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.3KG127100.1.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 TALE
Protein Properties Length: 305aa    MW: 32746.8 Da    PI: 5.0167
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG127100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox27.94.1e-092372702255
                          SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
             Homeobox  22 nrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                           +yp++e++ +LA+ +gL+ +q+ +WF N+R ++
  Pavir.3KG127100.1.p 237 WPYPTEEDKVRLAAVTGLDPKQINNWFINQRKRH 270
                          59*****************************885 PP
2ELK33.11.2e-11190211122
                  ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                          ELK++Ll+KYsg+L+ L++EF+
  Pavir.3KG127100.1.p 190 ELKEMLLKKYSGCLSRLRSEFL 211
                          9********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012551.7E-195296IPR005540KNOX1
PfamPF037904.0E-205493IPR005540KNOX1
SMARTSM012567.9E-25100151IPR005541KNOX2
PfamPF037912.3E-22104150IPR005541KNOX2
SMARTSM011881900109129IPR005539ELK domain
SMARTSM011883.6E-6190211IPR005539ELK domain
PROSITE profilePS5121310.423190210IPR005539ELK domain
PfamPF037891.4E-8190211IPR005539ELK domain
PROSITE profilePS5007112.552210273IPR001356Homeobox domain
SuperFamilySSF466891.24E-19212282IPR009057Homeodomain-like
SMARTSM003895.4E-14212277IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.603.8E-27215275IPR009057Homeodomain-like
CDDcd000861.23E-12222274No hitNo description
PfamPF059209.4E-17230269IPR008422Homeobox KN domain
PROSITE patternPS000270248271IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 305 aa     Download sequence    Send to blast
MEDLYSIHPG ISRAGGGGAA AAASEASGVA GGAGSPPPPP PQPSPPAADL TELVKAQIAG  60
HPRYPSLLSA YIECRKVGAP PEVATLLEEI GRERCAAAAA GGEVGLDPEL DEFMEAYCGV  120
LERYKEELSR PLDEAASFLS SIRTQLSTLC GGAASLSDEM VGSSEDEPCS GDTDATDLGQ  180
EHSSRMADRE LKEMLLKKYS GCLSRLRSEF LKKRKKGKLP KDARSALMDW WNTHYRWPYP  240
TEEDKVRLAA VTGLDPKQIN NWFINQRKRH WKPSEDMRFA LMEGVTGGGS SGTTLYFDTG  300
TIGP*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1205214LRSEFLKKRK
2211215KKRKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.168540.0root| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in globular stage embryo 3 days after pollination (DAP) in a small region just below the center of the ventral portion of the embryo. At coleoptile stages, expressed in the corresponding region of the epiblast and the central part of the embryo, but weakly in the shoot apical meristem (SAM). At the shoot apex differentiation stage, expressed in the cells surrounding the provascular tissue and radicle primordia. In nearly mature embryos (6 DAP), expressed around the basal part of the provascular tissue and radicle, and around the shoot region at the base of the first leaf primordium and the notch between the SAM and the second leaf primordium. Expressed uniformly in the inflorescence meristem, but after the transition from inflorescence to the floral phase, located specifically in the notches between the floral meristem and glume primordia. At later stages of flower development, uniformly expressed throughout the corpus of the meristem, and in the notches between glume primordia but less well defined than in the previous stage. {ECO:0000269|PubMed:10080693}.
UniprotDEVELOPMENTAL STAGE: Expressed in globular stage embryo 3 days after pollination (DAP) in a small region just below the center of the ventral portion of the embryo. At coleoptile stages, expressed in the corresponding region of the epiblast and the central part of the embryo, but weakly in the shoot apical meristem (SAM). At the shoot apex differentiation stage, expressed in the cells surrounding the provascular tissue and radicle primordia. In nearly mature embryos (6 DAP), expressed around the basal part of the provascular tissue and radicle, and around the shoot region at the base of the first leaf primordium, and the notch between the SAM and the second leaf primordium. Expressed uniformly in the inflorescence meristem, but after the transition from inflorescence to the floral phase, located specifically in the notches between the floral meristem and glume primordia. At later stages of flower development, uniformly expressed throughout the corpus of the meristem, and in the notches between glume primordia, but less well defined than in the previous stage. {ECO:0000269|PubMed:10080693, ECO:0000269|PubMed:10095070, ECO:0000269|PubMed:10488233}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that may be involved in shoot formation during embryogenesis. {ECO:0000269|PubMed:10080693}.
UniProtProbable transcription factor that may be involved in shoot formation during embryogenesis. {ECO:0000269|PubMed:10080693, ECO:0000269|PubMed:10488233}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.3KG127100.1.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
GenBankAF4571180.0AF457118.1 Zea mays knotted1-like homeodomain protein liguleless4a (lg4a) mRNA, complete cds.
GenBankBT0852520.0BT085252.1 Zea mays full-length cDNA clone ZM_BFb0343E20 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001105084.11e-178liguleless 4
SwissprotA2Y0071e-150KNOSA_ORYSI; Homeobox protein knotted-1-like 10
SwissprotQ7GDL51e-150KNOSA_ORYSJ; Homeobox protein knotted-1-like 10
TrEMBLA0A0A9BTH00.0A0A0A9BTH0_ARUDO; Uncharacterized protein
STRINGPavir.Ca00748.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP16983892
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G23380.14e-78KNOTTED1-like homeobox gene 6
Publications ? help Back to Top
  1. Ito Y,Eiguchi M,Kurata N
    KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice.
    Genesis, 2001. 30(4): p. 231-8
    [PMID:11536429]
  2. Postma-Haarsma AD, et al.
    Developmental regulation and downstream effects of the knox class homeobox genes Oskn2 and Oskn3 from rice.
    Plant Mol. Biol., 2002. 48(4): p. 423-41
    [PMID:11908517]
  3. 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]
  4. Kuijt SJ, et al.
    Different subcellular localization and trafficking properties of KNOX class 1 homeodomain proteins from rice.
    Plant Mol. Biol., 2004. 55(6): p. 781-96
    [PMID:15604716]
  5. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]
  6. Chu H, et al.
    A CLE-WOX signalling module regulates root meristem maintenance and vascular tissue development in rice.
    J. Exp. Bot., 2013. 64(17): p. 5359-69
    [PMID:24043854]
  7. Kuijt SJ, et al.
    Interaction between the GROWTH-REGULATING FACTOR and KNOTTED1-LIKE HOMEOBOX families of transcription factors.
    Plant Physiol., 2014. 164(4): p. 1952-66
    [PMID:24532604]
  8. Coudert Y, et al.
    Identification of CROWN ROOTLESS1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation.
    New Phytol., 2015. 206(1): p. 243-54
    [PMID:25442012]
  9. Xu Y, et al.
    OsARID3, an AT-rich Interaction Domain-containing protein, is required for shoot meristem development in rice.
    Plant J., 2015. 83(5): p. 806-17
    [PMID:26121094]
  10. Kir G, et al.
    RNA Interference Knockdown of BRASSINOSTEROID INSENSITIVE1 in Maize Reveals Novel Functions for Brassinosteroid Signaling in Controlling Plant Architecture.
    Plant Physiol., 2015. 169(1): p. 826-39
    [PMID:26162429]