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.9KG419900.1.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 AP2
Protein Properties Length: 449aa    MW: 47751.2 Da    PI: 6.7245
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9KG419900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP244.44.1e-14170229155
                  AP2   1 sgykGVrwdkkrgrWvAeIrd.pse.ng..kr.krfslgkfgtaeeAakaaiaarkkleg 55 
                          s y+GV++++++gr++A+++d  +   g  ++ ++++lg ++ +++Aa+a++ a++k++g
  Pavir.9KG419900.1.p 170 SIYRGVTRHRWTGRYEAHLWDnTCRkEGqkRKgRQVYLGGYDKEDKAARAYDIAALKYWG 229
                          57*******************554454475337**********99*************98 PP
2AP251.23.2e-16272324156
                  AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkklege 56 
                          s y+GV+++++ grW A+I  +     +k  +lg+f t+eeAa+a++ a++k++ge
  Pavir.9KG419900.1.p 272 SIYRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFATEEEAAEAYDIAALKFRGE 324
                          57****************988532...5**************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000182.35E-20170237No hitNo description
PfamPF008479.5E-11170229IPR001471AP2/ERF domain
SuperFamilySSF541711.31E-16170238IPR016177DNA-binding domain
SMARTSM003801.9E-25171243IPR001471AP2/ERF domain
PROSITE profilePS5103219.085171237IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.109.3E-16171238IPR001471AP2/ERF domain
PRINTSPR003671.2E-6172183IPR001471AP2/ERF domain
CDDcd000183.10E-11272333No hitNo description
PfamPF008478.5E-11272324IPR001471AP2/ERF domain
SuperFamilySSF541713.47E-18272332IPR016177DNA-binding domain
SMARTSM003803.1E-33273337IPR001471AP2/ERF domain
PROSITE profilePS5103219.414273331IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.108.0E-19273331IPR001471AP2/ERF domain
PRINTSPR003671.2E-6313333IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 449 aa     Download sequence    Send to blast
MSPPTSGAIS LSYGPAMGAG GLQDPLLLPF DDGFTDEDLL GADATLLGGA AADQTLLLLP  60
LCPGANGCGG SGSASAEGFG AQAAPASRAV TIAVGAADAG SFSLAPQPAP APVSWGVAAD  120
AGSFSIAPQP APAPVSWEVA TADAADGGSP APAPPSPALP LAHNTGSRTS IYRGVTRHRW  180
TGRYEAHLWD NTCRKEGQKR KGRQVYLGGY DKEDKAARAY DIAALKYWGA SATTNFPREN  240
YIREIEDMQN MRRQDVVGSL RRNSSGFSRG ASIYRGVTRH HQHGRWQARI GRVAGNKDLY  300
LGTFATEEEA AEAYDIAALK FRGENAVTNF EPSRYNLREI AQRDIPILRR LDQKPAPKAQ  360
SQAALDAPPF SQSQQSSNSL PPYFLPNLHQ PLPLQPPLAQ PLPIYNYSSG FGEPSFYWPY  420
GNVEQKVQHE SKLELVDGLL QLANSAAN*
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Accumulates in the basal embryo region that gives rise to hypocotyl, root, and root stem cells. Expressed in the root meristem throughout embryo development. {ECO:0000269|PubMed:15454085, ECO:0000269|PubMed:20190735}.
UniprotTISSUE SPECIFICITY: Expressed in roots, seedlings, flowers, and siliques. Also detected at low levels in leaves. In roots, specifically detected in the distal root meristem, including the QC. This tissue specificity is regulated by auxin gradient and depends on PIN proteins. {ECO:0000269|PubMed:15454085, ECO:0000269|PubMed:15635403, ECO:0000269|PubMed:15988559, ECO:0000269|PubMed:16424342, ECO:0000269|PubMed:20190735}.
