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 RrC9448_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family ARR-B
Protein Properties Length: 584aa    MW: 64295.2 Da    PI: 6.5572
Description ARR-B family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC9448_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1G2-like85.55.5e-27194247155
     G2-like   1 kprlrWtpeLHerFveaveqLGGsekAtPktilelmkvkgLtlehvkSHLQkYRl 55 
                 kpr++Wt eLH++Fv av+qL G ekA Pk+il+lm+v+ Lt+e+v+SHLQk+Rl
  RrC9448_p1 194 KPRVVWTVELHKKFVAAVNQL-GFEKARPKKILDLMNVEKLTRENVASHLQKFRL 247
                 79*******************.9*******************************8 PP
2Response_reg84.43.4e-28191271109
                   EEEESSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHH..ESEEEEESSCTTSEHHHHHHHHHHHTTTSEEEEEESTTTHHHHHHHHHTTES CS
  Response_reg   1 vlivdDeplvrellrqalekegyeevaeaddgeealellkekd..pDlillDiempgmdGlellkeireeepklpiivvtahgeeedalealkaGak 95 
                   vl vdD+++ +++l+++l + +y +v+++ ++++alell+e++  +Dl++ D++mp+mdG++ll+     e++lp+i+++ah++++++ + +  Ga 
    RrC9448_p1  19 VLAVDDDQTCLRILESLLHRCQY-HVTTTNQAQKALELLRENKnkFDLVISDVDMPDMDGFKLLELVGL-EMDLPVIMLSAHSDPKYVMKGVTHGAC 113
                   799********************.***************888888*******************87754.558************************ PP

                   EEEESS--HHHHHH CS
  Response_reg  96 dflsKpfdpeelvk 109
                   d+l Kp+ +eel +
    RrC9448_p1 114 DYLLKPVRIEELKN 127
                   ***********987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0363925.5E-1691584IPR017053Response regulator B-type, plant
SuperFamilySSF521721.85E-3516136IPR011006CheY-like superfamily
Gene3DG3DSA:3.40.50.23001.8E-4216167No hitNo description
SMARTSM004484.6E-3317129IPR001789Signal transduction response regulator, receiver domain
PROSITE profilePS5011043.28518133IPR001789Signal transduction response regulator, receiver domain
PfamPF000722.0E-2519127IPR001789Signal transduction response regulator, receiver domain
CDDcd001564.49E-2820132No hitNo description
PROSITE profilePS5129411.056191250IPR017930Myb domain
Gene3DG3DSA:1.10.10.601.4E-29191252IPR009057Homeodomain-like
SuperFamilySSF466893.58E-19192251IPR009057Homeodomain-like
TIGRFAMsTIGR015573.0E-23194247IPR006447Myb domain, plants
PfamPF002494.6E-8196245IPR001005SANT/Myb domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000160Biological Processphosphorelay signal transduction system
GO:0009414Biological Processresponse to water deprivation
GO:0010082Biological Processregulation of root meristem growth
GO:0010380Biological Processregulation of chlorophyll biosynthetic process
GO:0031537Biological Processregulation of anthocyanin metabolic process
GO:0048367Biological Processshoot system development
GO:0080022Biological Processprimary root development
GO:0080036Biological Processregulation of cytokinin-activated signaling pathway
GO:0080113Biological Processregulation of seed growth
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 584 aa     Download sequence    Send to blast
MTVEQDCVAL DQFPVGMRVL AVDDDQTCLR ILESLLHRCQ YHVTTTNQAQ KALELLRENK  60
NKFDLVISDV DMPDMDGFKL LELVGLEMDL PVIMLSAHSD PKYVMKGVTH GACDYLLKPV  120
RIEELKNIWQ HVVRSRFDKN RGSNNGDKKD GSGNEGVANS DQNNGRANRK RKDQYNEDED  180
EERDDNDDPS SQKKPRVVWT VELHKKFVAA VNQLGFEKAR PKKILDLMNV EKLTRENVAS  240
HLQKFRLYLK RISGNQQAIM ANSDLHFLQM SNGLDGFHHR PIPAGSGQFH GGAAAAAGMR  300
PFPPNGILGR LNTPSGIGGV RSLSLLLLQE CSCKPNRSWK VSPCPSLPLN HIDGGNILQG  360
LPMPLEFDQL QTNNNKSIIP GNSMSAFPSF PSTQQSSLPN NNSHLVLQGH PQVSPSAFPG  420
HQINKRLEHW SNAVSSSSST LPPPAQNSNS IMSHQFDDGS SSYSIPFCDS TIPLTPAMDT  480
NPRAFYRTTD LDSNANVQPG GVYYDSLQMR QSGNYGPTTD AMLSSNAKEG FIVGQQKLQS  540
GFMGAEAGSL DDIVNSTMKQ EQSQGDLSEG DLGYGGFSSL RTCL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1irz_A8e-27190253164ARR10-B
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins. Involved in the root-meristem size determination through the regulation of cell differentiation (PubMed:17363254). Involved in activating SHY2 during meristem growth and controls PIN expression via activation of SHY2 (PubMed:20605455). {ECO:0000250|UniProtKB:Q940D0, ECO:0000269|PubMed:17363254, ECO:0000269|PubMed:20605455}.
