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 Gorai.006G129400.1
Common NameB456_006G129400
Organism
Gossypium raimondii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family AP2
Protein Properties Length: 521aa    MW: 58012.7 Da    PI: 7.0589
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.006G129400.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP235.72.2e-11164220155
                 AP2   1 sgykGVrwdkkrgrWvAeIrd.pseng..kr.krfslgkfgtaeeAakaaiaarkkleg 55 
                         s y+GV++++++gr++A+++d  +     ++ k  + g ++ +e+Aa+a++ a++k++g
  Gorai.006G129400.1 164 SIYRGVTRHRWTGRYEAHLWDnSCR-RegQSrKGRQ-GGYDKEEKAARAYDLAALKYWG 220
                         57*******************5444.2455536655.779999**************98 PP
2AP242.81.3e-13265314355
                 AP2   3 ykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                         y+GV+++++ grW A+I  +     +k  +lg+f  +eeAa+a++ a+ k++g
  Gorai.006G129400.1 265 YRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFSAEEEAAEAYDIAAIKFRG 314
                         9***************988532...5************************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000186.92E-20164230No hitNo description
PfamPF008478.5E-9164220IPR001471AP2/ERF domain
SuperFamilySSF541717.19E-15164230IPR016177DNA-binding domain
Gene3DG3DSA:3.30.730.103.1E-12165229IPR001471AP2/ERF domain
PROSITE profilePS5103217.504165228IPR001471AP2/ERF domain
SMARTSM003803.2E-23165234IPR001471AP2/ERF domain
PRINTSPR003673.3E-6166177IPR001471AP2/ERF domain
CDDcd000188.09E-17263322No hitNo description
SuperFamilySSF541714.38E-17263323IPR016177DNA-binding domain
Gene3DG3DSA:3.30.730.103.4E-17264322IPR001471AP2/ERF domain
SMARTSM003802.4E-31264328IPR001471AP2/ERF domain
PROSITE profilePS5103218.874264322IPR001471AP2/ERF domain
PfamPF008472.4E-8265314IPR001471AP2/ERF domain
PRINTSPR003673.3E-6304324IPR001471AP2/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: 521 aa     Download sequence    Send to blast
MNSNNWLSFP LSPSNSSLHS SQPHDHHQFN VGLVNANMEN PFQTQEWNLI NTHDNTSEVP  60
KVADFLGVSK SQTPSLDLVA LNAIHQSNHP ADYSFQHNNI VQVQNSTTVI ASNNNYELLE  120
NATNLQSLAL SMGSGKGSTS AENSANIVEA PTRRTCDTFG QRTSIYRGVT RHRWTGRYEA  180
HLWDNSCRRE GQSRKGRQGG YDKEEKAARA YDLAALKYWG TSTTTNFPIS NYEKEIEEMK  240
HMTRQEFVAA IRRKSSGFSR GASMYRGVTR HHQHGRWQAR IGRVAGNKDL YLGTFSAEEE  300
AAEAYDIAAI KFRGLNAVTN FDMNRYDVKA ILERNTLPIG GGAAKRLKEA QALESSRKRE  360
EMIALGSSFQ YGSSSTSRLP QAYPLMQFDH QPQQQPLLTL QNHDINSQYT QEDTSSSTFH  420
RNYIQTQLQL HQQFYNNTYI QNNPDLLHGL MNLSCSSPSV VDNNGGSGSS GSYSGGYVGN  480
STEEVGLVKV DYDMQSGGYG GWSVDSVQGS NPGVYPMWNE *
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}.
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
GenBankJF4956176e-92JF495617.1 Gossypium herbaceum clone NBRI_Gh_M126 simple sequence repeat marker, genomic sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012485416.10.0PREDICTED: AP2-like ethylene-responsive transcription factor PLT2
SwissprotQ5YGP70.0PLET2_ARATH; AP2-like ethylene-responsive transcription factor PLT2
TrEMBLA0A0D2S2D00.0A0A0D2S2D0_GOSRA; Uncharacterized protein
STRINGGorai.006G129400.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM30152767
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. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  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. 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]
  15. 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]
  16. 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]