Functional Description ? help Back to Top
Source Description
UniProtProbably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). Master regulator of basal/root fate. Essential for root quiescent center (QC) and columella specification, stem cell activity, as well as for establishment of the stem cell niche during embryogenesis. Modulates the root polar auxin transport by regulating the distribution of PIN genes. Essential role in respecifying pattern and polarity in damaged roots. Direct target of the transcriptional corepressor TPL. Expression levels and patterns regulated post-transcriptionally by root meristem growth factors (RGFs). {ECO:0000250, ECO:0000269|PubMed:15454085, ECO:0000269|PubMed:15635403, ECO:0000269|PubMed:16424342, ECO:0000269|PubMed:20190735}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9KG419900.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin accumulation. {ECO:0000269|PubMed:15454085}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025792711.10.0AP2-like ethylene-responsive transcription factor AIL7
SwissprotQ5YGP71e-104PLET2_ARATH; AP2-like ethylene-responsive transcription factor PLT2
TrEMBLA0A2S3IR720.0A0A2S3IR72_9POAL; Uncharacterized protein
STRINGPavir.Ib00501.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP135792631
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G57390.15e-94AINTEGUMENTA-like 5
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Lee DK,Sieburth LE
    The bps signal: embryonic arrest from an auxin-independent mechanism in bypass triple mutants.
    Plant Signal Behav, 2012. 7(6): p. 698-700
    [PMID:22580686]
  3. Hong LW,Yan DW,Liu WC,Chen HG,Lu YT
    TIME FOR COFFEE controls root meristem size by changes in auxin accumulation in Arabidopsis.
    J. Exp. Bot., 2014. 65(1): p. 275-86
    [PMID:24277277]
  4. Tian H,Jia Y,Niu T,Yu Q,Ding Z
    The key players of the primary root growth and development also function in lateral roots in Arabidopsis.
    Plant Cell Rep., 2014. 33(5): p. 745-53
    [PMID:24504658]
  5. Zhao Q, et al.
    Sulfur nutrient availability regulates root elongation by affecting root indole-3-acetic acid levels and the stem cell niche.
    J Integr Plant Biol, 2014. 56(12): p. 1151-63
    [PMID:24831283]
  6. Huang JB, et al.
    ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis.
    Plant Cell, 2014. 26(9): p. 3501-18
    [PMID:25217509]
  7. Yang S, et al.
    The Arabidopsis SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA Targets Directly to PINs and Is Required for Root Stem Cell Niche Maintenance.
    Plant Cell, 2015. 27(6): p. 1670-80
    [PMID:25991732]
  8. Jia Y, et al.
    The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development.
    J. Exp. Bot., 2015. 66(15): p. 4631-42
    [PMID:25998905]
  9. Zhang M, et al.
    A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis.
    Plant J., 2015. 83(4): p. 582-99
    [PMID:26072661]
  10. Shinohara H,Mori A,Yasue N,Sumida K,Matsubayashi Y
    Identification of three LRR-RKs involved in perception of root meristem growth factor in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(14): p. 3897-902
    [PMID:27001831]
  11. Ou Y, et al.
    RGF1 INSENSITIVE 1 to 5, a group of LRR receptor-like kinases, are essential for the perception of root meristem growth factor 1 in Arabidopsis thaliana.
    Cell Res., 2016. 26(6): p. 686-98
    [PMID:27229312]
  12. Santuari L, et al.
    The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots.
    Plant Cell, 2016. 28(12): p. 2937-2951
    [PMID:27920338]
  13. Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z
    ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis .
    J Integr Plant Biol, 2017. 59(1): p. 30-43
    [PMID:28074634]
  14. Du Y,Scheres B
    PLETHORA transcription factors orchestrate de novo organ patterning during Arabidopsis lateral root outgrowth.
    Proc. Natl. Acad. Sci. U.S.A., 2017. 114(44): p. 11709-11714
    [PMID:29078398]
  15. Bustillo-Avendaño E, et al.
    Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis.
    Plant Physiol., 2018. 176(2): p. 1709-1727
    [PMID:29233938]