GVAGSYNGAL QVMSMEFQVP  300
SPLVPTRESY FARYCKNNPD GTWAVVDVSL DSLRPNPVLK CRRRPSGCLI QEMPNGYSKV  360
TWVEHVEVDD RSVHNLYRPL VNSGLAFGAK RWVGTLDRQC ERLASAMASN IPNGDLGVIT  420
SIEGRKSMLK LAERMVASFC GGVTASAAHQ WTTLSGSGAE DVRVMTRKSV DDPGRPPGIV  480
LNAATSFWLP VPPKRVFDFL RDETSRSEWD ILSNGGAVQE MAHIANGRDH GNCVSLLRVN  540
SANSNQSNML ILQESCTDAS GSYVVYAPVD VVAMNVVLNG GDPDYVALLP SGFAILPDGP  600
PGAPNGEISA GLEAGGGSLL TVAFQILVDS VPTAKLSLGS VATVNSLIAC TVERIKAAVC  660
AEGNPQ*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.94400.0callus| leaf| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Specifically expressed in the L1-layer of the meristem and protoderm (epidermis) of leaf primordia. During leaf development, expressed in protoderm from plastochron 1 (P1) to P4 and down-regulated at P5 to then disappear. Expressed in the epidermis of primary rachis branch, and in the protoderm of secondary rachis branch primordia. Expressed similarly in L1-layer or protoderm in young and developed floral shoots. During embryogenesis, expressed in the outermost (epidermal) cells 2 days after pollination (DAP) and later at 4 DAP in protodermal cells without any organ differentiation. In nearly mature embryo, strongly expressed in protoderm in the shoot apical meristem (SAM) and lateral organ primordia. {ECO:0000269|PubMed:11846882}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that may be involved in protoderm differentiation and radial pattern formation during early embryogenesis. {ECO:0000269|PubMed:11846882}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.6KG093100.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ2509870.0AJ250987.1 Zea mays mRNA for OCL5 protein (ocl5 gene).
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025821536.10.0homeobox-leucine zipper protein ROC1-like
SwissprotQ6ZAR00.0ROC1_ORYSJ; Homeobox-leucine zipper protein ROC1
TrEMBLA0A2T7D4B80.0A0A2T7D4B8_9POAL; Uncharacterized protein
STRINGPavir.Fa02028.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP79938147
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G05230.40.0homeodomain GLABROUS 2
Publications ? help Back to Top
  1. Lee JH, et al.
    Characterization of Arabidopsis and rice DWD proteins and their roles as substrate receptors for CUL4-RING E3 ubiquitin ligases.
    Plant Cell, 2008. 20(1): p. 152-67
    [PMID:18223036]
  2. Yi J, et al.
    OsMPK6 plays a critical role in cell differentiation during early embryogenesis in Oryza sativa.
    J. Exp. Bot., 2016. 67(8): p. 2425-37
    [PMID:26912801]
  3. Dou M,Cheng S,Zhao B,Xuan Y,Shao M
    The Indeterminate Domain Protein ROC1 Regulates Chilling Tolerance via Activation of DREB1B/CBF1 in Rice.
    Int J Mol Sci, 2016. 17(3): p. 233
    [PMID:26927068]
  4. Chou IT,Gasser CS
    Characterization of the cyclophilin gene family of Arabidopsis thaliana and phylogenetic analysis of known cyclophilin proteins.
    Plant Mol. Biol., 1997. 35(6): p. 873-92
    [PMID:9426607]