PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Rsa1.0_04557.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 611aa MW: 67530.2 Da PI: 6.5163

Description

ARR-B family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_04557.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	G2-like	90.6	1.4e-28	239	292	1	55
G2-like 1 kprlrWtpeLHerFveaveqLGGsekAtPktilelmkvkgLtlehvkSHLQkYRl 55 kpr++W+ eLH++Fv av+qL G ekA+Pk+ilelm+v+gLt+e+v+SHLQkYR+ Rsa1.0_04557.1_g00001.1 239 KPRVVWSVELHQQFVAAVNQL-GVEKAVPKKILELMNVPGLTRENVASHLQKYRI 292 79*****************.******************************7 PP
2	Response_reg	73.9	6.4e-25	36	144	1	109
EEEESSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHH..ESEEEEESSCTTSEHHHHHHHHHHHTTTSEEEEEESTTTHH CS Response_reg 1 vlivdDeplvrellrqalekegyeevaeaddgeealellkekd..pDlillDiempgmdGlellkeireeepklpiivvtahgeee 84 vl+vdD+p+ + +l+++l+ y ev+ + +e al ll++++ +D+++ D+ mp+mdG++ll++ e +lp+i+++a ++++ Rsa1.0_04557.1_g00001.1 36 VLVVDDDPTCLVILEKMLRTCLY-EVTKCNRAEMALSLLRKNKhgFDIVISDVHMPDMDGFKLLEHVGLEM-DLPVIMMSADDSKS 119 89*******************.***********888889******************6644.8********* PP HHHHHHHTTESEEEESS--HHHHHH CS Response_reg 85 dalealkaGakdflsKpfdpeelvk 109 +l+ + Ga d+l Kp+ +e+l + Rsa1.0_04557.1_g00001.1 120 VVLKGVTHGAVDYLIKPVRMEALKN 144 ******************99986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PIRSF	PIRSF036392	4.7E-174	15	603	IPR017053	Response regulator B-type, plant
SuperFamily	SSF52172	3.13E-35	32	161	IPR011006	CheY-like superfamily
Gene3D	G3DSA:3.40.50.2300	2.6E-41	33	183	No hit	No description
SMART	SM00448	4.5E-30	34	146	IPR001789	Signal transduction response regulator, receiver domain
PROSITE profile	PS50110	41.45	35	150	IPR001789	Signal transduction response regulator, receiver domain
Pfam	PF00072	3.3E-22	36	144	IPR001789	Signal transduction response regulator, receiver domain
CDD	cd00156	7.32E-27	37	149	No hit	No description
PROSITE profile	PS51294	11.54	236	295	IPR017930	Myb domain
SuperFamily	SSF46689	1.42E-19	237	296	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	7.9E-30	238	297	IPR009057	Homeodomain-like
TIGRFAMs	TIGR01557	2.9E-24	239	292	IPR006447	Myb domain, plants
Pfam	PF00249	3.9E-8	241	291	IPR001005	SANT/Myb domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000160	Biological Process	phosphorelay signal transduction system
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 611 aa Download sequence Send to blast
MMNPLNGRGG GLGGSSSGKN QGGESVVEMF PSGLRVLVVD DDPTCLVILE KMLRTCLYEV 60 TKCNRAEMAL SLLRKNKHGF DIVISDVHMP DMDGFKLLEH VGLEMDLPVI MMSADDSKSV 120 VLKGVTHGAV DYLIKPVRME ALKNIWQHVV RKRRIEWSMP TTTHSGSVEE TTGERQQQQQ 180 QQQREAVSAD DDDNNSSSVN EGNNNNNNWR SSSGSSSRKR KDEEGEEQGD EEDASNLKKP 240 RVVWSVELHQ QFVAAVNQLG VEKAVPKKIL ELMNVPGLTR ENVASHLQKY RIYLRRLGGV 300 SQHHQGSLNN SFMTGQDASF GSLPTLNAFD LQALGQLPAQ SLAQLQASGL TRPAALVSKP 360 GFPGGSTTIV DERSIFSFDN SKMNLLHGVP TGMEPRQLAG LQQQHGMTIQ QQIAAVRAGH 420 SLRRPQQQTF SRPQQSSSIR QPMLPNRVSE ISGFSSGRSS SIPESSSRVL PTSYANLSTQ 480 QQSLAFSNFQ QELPHDMLFS SRQNDWDLRS MLSSSHQDAF SNSEAYSSSR NNNNTSRNQQ 540 QQQQQQGMVS HHQVYGNGGG SSLKVKSETM AFHEQYSNQE DLMSALLKQE GIGPVDTEFD 600 FDAYSIDDIP V

