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 Ciclev10007639m
Common NameCICLE_v10007639mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family ARR-B
Protein Properties Length: 696aa    MW: 77100.9 Da    PI: 7.2572
Description ARR-B family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10007639mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1G2-like89.72.6e-28199252155
          G2-like   1 kprlrWtpeLHerFveaveqLGGsekAtPktilelmkvkgLtlehvkSHLQkYRl 55 
                      kpr++W+ eLH++Fv av+qL G++kA+Pk+il+lm+v+ Lt+e+v+SHLQkYRl
  Ciclev10007639m 199 KPRVVWSVELHRKFVAAVNQL-GIDKAVPKKILDLMNVEKLTRENVASHLQKYRL 252
                      79*******************.********************************8 PP
2Response_reg76.31.1e-25171251109
                      EEEESSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHH..ESEEEEESSCTTSEHHHHHHHHHHHTTTSEEEEEESTTTHHHHHHHHHT CS
     Response_reg   1 vlivdDeplvrellrqalekegyeevaeaddgeealellkekd..pDlillDiempgmdGlellkeireeepklpiivvtahgeeedalealka 92 
                      vl vdD+p+ + ll+++l++ +y +v++++++  al+ll+e++  +Dl++ D+ mp+mdG++ll+     e++lp+i+++++g+++++ + +  
  Ciclev10007639m  17 VLAVDDDPTCLLLLETLLRRCQY-HVTTTSQAITALKLLRENKnkFDLVISDVHMPDMDGFKLLELVGL-EMDLPVIMLSGNGDPKLVMKGITH 108
                      799********************.***************888888*******************87754.558********************* PP

                      TESEEEESS--HHHHHH CS
     Response_reg  93 GakdflsKpfdpeelvk 109
                      Ga d+l Kp+ +eel +
  Ciclev10007639m 109 GACDYLLKPVRIEELKN 125
                      **************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0363921.4E-1691667IPR017053Response regulator B-type, plant
SuperFamilySSF521723.84E-3613137IPR011006CheY-like superfamily
Gene3DG3DSA:3.40.50.23001.4E-4114150No hitNo description
SMARTSM004484.3E-3115127IPR001789Signal transduction response regulator, receiver domain
PROSITE profilePS5011042.32816131IPR001789Signal transduction response regulator, receiver domain
PfamPF000726.7E-2317125IPR001789Signal transduction response regulator, receiver domain
CDDcd001561.88E-2218130No hitNo description
SuperFamilySSF466897.17E-20196256IPR009057Homeodomain-like
PROSITE profilePS5129412.269196255IPR017930Myb domain
Gene3DG3DSA:1.10.10.602.1E-30196257IPR009057Homeodomain-like
TIGRFAMsTIGR015575.0E-25199252IPR006447Myb domain, plants
PfamPF002491.2E-6201251IPR001005SANT/Myb domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000160Biological Processphosphorelay signal transduction system
GO:0006355Biological Processregulation of transcription, DNA-templated
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:0016021Cellular Componentintegral component of membrane
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 696 aa     Download sequence    Send to blast
MTVEHVNGDQ FPSGLRVLAV DDDPTCLLLL ETLLRRCQYH VTTTSQAITA LKLLRENKNK  60
FDLVISDVHM PDMDGFKLLE LVGLEMDLPV IMLSGNGDPK LVMKGITHGA CDYLLKPVRI  120
EELKNIWQHV VRRKKIDAKD RNNSDNQDKP HNGSGQAEGM GNSDQNGKLN KKRKDQNEDE  180
DDEDDEDDHN HEDPTTQKKP RVVWSVELHR KFVAAVNQLG IDKAVPKKIL DLMNVEKLTR  240
ENVASHLQKY RLYLKRISCV ANQQANMVAA LGSSDPSYLR MSSVNGLGNY HTVGGPGQFQ  300
NSTFRSFPAS GMLGRLNAPA GLGMHGLPSS GMIPMRHAQN SDNTTNDQGK FHPALLPGSH  360
SGNILQGMPT SLELDQLQLN KNITSISELP NTKDNTTFHV SSGFPDARIG FGRSTNPLLD  420
VNNNPLFLEG HPQEAHSNKM FGNQSLMSLN SGSSSRLPDH GRCNDNWSSA VQSSGIQPNS  480
FSLGGDYKQP TLHPGHLRDN LSTMALPIGN SPCDVSSLHP LSNRFQDPKA DLQFQAVQDA  540
PCRSNVMFSP LNSAVSINGD VGPLGQCLDT NKTFFHRSNE FDSLGQSNFV DHFSMKINEV  600
QRSSMQASSN LKEGYLMGQQ KTQGSYISTS VDSLEDLFMS SMVKEVRSYN LAFSSCQNAF  660
INSFYTTLTI IVKNLLNLFN CLLLWFRTKR RKFSI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1irz_A2e-26195258164ARR10-B
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Detected immediately after seed germination. {ECO:0000269|PubMed:17363254}.
UniprotTISSUE SPECIFICITY: Detected in the whole plant. Predominantly expressed in leaves. Expressed at the root transition zone (PubMed:17363254). {ECO:0000269|PubMed:15173562, ECO:0000269|PubMed:17363254}.
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_006450309.10.0two-component response regulator ARR12 isoform X1
SwissprotP625981e-150ARR12_ARATH; Two-component response regulator ARR12
TrEMBLV4TSK60.0V4TSK6_9ROSI; Two-component response regulator
STRINGXP_006450308.10.0(Citrus clementina)
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
AT2G25180.11e-142response 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]