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.2NG030700.1.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: 341aa    MW: 37287.1 Da    PI: 6.524
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.2NG030700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox30.18.5e-102663012055
                          HHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
             Homeobox  20 eknrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                          +k +yps++e+  LA+++gL+++q+ +WF N+R ++
  Pavir.2NG030700.1.p 266 YKWPYPSETEKIALAESTGLDQKQINNWFINQRKRH 301
                          4679*****************************885 PP
2ELK37.93.8e-13221242122
                  ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                          ELK qLl+KYsgyL+sL+qEFs
  Pavir.2NG030700.1.p 221 ELKYQLLKKYSGYLSSLRQEFS 242
                          9********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012553.2E-2276120IPR005540KNOX1
PfamPF037903.7E-2278118IPR005540KNOX1
SMARTSM012561.7E-30123174IPR005541KNOX2
PfamPF037912.9E-24129172IPR005541KNOX2
SMARTSM011881.2E-7221242IPR005539ELK domain
PROSITE profilePS5121311.627221241IPR005539ELK domain
PfamPF037894.0E-10221242IPR005539ELK domain
PROSITE profilePS5007112.892241304IPR001356Homeobox domain
SuperFamilySSF466891.15E-19242315IPR009057Homeodomain-like
SMARTSM003894.4E-13243308IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.607.3E-28246305IPR009057Homeodomain-like
CDDcd000861.81E-12253305No hitNo description
PfamPF059209.4E-17261300IPR008422Homeobox KN domain
PROSITE patternPS000270279302IPR017970Homeobox, 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: 341 aa     Download sequence    Send to blast
MDQGFGNLGV GGSSSGGSNS ANAAASSSSF LQLPLPTAAA AGPAYYGTPL ALLHQAAGPS  60
PYGKHAAAEI SPAEAESIKA KIVAHPQYSA LLAAYLDCQK VGAPPDVLER LTAMAAKLDA  120
RPPRRHEPRD PELDQFMEAY CNMLVKYREE LTRPIDEAME FLKRVEAQLD SIAGAGAGSS  180
AARLSLADGK SEGVGSSEDD MDASGRENEP PEIDPRAEDK ELKYQLLKKY SGYLSSLRQE  240
FSKKKKKGKL PKEARQKLLH WWELHYKWPY PSETEKIALA ESTGLDQKQI NNWFINQRKR  300
HWKPSEDMPF VMMEGFHPQN AAALYLDGPF MADGMYRLGS *
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.2NG030700.1.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-177KNOSC_ORYSI; Homeobox protein knotted-1-like 12
SwissprotO804161e-177KNOSC_ORYSJ; Homeobox protein knotted-1-like 12
TrEMBLA0A368PV500.0A0A368PV50_SETIT; Uncharacterized protein
STRINGPavir.Ba03909.1.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
AT4G08150.17e-96KNOTTED-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]