Sequence ? help Back to Top

Protein Sequence Length: 611 aa Download sequence Send to blast

MMNPLNGRGG GLGGSSSGKN QGGESVVEMF PSGLRVLVVD DDPTCLVILE KMLRTCLYEV  60
TKCNRAEMAL SLLRKNKHGF DIVISDVHMP DMDGFKLLEH VGLEMDLPVI MMSADDSKSV  120
VLKGVTHGAV DYLIKPVRME ALKNIWQHVV RKRRIEWSMP TTTHSGSVEE TTGERQQQQQ  180
QQQREAVSAD DDDNNSSSVN EGNNNNNNWR SSSGSSSRKR KDEEGEEQGD EEDASNLKKP  240
RVVWSVELHQ QFVAAVNQLG VEKAVPKKIL ELMNVPGLTR ENVASHLQKY RIYLRRLGGV  300
SQHHQGSLNN SFMTGQDASF GSLPTLNAFD LQALGQLPAQ SLAQLQASGL TRPAALVSKP  360
GFPGGSTTIV DERSIFSFDN SKMNLLHGVP TGMEPRQLAG LQQQHGMTIQ QQIAAVRAGH  420
SLRRPQQQTF SRPQQSSSIR QPMLPNRVSE ISGFSSGRSS SIPESSSRVL PTSYANLSTQ  480
QQSLAFSNFQ QELPHDMLFS SRQNDWDLRS MLSSSHQDAF SNSEAYSSSR NNNNTSRNQQ  540
QQQQQQGMVS HHQVYGNGGG SSLKVKSETM AFHEQYSNQE DLMSALLKQE GIGPVDTEFD  600
FDAYSIDDIP V

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1irz_A	2e-22	238	297	4	63	ARR10-B
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional 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. Regulates SHY2 by binding to its promoter (PubMed:19039136). Involved in the root-meristem size determination through the regulation of cell differentiation (PubMed:17363254). {ECO:0000269\|PubMed:11574878, ECO:0000269\|PubMed:11691951, ECO:0000269\|PubMed:17363254, ECO:0000269\|PubMed:19039136}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_04557.1_g00001.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by gibberellin. {ECO:0000269\|PubMed:20605455}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK353418	1e-151	AK353418.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-42-G14.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018493413.1	0.0	PREDICTED: two-component response regulator ARR1-like
Swissprot	Q940D0	0.0	ARR1_ARATH; Two-component response regulator ARR1
TrEMBL	A0A398A1K8	0.0	A0A398A1K8_BRACM; Two-component response regulator
STRING	Bra001643.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2403	27	73

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G16857.2	0.0	response regulator 1

Publications ? help Back to Top
Bürkle L,Meyer S,Dortay H,Lehrach H,Heyl A In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system. Funct. Integr. Genomics, 2005. 5(3): p. 175-83 [PMID:15714319] Moubayidin L, et al. Spatial coordination between stem cell activity and cell differentiation in the root meristem. Dev. Cell, 2013. 26(4): p. 405-15 [PMID:23987513] 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] Kurepa J,Li Y,Perry SE,Smalle JA Ectopic expression of the phosphomimic mutant version of Arabidopsis response regulator 1 promotes a constitutive cytokinin response phenotype. BMC Plant Biol., 2014. 14: p. 28 [PMID:24423196] 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] Marín-de la Rosa N, et al. Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins. PLoS Genet., 2015. 11(7): p. e1005337 [PMID:26134422] D'Alessandro S,Golin S,Hardtke CS,Lo Schiavo F,Zottini M The co-chaperone p23 controls root development through the modulation of auxin distribution in the Arabidopsis root meristem. J. Exp. Bot., 2015. 66(16): p. 5113-22 [PMID:26163704] 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] Moubayidin L, et al. A SCARECROW-based regulatory circuit controls Arabidopsis thaliana meristem size from the root endodermis. Planta, 2016. 243(5): p. 1159-68 [PMID:26848984] Muraro D, et al. A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana. J. Theor. Biol., 2016. 404: p. 182-205 [PMID:27157127] 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] Kobayashi K, et al. Shoot Removal Induces Chloroplast Development in Roots via Cytokinin Signaling. Plant Physiol., 2017. 173(4): p. 2340-2355 [PMID:28193764] 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] Kushwah S,Laxmi A The interaction between glucose and cytokinin signaling in controlling Arabidopsis thaliana seedling root growth and development. Plant Signal Behav, 2017. 12(5): p. e1312241 [PMID:28467152] 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] 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] Liu B,De Storme N,Geelen D Cold interferes with male meiotic cytokinesis in Arabidopsis thaliana independently of the AHK2/3-AHP2/3/5 cytokinin signaling module. Cell Biol. Int., 2017. 41(8): p. 879-889 [PMID:28618065] 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] 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] Rong XF, et al. Type-B ARRs Control Carpel Regeneration Through Mediating AGAMOUS Expression in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 756-764 [PMID:29186581] 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] Waldie T,Leyser O Cytokinin Targets Auxin Transport to Promote Shoot Branching. Plant Physiol., 2018. 177(2): p. 803-818 [PMID:29717021]