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_018478453.10.0PREDICTED: two-component response regulator ARR12
SwissprotP625980.0ARR12_ARATH; Two-component response regulator ARR12
TrEMBLA0A078HC850.0A0A078HC85_BRANA; Two-component response regulator
TrEMBLA0A397ZTX90.0A0A397ZTX9_BRACM; Two-component response regulator
TrEMBLA0A3P6CIE10.0A0A3P6CIE1_BRACM; Two-component response regulator
STRINGBra032035.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM19812879
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G25180.10.0response regulator 12
Publications ? help Back to Top
  1. Takahashi N, et al.
    Cytokinins control endocycle onset by promoting the expression of an APC/C activator in Arabidopsis roots.
    Curr. Biol., 2013. 23(18): p. 1812-7
    [PMID:24035544]
  2. Cortleven A, et al.
    A novel protective function for cytokinin in the light stress response is mediated by the Arabidopsis histidine kinase2 and Arabidopsis histidine kinase3 receptors.
    Plant Physiol., 2014. 164(3): p. 1470-83
    [PMID:24424319]
  3. Kim HJ,Kieber JJ,Schaller GE
    The rice F-box protein KISS ME DEADLY2 functions as a negative regulator of cytokinin signalling.
    Plant Signal Behav, 2013. 8(12): p. e26434
    [PMID:24675172]
  4. Choi SH, et al.
    Gene duplication of type-B ARR transcription factors systematically extends transcriptional regulatory structures in Arabidopsis.
    Sci Rep, 2014. 4: p. 7197
    [PMID:25425016]
  5. Jiang L, et al.
    Strigolactones spatially influence lateral root development through the cytokinin signaling network.
    J. Exp. Bot., 2016. 67(1): p. 379-89
    [PMID:26519957]
  6. Cortleven A, et al.
    Cytokinin Regulates the Etioplast-Chloroplast Transition through the Two-Component Signaling System and Activation of Chloroplast-Related Genes.
    Plant Physiol., 2016. 172(1): p. 464-78
    [PMID:27388681]
  7. Kobayashi K, et al.
    Shoot Removal Induces Chloroplast Development in Roots via Cytokinin Signaling.
    Plant Physiol., 2017. 173(4): p. 2340-2355
    [PMID:28193764]
  8. Zhang TQ, et al.
    A Two-Step Model for de Novo Activation of WUSCHEL during Plant Shoot Regeneration.
    Plant Cell, 2017. 29(5): p. 1073-1087
    [PMID:28389585]
  9. Meng WJ, et al.
    Type-B ARABIDOPSIS RESPONSE REGULATORs Specify the Shoot Stem Cell Niche by Dual Regulation of WUSCHEL.
    Plant Cell, 2017. 29(6): p. 1357-1372
    [PMID:28576846]
  10. Kobayashi K,Iwase A
    Simultaneous but spatially different regulation of non-photosynthetic callus formation and photosynthetic root development after shoot removal.
    Plant Signal Behav, 2017. 12(6): p. e1338999
    [PMID:28594268]
  11. Dai X, et al.
    ARR12 promotes de novo shoot regeneration in Arabidopsis thaliana via activation of WUSCHEL expression.
    J Integr Plant Biol, 2017. 59(10): p. 747-758
    [PMID:28681564]
  12. Zhang F,May A,Irish VF
    Type-B ARABIDOPSIS RESPONSE REGULATORs Directly Activate WUSCHEL.
    Trends Plant Sci., 2017. 22(10): p. 815-817
    [PMID:28886911]
  13. Yan Z, et al.
    Type B Response Regulators Act As Central Integrators in Transcriptional Control of the Auxin Biosynthesis Enzyme TAA1.
    Plant Physiol., 2017. 175(3): p. 1438-1454
    [PMID:28931628]
  14. 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]