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 Glyma.12G056300.1.p
Common NameGLYMA_12G056300, LOC100788471
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja
Family AP2
Protein Properties Length: 554aa    MW: 61370.2 Da    PI: 6.6209
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Glyma.12G056300.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP2476.4e-15163222155
                  AP2   1 sgykGVrwdkkrgrWvAeIrd.pse.ng..kr.krfslgkfgtaeeAakaaiaarkkleg 55 
                          s y+GV++++++gr++A+++d  +   g  ++ ++++lg ++ +e+Aa+a++ a++k++g
  Glyma.12G056300.1.p 163 SIYRGVTRHRWTGRYEAHLWDnSCRrEGqsRKgRQVYLGGYDKEEKAARAYDLAALKYWG 222
                          57*******************666664477446*************************98 PP

2AP247.16.1e-15267316355
                  AP2   3 ykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                          y+GV+++++ grW A+I  +     +k  +lg+f t+eeAa+a++ a+ k++g
  Glyma.12G056300.1.p 267 YRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFSTEEEAAEAYDIAAIKFRG 316
                          9***************988532...5************************998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000181.10E-22163232No hitNo description
SuperFamilySSF541712.75E-17163232IPR016177DNA-binding domain
PfamPF008477.2E-12163222IPR001471AP2/ERF domain
PROSITE profilePS5103219.256164230IPR001471AP2/ERF domain
SMARTSM003805.8E-30164236IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.107.8E-16164231IPR001471AP2/ERF domain
PRINTSPR003672.4E-6165176IPR001471AP2/ERF domain
SuperFamilySSF541715.43E-18265326IPR016177DNA-binding domain
CDDcd000184.17E-24265326No hitNo description
PROSITE profilePS5103219.375266324IPR001471AP2/ERF domain
SMARTSM003808.6E-33266330IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.103.1E-18266325IPR001471AP2/ERF domain
PfamPF008471.5E-9267316IPR001471AP2/ERF domain
PRINTSPR003672.4E-6306326IPR001471AP2/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:0010073Biological Processmeristem maintenance
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: 554 aa     Download sequence    Send to blast
MNNNWLSFPL SPTHSSLPAH DLQATQYHQF SLGLVNENMD NPFQNHDWNL INTHSSNEIP  60
KVADFLGVSK SENQSDLAAL NEIHSNDSDY LFTNNSLVPM QNPVLDTPSN EYQENANSNL  120
QSLTLSMGSG KDSTCETSGE NSTNTTVEVA PRRTLDTFGQ RTSIYRGVTR HRWTGRYEAH  180
LWDNSCRREG QSRKGRQVYL GGYDKEEKAA RAYDLAALKY WGTSTTTNFP ISNYEKELDE  240
MKHMTRQEFV AAIRRKSSGF SRGASMYRGV TRHHQHGRWQ ARIGRVAGNK DLYLGTFSTE  300
EEAAEAYDIA AIKFRGLNAV TNFDMSRYDV KAILESNTLP IGGGAAKRLK EAQALESSRK  360
REEMIALGSS STFQYGTSAS SSRLHAYPLM QHHHQFEQPQ PLLTLQNHDI SSSHFSHQQD  420
PLHHQGYIQT QLQLHQQSGA SSYSFQNNAQ FYNGYLQNHP ALLQGMMNMG SSSSSSSVLE  480
NNNSNNNNNN VGGFVGSGFG MASNATAGNT VGTAEELGLV KVDYDMPAGG YGGWSAADSM  540
QTSNGGVFTM WND*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Gma.342690.0somatic embryo
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
PlantRegMapGlyma.12G056300.1.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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU6773810.0EU677381.1 Glycine max PLETHORA 2 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006592171.10.0AP2-like ethylene-responsive transcription factor PLT2 isoform X1
SwissprotQ5YGP70.0PLET2_ARATH; AP2-like ethylene-responsive transcription factor PLT2
TrEMBLI1LQI00.0I1LQI0_SOYBN; Uncharacterized protein
STRINGGLYMA12G06010.10.0(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF49423152
Representative plantOGRP11217209
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G51190.10.0AP2 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. 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]