PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os03g19900.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family AP2
Protein Properties Length: 491aa    MW: 52869.6 Da    PI: 7.3239
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g19900.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP249.98e-16294346156
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkklege 56 
                       s y+GV+++++ grW A+I  +     +k  +lg+f t+eeAa+a++ a++k++g+
  LOC_Os03g19900.1 294 SIYRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFATEEEAAEAYDVAALKFRGA 346
                       57****************988532...5*************************985 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003807.9E-8134265IPR001471AP2/ERF domain
PROSITE profilePS5103212.774134259IPR001471AP2/ERF domain
PRINTSPR003675.4E-6135146IPR001471AP2/ERF domain
SuperFamilySSF541719.81E-6231260IPR016177DNA-binding domain
Gene3DG3DSA:3.30.730.107.8E-7232260IPR001471AP2/ERF domain
PRINTSPR003675.4E-6241261IPR001471AP2/ERF domain
PfamPF008475.8E-11294345IPR001471AP2/ERF domain
CDDcd000188.52E-12294355No hitNo description
SuperFamilySSF541713.86E-18294354IPR016177DNA-binding domain
SMARTSM003801.4E-32295359IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.103.5E-19295353IPR001471AP2/ERF domain
PROSITE profilePS5103219.48295353IPR001471AP2/ERF 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
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 491 aa     Download sequence    Send to blast
MSPPTNGAIS LAFPPMGPLP ADALIYPFDG LSYDDFVLPV AAAPQHPLPV AVADPAPLLL  60
LPPPSSCTCN GASSGMGAVA PRTLALGATT DGSVMTPTSW GSDGGGGGSS SARAVRSPSP  120
VLPLVQGTGQ RTSCYRGVTR HRWTGRYEAH LWDNTCRREG QKRKGRQVTT PVELFLLSVL  180
VDWHLATNFC TLLDTLAELH SAVVPFFFLR KDYQWFHDSD TMTCCFFAFS GYDIEDKAAR  240
AYDLAALKYW GANATTNFPK ESYVKEIEEM QKMSKQELVA SLRRKSSGFS RGASIYRGVT  300
RHHQHGRWQA RIGRVAGNKD LYLGTFATEE EAAEAYDVAA LKFRGANAVT NFEPSRYNLE  360
AISQSDLPIS VSGRRHNSSS NSNNPAPEAG GQITLMSSPP ISQQSSSAPP YLIHNLLQFQ  420
PCGPPYAPPP PPPPPPPPPQ ALPLPGSYNF AEPVGFYWPY GDGEEQKVQL NSNMVGMASG  480
GFLHLANAAN *
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.563140.0callus
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1154526520.0
Expression AtlasQ10MD4-
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
PlantRegMapLOC_Os03g19900.1
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-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g19900
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1098390.0AK109839.1 Oryza sativa Japonica Group cDNA clone:002-148-D11, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015629274.10.0AP2-like ethylene-responsive transcription factor AIL7
SwissprotQ5YGP89e-87PLET1_ARATH; AP2-like ethylene-responsive transcription factor PLT1
TrEMBLQ10MD40.0Q10MD4_ORYSJ; AP2 domain containing protein
STRINGONIVA03G15980.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP135792631
Representative plantOGRP11217209
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G10510.35e-87AINTEGUMENTA-like 6
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]