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

RrC4050_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

GRAS

Protein Properties

Length: 523aa MW: 58241.3 Da PI: 5.2308

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4050_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	372.9	4e-114	137	521	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalkl..fsevsPilkfshltaN 99 + Lle+A+a+s++d+++aq++L++l+el+sp+gd+ q+la yf++AL +r+++s++ +y+++ + +++ek+ s e + ++ f+evsP+ +f+h++aN RrC4050_p1 137 SILLEAARAFSDKDTARAQQILWTLNELSSPYGDTEQKLAYYFLQALFNRMTSSGELCYRTMVTAAATEKTCSFESMRKTVlkFQEVSPWATFGHVAAN 235 689*********************************************************999999999776666555579************ PP GRAS 100 qaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg.......skeeleetgerLakfAeelgvpfefnvlvak.rledle 190 aIleav+ge ++Hi+D++ + ++QWp+Ll+aLa+R++++p+lR+T+++ +s s+++++e+g+r++kfA+ +gvpf fn++++ +l++++ RrC4050_p1 236 GAILEAVDGEAKIHIVDISSTFCTQWPTLLEALATRSDDTPHLRLTTIVVGQSPpptdqtaSHRMMKEIGNRMEKFARLMGVPFTFNTIHHVgDLSKFD 334 *******************************************998766677889999***********************6666** PP GRAS 191 leeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh.nse.....sFlerflealeyysalfdsleaklpreseeri 283 l+ L++kp+E+laVn+v ++ + + ++rd+v++ +++l+P++v+vve+ead+ +++ +Fl+ f e+l+++ ++f+sle+++pr+s r RrC4050_p1 335 LNGLEIKPDEVLAVNCVGAMRGIA----PGGNPRDAVISNFRRLRPRIVTVVEEEADLvGEQevfddEFLRLFGESLRWFRVCFESLEESFPRTSTGRL 429 *******************8....666778*******************97665788889*************************** PP GRAS 284 kvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdg..yrveeesgslv.lgWkdrpLvsvSaWr 374 ++Er+ gr+iv++vace + + er+et+ekW++r+++ GF +v +s+++a+++++llr++k +g +v++++++ + l+W+d+p+v++SaWr RrC4050_p1 430 VLERA-AGRAIVDLVACEPSGSMERRETAEKWSMRMRNGGFDAVGYSDEVADDVRALLRRYK-EGvwSMVQCSDAAGIfLCWRDQPVVWASAWR 521 *.****************************************************.4444788876665555************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	50.875	109	499	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.4E-111	137	521	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008356	Biological Process	asymmetric cell division
GO:0009956	Biological Process	radial pattern formation
GO:0045930	Biological Process	negative regulation of mitotic cell cycle
GO:0048366	Biological Process	leaf development
GO:0055072	Biological Process	iron ion homeostasis
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 523 aa Download sequence Send to blast
MDTLFTLVSL QQQQSDSIIT NKSSTTTGSP QTAYHYKFPQ SDVVEECFNS FMDEEDLSSS 60 SSHHNHHLNN NPSSYYSPFT TPTQYHHATS PTPAAVAASA SLTSPYSSGN HLDPSAFSIP 120 HTPPSFDFSA NAKWADSILL EAARAFSDKD TARAQQILWT LNELSSPYGD TEQKLAYYFL 180 QALFNRMTSS GELCYRTMVT AAATEKTCSF ESMRKTVLKF QEVSPWATFG HVAANGAILE 240 AVDGEAKIHI VDISSTFCTQ WPTLLEALAT RSDDTPHLRL TTIVVGQSPP PTDQTASHRM 300 MKEIGNRMEK FARLMGVPFT FNTIHHVGDL SKFDLNGLEI KPDEVLAVNC VGAMRGIAPG 360 GNPRDAVISN FRRLRPRIVT VVEEEADLVG EQEVFDDEFL RLFGESLRWF RVCFESLEES 420 FPRTSTGRLV LERAAGRAIV DLVACEPSGS MERRETAEKW SMRMRNGGFD AVGYSDEVAD 480 DVRALLRRYK EGVWSMVQCS DAAGIFLCWR DQPVVWASAW RPT

Sequence ? help Back to Top

Protein Sequence Length: 523 aa Download sequence Send to blast

MDTLFTLVSL QQQQSDSIIT NKSSTTTGSP QTAYHYKFPQ SDVVEECFNS FMDEEDLSSS  60
SSHHNHHLNN NPSSYYSPFT TPTQYHHATS PTPAAVAASA SLTSPYSSGN HLDPSAFSIP  120
HTPPSFDFSA NAKWADSILL EAARAFSDKD TARAQQILWT LNELSSPYGD TEQKLAYYFL  180
QALFNRMTSS GELCYRTMVT AAATEKTCSF ESMRKTVLKF QEVSPWATFG HVAANGAILE  240
AVDGEAKIHI VDISSTFCTQ WPTLLEALAT RSDDTPHLRL TTIVVGQSPP PTDQTASHRM  300
MKEIGNRMEK FARLMGVPFT FNTIHHVGDL SKFDLNGLEI KPDEVLAVNC VGAMRGIAPG  360
GNPRDAVISN FRRLRPRIVT VVEEEADLVG EQEVFDDEFL RLFGESLRWF RVCFESLEES  420
FPRTSTGRLV LERAAGRAIV DLVACEPSGS MERRETAEKW SMRMRNGGFD AVGYSDEVAD  480
DVRALLRRYK EGVWSMVQCS DAAGIFLCWR DQPVVWASAW RPT

