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.9NG072500.1.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: 337aa    MW: 37242.9 Da    PI: 6.649
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9NG072500.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox28.62.4e-092582932055
                          HHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
             Homeobox  20 eknrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                          +k +yps++e+  LA+ +gL+++q+ +WF N+R ++
  Pavir.9NG072500.1.p 258 YKWPYPSETEKLALAETTGLDQKQINNWFINQRKRR 293
                          4679***************************99763 PP
2ELK439.4e-15213234122
                  ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                          ELKhqLlrKY+gyLg+L+qEFs
  Pavir.9NG072500.1.p 213 ELKHQLLRKYGGYLGGLRQEFS 234
                          9********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012553.3E-2180124IPR005540KNOX1
PfamPF037903.3E-2281122IPR005540KNOX1
SMARTSM012562.0E-27132183IPR005541KNOX2
PfamPF037914.4E-23137182IPR005541KNOX2
SMARTSM011884.2E-8213234IPR005539ELK domain
PROSITE profilePS5121311.575213233IPR005539ELK domain
PfamPF037893.6E-11213234IPR005539ELK domain
PROSITE profilePS5007112.957233296IPR001356Homeobox domain
SuperFamilySSF466898.55E-19234305IPR009057Homeodomain-like
SMARTSM003891.5E-10235300IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.602.8E-26238299IPR009057Homeodomain-like
CDDcd000863.16E-11245296No hitNo description
PfamPF059202.0E-16253292IPR008422Homeobox KN domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 337 aa     Download sequence    Send to blast
MDSFRDLGGG GGSSASKASF LQLPLPASSS AQGFPSPDGH HHISRLALQQ LLADPSGSQS  60
SHRMAGAVLQ REISPVDHAE TIKAKIMSHP QYSALVAAYL DCQKVGAPPD VSDRLSAMAA  120
KLDAQPGPSW RRHEPARADP ELDQFMEAYC NMLVKYQEEL ARPIHEAAEF FKSVERQLDS  180
ITDSNYCEGA GSSEDDQDAS CPEEIDPCAE DKELKHQLLR KYGGYLGGLR QEFSKRKKKG  240
KLPKEARQKL LHWWELHYKW PYPSETEKLA LAETTGLDQK QINNWFINQR KRRWKPTSED  300
MPFAMVEAAG GFHAPQGTAA AAAVLYMADG MYRLGS*
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, mainly expressed in the basal and central parts of the ventral side of the embryo, in cells just below the coleoptile, and corresponding to the epiblast and part of the shoot region. At the shoot apex differentiation stage, expressed in the shoot apical meristem (SAM) and the epiblast, but not in the region between the SAM and epiblast. Expressed also in the cells surrounding the ventral side of the root apical meristem. Expression pattern is maintained in subsequent stages after the second leaf primordium is formed. During inflorescence development, expressed only in the corpus of the rachis primordium, but not in the tunica layer (L1). After floral induction, expressed in both tunica and corpus, but not in floral organ primordia. Later in flower development, expression in the corpus of the floral meristem disappears. {ECO:0000269|PubMed:10488233}.
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}.
UniProtProbable transcription factor that may be involved in shoot formation during embryogenesis. {ECO:0000269|PubMed:10488233}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00671PBMTransfer from GRMZM2G135447Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9NG072500.1.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-113KNOSC_ORYSI; Homeobox protein knotted-1-like 12
SwissprotO804161e-113KNOSC_ORYSJ; Homeobox protein knotted-1-like 12
SwissprotQ10ED21e-113KNOS8_ORYSJ; Homeobox protein knotted-1-like 8
TrEMBLA0A2T7C0H00.0A0A2T7C0H0_9POAL; Uncharacterized protein
STRINGPavir.Ia00428.1.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
AT4G08150.11e-85KNOTTED-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. 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]
  6. 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]
  7. 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]