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.2KG044000.1.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: 346aa    MW: 37742.6 Da    PI: 6.5238
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.2KG044000.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox308.7e-102713062055
                          HHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
             Homeobox  20 eknrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                          +k +yps++e+  LA+++gL+++q+ +WF N+R ++
  Pavir.2KG044000.1.p 271 YKWPYPSETEKIALAESTGLDQKQINNWFINQRKRH 306
                          4679*****************************885 PP
2ELK37.93.9e-13226247122
                  ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                          ELK qLl+KYsgyL+sL+qEFs
  Pavir.2KG044000.1.p 226 ELKYQLLKKYSGYLSSLRQEFS 247
                          9********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012554.6E-2281125IPR005540KNOX1
PfamPF037903.4E-2282123IPR005540KNOX1
SMARTSM012569.9E-31128179IPR005541KNOX2
PfamPF037912.9E-24134177IPR005541KNOX2
SMARTSM011881.2E-7226247IPR005539ELK domain
PROSITE profilePS5121311.627226246IPR005539ELK domain
PfamPF037894.1E-10226247IPR005539ELK domain
PROSITE profilePS5007112.892246309IPR001356Homeobox domain
SuperFamilySSF466891.2E-19247320IPR009057Homeodomain-like
SMARTSM003894.4E-13248313IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.607.5E-28251310IPR009057Homeodomain-like
CDDcd000867.78E-13258310No hitNo description
PfamPF059209.6E-17266305IPR008422Homeobox KN domain
PROSITE patternPS000270284307IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0001708Biological Processcell fate specification
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010051Biological Processxylem and phloem pattern formation
GO:0010089Biological Processxylem development
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 346 aa     Download sequence    Send to blast
MDQGFGNLGV GGGSSSGGSN SNPAKAVASS SFLQLPLSTA GPAYYGAPLA LLHQAAAGPS  60
SSSQPPYGKQ HAAEISPAEA DAIKAKIVAH PQYSALLAAY LDCQKVGAPP DVLERLTAMA  120
AKLDARPPGR HEPRDPELDQ FMEAYCNMLV KYREELTRPI DEAMEFLKRV EAQLDSIAGA  180
AGGSSAARLS LADGKSEGVG SSEDDMDASG RENEPPEIDP RAEDKELKYQ LLKKYSGYLS  240
SLRQEFSKKK KKGKLPKEAR QKLLHWWELH YKWPYPSETE KIALAESTGL DQKQINNWFI  300
NQRKRHWKPS EDMPFVMMEG FHPQNAAALY LDGPFMADGM YRLGS*
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.2KG044000.1.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
GenBankBT0333610.0BT033361.1 Zea mays full-length cDNA clone ZM_BFb0146E21 mRNA, complete cds.
GenBankKJ7275690.0KJ727569.1 Zea mays clone pUT5429 HB transcription factor (HB132) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004955415.10.0homeobox protein rough sheath 1
SwissprotO650341e-175KNOSC_ORYSI; Homeobox protein knotted-1-like 12
SwissprotO804161e-175KNOSC_ORYSJ; Homeobox protein knotted-1-like 12
TrEMBLA0A368PV500.0A0A368PV50_SETIT; Uncharacterized protein
STRINGPavir.Bb00225.1.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-104KNOTTED-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]