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.6NG083100.1.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: 780aa    MW: 83987.8 Da    PI: 5.633
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6NG083100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox64.31.7e-20100156157
                          TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHHC CS
             Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakekk 57 
                          +++ +++t++q++e+e++F+++++p+ ++r+eL+++lgL+  qVk+WFqN+R+++k+
  Pavir.6NG083100.1.p 100 KKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKN 156
                          688999************************************************995 PP
2START191.63.9e-602975151206
                          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.6NG083100.1.p 297 ELAVAAMDELLRMARLDAPLWTTGAagAQLDEEEYGRMFPGGLGprqygLRPEASRDGAVVIMTRDSLVEILMDANRfaaVFSSIVSRAS 386
                          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.6NG083100.1.p 387 THEVLSTGvagsynGALQVMSMEFQVPSPLVPtRESYFARYCKNNPDGTWAVVDVSLDSLRPNP----VLKCRRRPSGCLIQEMPNGYSK 472
                          ***************************************************************9....7********************* PP

                          EEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
                START 164 vtwvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206
                          vtwvehv++++r++h+l+r+lv+sgla+gak+wv  l+rqce+
  Pavir.6NG083100.1.p 473 VTWVEHVEVDDRSVHNLYRPLVNSGLAFGAKRWVGSLDRQCER 515
                          *****************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.601.2E-2379141IPR009057Homeodomain-like
SuperFamilySSF466897.1E-2084157IPR009057Homeodomain-like
PROSITE profilePS5007117.02297157IPR001356Homeobox domain
SMARTSM003891.1E-1998161IPR001356Homeobox domain
CDDcd000861.46E-19100158No hitNo description
PfamPF000464.2E-18100155IPR001356Homeobox domain
PROSITE patternPS000270132155IPR017970Homeobox, conserved site
Gene3DG3DSA:1.10.10.608.9E-4142184IPR009057Homeodomain-like
CDDcd146860.00819153177No hitNo description
PROSITE profilePS5084838.693288518IPR002913START domain
SuperFamilySSF559617.69E-32289517No hitNo description
CDDcd088752.17E-116292514No hitNo description
SMARTSM002341.1E-53297515IPR002913START domain
PfamPF018527.4E-50298515IPR002913START domain
Gene3DG3DSA:3.30.530.201.1E-5389515IPR023393START-like domain
SuperFamilySSF559612.09E-24537770No 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: 780 aa     Download sequence    Send to blast
MTPARHMPAM IGRNGVAYGS SSALSLSQAD LLDSHQLQQE FQQQLFDQIP AGGVDSGDNI  60
IHGRSDTLAD EFESKSCSEN PDGTSGDDGQ EDPNQRPNKK KRYHRHTQHQ IQEMEAFFKE  120
CPHPDDKQRK ELSRELGLEP LQVKFWFQNK RTQMKNQHER QENAQLRAEN DKLRAENMRY  180
KEALSTASCP SCGGPAALGE MSFDEHHLRL ENARLRDEID RISGIAAKHV GKPMVSFPVL  240
SSPLAAAAAR SPLDVVGAFG SAGLGPDPLF GVGTGAGELL RSMSTGQLDA DKPMIVELAV  300
AAMDELLRMA RLDAPLWTTG AAGAQLDEEE YGRMFPGGLG PRQYGLRPEA SRDGAVVIMT  360
RDSLVEILMD ANRFAAVFSS IVSRASTHEV LSTGVAGSYN GALQVMSMEF QVPSPLVPTR  420
ESYFARYCKN NPDGTWAVVD VSLDSLRPNP VLKCRRRPSG CLIQEMPNGY SKVTWVEHVE  480
VDDRSVHNLY RPLVNSGLAF GAKRWVGSLD RQCERLASAM ASNIPNGDLG VITSIEGRKS  540
MLKLAERMVA SFCGGVTASA AHQWTTLSGS GAEDVRVMTR KSVDDPGRPP GIVLNAATSF  600
WLPVPPKRVF DFLRDETSRS EWDILSNGGA VQEMAHIANG RDHGNCVSLL RVNSANSNQS  660
NMLILQESCT DASGSYVVYA PVDVVAMNVV LNGGDPDYVA LLPSGFAILP DGPPGASPHG  720
EISAGLEAGG GSLLTVAFQI LVDSVPTAKL SLGSVATVNS LIACTVERIK AAVCAEGPQ*
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.6NG083100.1.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
TrEMBLA0A2S3I0P40.0A0A2S3I0P4_9POAL; Uncharacterized protein
STRINGPavir.J09537.1.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
AT4G21750.20.0HD-ZIP family protein
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]