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.J435100.1.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: 339aa    MW: 37230.7 Da    PI: 6.5134
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.J435100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox28.33e-092622952255
                        SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
           Homeobox  22 nrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                         +yps++e+  LA+ +gL+++q+ +WF N+R ++
  Pavir.J435100.1.p 262 WPYPSETEKLALAETTGLDQKQINNWFINQRKRH 295
                        69*****************************885 PP
2ELK439.5e-15215236122
                ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                        ELKhqLlrKY+gyLg+L+qEFs
  Pavir.J435100.1.p 215 ELKHQLLRKYGGYLGGLRQEFS 236
                        9********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012559.3E-2181125IPR005540KNOX1
PfamPF037901.5E-2182123IPR005540KNOX1
SMARTSM012562.0E-28133184IPR005541KNOX2
PfamPF037911.7E-23138183IPR005541KNOX2
PfamPF037893.6E-11215236IPR005539ELK domain
PROSITE profilePS5121311.575215235IPR005539ELK domain
SMARTSM011884.2E-8215236IPR005539ELK domain
PROSITE profilePS5007113.248235298IPR001356Homeobox domain
SuperFamilySSF466892.05E-19236307IPR009057Homeodomain-like
SMARTSM003892.6E-12237302IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.603.6E-27240302IPR009057Homeodomain-like
CDDcd000864.97E-12247298No hitNo description
PfamPF059201.4E-16255294IPR008422Homeobox KN domain
PROSITE patternPS000270273296IPR017970Homeobox, 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: 339 aa     Download sequence    Send to blast
MDGFRDLGGG GGSSASKASS FLQLPLAASS SAQGFPSPDG HHHSSRLALQ QLLADPSGSQ  60
SSHQMDGAAD LRREISPVDA ETIKAKIMSH PQYSALVAAY LDCRKVGAPP DVSDRLSAMA  120
AKLDAQPGPS RRRHEPARAD PELDQFMEAY CNMLVKYQEE LARPIQEAAE FFKSVERQLD  180
SITDSNNCEG AGSSEDEQQD TSCPEEIDPC AEDKELKHQL LRKYGGYLGG LRQEFSKRKK  240
KGKLPKEARQ KLLRWWELHC KWPYPSETEK LALAETTGLD QKQINNWFIN QRKRHWKPAS  300
EDMPFAMVEA AGGFHAPQQG AAAAAALYVA DGMYRLGS*
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the embryo at 4 days after pollination (DAP) in the ventral and basal part of the embryo including the initial of the shoot apical meristem (SAM). At 5 DAP, expressed at the ventral side of the embryo, but the expression within SAM is down-regulated. At 7 DAP, expression is restricted to the boundaries between the embryonic organs, between the scutellum and the coleoptile, the coleoptile and the second leaf primordium, the shoot apical meristem and the first leaf primordium, the first leaf primordium and the coleoptile, the coleoptile and the epiblast and at the tip of the epiblast, but not in the leaf primordia. {ECO:0000269|PubMed:10080693}.
UniprotDEVELOPMENTAL STAGE: Expressed in the embryo at 4 days after pollination (DAP) in the ventral and basal part of the embryo, including the initial of the shoot apical meristem (SAM). At 5 DAP, expressed at the ventral side of the embryo, but the expression within SAM is down-regulated. At 7 DAP, expression is restricted to the boundaries between the embryonic organs, between the scutellum and the coleoptile, the coleoptile and the second leaf primordium, the shoot apical meristem and the first leaf primordium, the first leaf primordium and the coleoptile, the coleoptile and the epiblast and at the tip of the epiblast, but not in the leaf primordia. {ECO:0000269|PubMed:10080693, ECO:0000269|PubMed:10095070, ECO:0000269|PubMed:9869405}.
UniprotTISSUE SPECIFICITY: Expressed in stems, rachis and inflorescence. {ECO:0000269|PubMed:9869405}.
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:9869405}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.J435100.1.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
GenBankEU9663730.0EU966373.1 Zea mays clone 293957 homeobox protein rough sheath 1 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025795146.10.0homeobox protein knotted-1-like 12 isoform X3
SwissprotO650341e-111KNOSC_ORYSI; Homeobox protein knotted-1-like 12
SwissprotO804161e-111KNOSC_ORYSJ; Homeobox protein knotted-1-like 12
TrEMBLA0A2T7C0H00.0A0A2T7C0H0_9POAL; Uncharacterized protein
STRINGPavir.J02443.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP40613873
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G08150.12e-84KNOTTED-like from Arabidopsis thaliana
Publications ? help Back to Top
  1. Sato Y, et al.
    Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants.
    EMBO J., 1999. 18(4): p. 992-1002
    [PMID:10022841]
  2. 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]
  3. Nagasaki H,Sakamoto T,Sato Y,Matsuoka M
    Functional analysis of the conserved domains of a rice KNOX homeodomain protein, OSH15.
    Plant Cell, 2001. 13(9): p. 2085-98
    [PMID:11549765]
  4. 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]
  5. 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]
  6. Yin H, et al.
    SUI-family genes encode phosphatidylserine synthases and regulate stem development in rice.
    Planta, 2013. 237(1): p. 15-27
    [PMID:22956125]