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_B	0.0	52	523	3	475	Protein SHORT-ROOT
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Essential for both cell division and cell specification. Regulates the radial organization of the shoot axial organs and is required for normal shoot gravitropism. Directly controls the transcription of SCR, and when associated with SCR, of MGP, RLK, TRI, NUC and SCL3. {ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:12569126, ECO:0000269\|PubMed:15314023, ECO:0000269\|PubMed:16640459, ECO:0000269\|PubMed:17446396, ECO:0000269\|PubMed:9670559}.

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	AF233752	0.0	AF233752.1 Arabidopsis thaliana short-root protein (shr) gene, complete cds.
GenBank	AL035605	0.0	AL035605.1 Arabidopsis thaliana DNA chromosome 4, BAC clone F19F18 (ESSA project).
GenBank	AL161591	0.0	AL161591.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 87.
GenBank	BT033026	0.0	BT033026.1 Arabidopsis thaliana unknown protein (At4g37650) mRNA, complete cds.
GenBank	CP002687	0.0	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018450543.1	0.0	PREDICTED: protein SHORT-ROOT-like
Swissprot	Q9SZF7	0.0	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A078I1S6	0.0	A0A078I1S6_BRANA; BnaA08g15740D protein
TrEMBL	A0A3P6C869	0.0	A0A3P6C869_BRACM; Uncharacterized protein
STRING	Bo7g118650.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6104	25	47

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	0.0	GRAS family protein

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Muraro D, et al. Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(2): p. 857-62 [PMID:24381155] 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] Gao X,Wang C,Cui H Identification of bundle sheath cell fate factors provides new tools for C3-to-C4 engineering. Plant Signal Behav, 2018. [PMID:24819776] Ahrazem O, et al. Ectopic expression of a stress-inducible glycosyltransferase from saffron enhances salt and oxidative stress tolerance in Arabidopsis while alters anchor root formation. Plant Sci., 2015. 234: p. 60-73 [PMID:25804810] 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] 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] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Miguel A,Milhinhos A,Novák O,Jones B,Miguel CM The SHORT-ROOT-like gene PtSHR2B is involved in Populus phellogen activity. J. Exp. Bot., 2016. 67(5): p. 1545-55 [PMID:26709311] Gong X, et al. SEUSS Integrates Gibberellin Signaling with Transcriptional Inputs from the SHR-SCR-SCL3 Module to Regulate Middle Cortex Formation in the Arabidopsis Root. Plant Physiol., 2016. 170(3): p. 1675-83 [PMID:26818732] Kim ES, et al. HAWAIIAN SKIRT regulates the quiescent center-independent meristem activity in Arabidopsis roots. Physiol Plant, 2016. 157(2): p. 221-33 [PMID:26968317] Lee SA, et al. Interplay between ABA and GA Modulates the Timing of Asymmetric Cell Divisions in the Arabidopsis Root Ground Tissue. Mol Plant, 2016. 9(6): p. 870-84 [PMID:26970019] Li Q,Zhao Y,Yue M,Xue Y,Bao S The Protein Arginine Methylase 5 (PRMT5/SKB1) Gene Is Required for the Maintenance of Root Stem Cells in Response to DNA Damage. J Genet Genomics, 2016. 43(4): p. 187-97 [PMID:27090604] Clark NM, et al. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. Elife, 2017. [PMID:27288545] Yoon EK, et al. Conservation and Diversification of the SHR-SCR-SCL23 Regulatory Network in the Development of the Functional Endodermis in Arabidopsis Shoots. Mol Plant, 2016. 9(8): p. 1197-1209 [PMID:27353361] Waszczak C, et al. SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions. Plant Cell, 2016. 28(8): p. 1844-59 [PMID:27432873] Yu Q, et al. A P-Loop NTPase Regulates Quiescent Center Cell Division and Distal Stem Cell Identity through the Regulation of ROS Homeostasis in Arabidopsis Root. PLoS Genet., 2016. 12(9): p. e1006175 [PMID:27583367] Sparks EE, et al. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Dev. Cell, 2016. 39(5): p. 585-596 [PMID:27923776] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Henry S, et al. SHR overexpression induces the formation of supernumerary cell layers with cortex cell identity in rice. Dev. Biol., 2017. 425(1): p. 1-7 [PMID:28263767] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Díaz-Triviño S,Long Y,Scheres B,Blilou I Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems. Methods Mol. Biol., 2017. 1629: p. 83-103 [PMID:28623581] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Yu Q, et al. Cell-Fate Specification in Arabidopsis Roots Requires Coordinative Action of Lineage Instruction and Positional Reprogramming. Plant Physiol., 2017. 175(2): p. 816-827 [PMID:28821591] Spiegelman Z,Lee CM,Gallagher KL KinG Is a Plant-Specific Kinesin That Regulates Both Intra- and Intercellular Movement of SHORT-ROOT. Plant Physiol., 2018. 176(1): p. 392-405 [PMID:29122988] 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]