PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Itr_sc000505.1_g00006.1
Organism
Ipomoea trifida
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea
Family AP2
Protein Properties Length: 618aa    MW: 66857.4 Da    PI: 7.2206
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Itr_sc000505.1_g00006.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP233.51.1e-10225281155
                      AP2   1 sgykGVrwdkkrgrWvAeIrd.pseng..kr.krfslgkfgtaeeAakaaiaarkkleg 55 
                              s y+GV++++++gr++A+++d  +     ++ k  + g ++ +++Aa+a++ a++k++g
  Itr_sc000505.1_g00006.1 225 SIYRGVTRHRWTGRYEAHLWDnSCR-RegQSrKGRQ-GGYDKEDKAARAYDLAALKYWG 281
                              57*******************5444.2455535555.7799999*************98 PP
2AP246.97e-15326375355
                      AP2   3 ykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                              y+GV+++++ grW A+I  +     +k  +lg+f t+eeAa+a++ a+ k++g
  Itr_sc000505.1_g00006.1 326 YRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFSTEEEAAEAYDIAAIKFRG 375
                              9***************988532...5************************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF008473.2E-8225281IPR001471AP2/ERF domain
SuperFamilySSF541713.27E-14225291IPR016177DNA-binding domain
CDDcd000182.33E-18225291No hitNo description
SMARTSM003802.6E-22226295IPR001471AP2/ERF domain
PROSITE profilePS5103217.201226289IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.101.9E-11226290IPR001471AP2/ERF domain
PRINTSPR003673.0E-6227238IPR001471AP2/ERF domain
CDDcd000181.07E-23324385No hitNo description
SuperFamilySSF541716.34E-18324385IPR016177DNA-binding domain
SMARTSM003808.6E-33325389IPR001471AP2/ERF domain
PROSITE profilePS5103219.375325383IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.103.6E-18325384IPR001471AP2/ERF domain
PfamPF008471.7E-9326375IPR001471AP2/ERF domain
PRINTSPR003673.0E-6365385IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000723Biological Processtelomere maintenance
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007389Biological Processpattern specification process
GO:0010449Biological Processroot meristem growth
GO:0019827Biological Processstem cell population maintenance
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 618 aa     Download sequence    Send to blast
MGSMNSNNWL SFPLSPSQAA AQSHHFSVGL VNDSLDTSFQ NPEVMISPEP APVPPGANVG  60
GPQTVKRTER KTSLGARLGH YWPFAQHKWN LISTQGSNEV PKVADFLGVG KVDCNQPDLV  120
SYNDIQANEP DYLFSSNAGG LLPVQTGGVT VAAGAGGGFE LQENNACNMQ SLTLSMGTSG  180
KGSATTHASP SGNATASGSA ENSNTSIVEA ATPRRALDTF GQRTSIYRGV TRHRWTGRYE  240
AHLWDNSCRR EGQSRKGRQG GYDKEDKAAR AYDLAALKYW GTSTTTNFPI SNYEKELEEM  300
KHMTRQEFVA AIRRKSSGFS RGASMYRGVT RHHQHGRWQA RIGRVAGNKD LYLGTFSTEE  360
EAAEAYDIAA IKFRGLNAVT NFDMSRYDVK AILESNTLPI GGGAAKRLKE AQALESSRKR  420
DQEMLALNSS FHYSATTGPI HAAAAAAAYP LMQPFDAQPL LTLQNQDFSH HYAPQESPYT  480
YIQTHLQLHH QQQQHSPSYL NPSPQTSQYY NNNNNNNNNN PYLQSGNPGL LHGLMNMGGS  540
SSSVMDNNGG TSSGSYSGGG YLGNSTLGMA TNSNSGGGGD QELAVVKVDY DMPSGTYAGW  600
SNDSVQGSNP NIFSMWND
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00368DAPTransfer from AT3G20840Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin accumulation. {ECO:0000269|PubMed:15454085}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_019163643.10.0PREDICTED: AP2-like ethylene-responsive transcription factor PLT1
RefseqXP_019163644.10.0PREDICTED: AP2-like ethylene-responsive transcription factor PLT1
SwissprotQ5YGP80.0PLET1_ARATH; AP2-like ethylene-responsive transcription factor PLT1
TrEMBLA0A068VG920.0A0A068VG92_COFCA; Uncharacterized protein
STRINGEOY325840.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA22462457
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G20840.10.0AP2 family protein
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. García-Cruz KV, et al.
    The MADS-box XAANTAL1 increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell-cycle components.
    Ann. Bot., 2018.
    [PMID:27474508]
  13. 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]
  14. Franssen HJ,Kulikova O,Willemsen V,Heidstra R
    Cis-regulatory PLETHORA promoter elements directing root and nodule expression are conserved between Arabidopsis thaliana and Medicago truncatula.
    Plant Signal Behav, 2017. 12(2): p. e1278102
    [PMID:28067580]
  15. 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]
  16. 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]
  17. 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]
  18. Ercoli MF, et al.
    GIF Transcriptional Coregulators Control Root Meristem Homeostasis.
    Plant Cell, 2018. 30(2): p. 347-359
    [PMID:29352064]
  19. Xu C, et al.
    Control of auxin-induced callus formation by bZIP59-LBD complex in Arabidopsis regeneration.
    Nat Plants, 2018. 4(2): p. 108-115
    [PMID:29358751]