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

RrC916_p5

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: 493aa MW: 55242.8 Da PI: 5.8225

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC916_p5	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	331.2	2e-101	146	482	3	329
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalkl..fsevsPilkfshltaNq 100 + Lle+A+a+s++d+++a+++L++l+el+sp+gd+ q+la+yf++AL +r+++s++++y+++ + +++ek+ s e + ++ f+evsP+ +f+h++aN RrC916_p5 146 SILLEAARAFSDKDTARARQILWTLNELSSPYGDTDQKLASYFLQALFNRMTGSGERCYRTMVTAASTEKTCSFESTRKTVlkFQEVSPWATFGHVAANG 245 689**********************************************************99999999665554444468************* PP GRAS 101 aIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg......skeeleetgerLakfAeelgvpfefnvlvak.rledlelee 193 aIleav+ge ++Hi+D++ + ++QWp+Ll+aLa+R++++p+lR+T+v+ ++++ s+++++e+g+r++kfA+ +gvpf+fn++++ +l++++l+e RrC916_p5 246 AILEAVDGEAKIHIVDISSTFCTQWPTLLEALATRSDDTPHLRLTTVVVANKFvndqtaSHRMMKELGNRMEKFARLMGVPFKFNIIHHVgDLSEFDLNE 345 ********************************************999889999999**********************96666***** PP GRAS 194 LrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh.nse.....sFlerflealeyysalfdsleaklpreseerikvEr 287 L+vk +E+la+n+v ++h + + ++rd+v++ +++l+P++v+++e+ead+ ++e +Fl+ f e+l+++ ++f+sle+++pr+s+er ++Er RrC916_p5 346 LDVKADEVLAINCVGAMHGIA----PRGNPRDAVISNFRRLRPRIVTIIEEEADLvGEEegfddEFLRSFGECLRWFRVCFESLEESFPRTSNERLMLER 441 ****************8....888899********************7665888889******************************* PP GRAS 288 ellgreivnvvacegaerrerhetlekWrerleeaGFkpvpl 329 + g +iv++vace + ++er+et++kW++r+++ G++p + RrC916_p5 442 V-AGCAIVDLVACEPSGSTERRETARKWSRRMRNGGLGPWGI 482 9.*********************************99876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	47.928	118	493	IPR005202	Transcription factor GRAS
Pfam	PF03514	6.8E-99	146	482	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 493 aa Download sequence Send to blast
MDTLFRLVSL QQQQQSDSII TNQSSLSRTS TTTTGSPQTA YHYNHNNFPT NDVVEECFNF 60 FMDEEDLSSS SSHHNHHHPT SSYYSPFTTP TQYHPATSST PPSAPDAAAL ASPYSSSGHH 120 NDPSAFSIPQ TPPSFDFSSN AKWADSILLE AARAFSDKDT ARARQILWTL NELSSPYGDT 180 DQKLASYFLQ ALFNRMTGSG ERCYRTMVTA ASTEKTCSFE STRKTVLKFQ EVSPWATFGH 240 VAANGAILEA VDGEAKIHIV DISSTFCTQW PTLLEALATR SDDTPHLRLT TVVVANKFVN 300 DQTASHRMMK ELGNRMEKFA RLMGVPFKFN IIHHVGDLSE FDLNELDVKA DEVLAINCVG 360 AMHGIAPRGN PRDAVISNFR RLRPRIVTII EEEADLVGEE EGFDDEFLRS FGECLRWFRV 420 CFESLEESFP RTSNERLMLE RVAGCAIVDL VACEPSGSTE RRETARKWSR RMRNGGLGPW 480 GIVMKWRMTS ELC

Sequence ? help Back to Top

Protein Sequence Length: 493 aa Download sequence Send to blast

MDTLFRLVSL QQQQQSDSII TNQSSLSRTS TTTTGSPQTA YHYNHNNFPT NDVVEECFNF  60
FMDEEDLSSS SSHHNHHHPT SSYYSPFTTP TQYHPATSST PPSAPDAAAL ASPYSSSGHH  120
NDPSAFSIPQ TPPSFDFSSN AKWADSILLE AARAFSDKDT ARARQILWTL NELSSPYGDT  180
DQKLASYFLQ ALFNRMTGSG ERCYRTMVTA ASTEKTCSFE STRKTVLKFQ EVSPWATFGH  240
VAANGAILEA VDGEAKIHIV DISSTFCTQW PTLLEALATR SDDTPHLRLT TVVVANKFVN  300
DQTASHRMMK ELGNRMEKFA RLMGVPFKFN IIHHVGDLSE FDLNELDVKA DEVLAINCVG  360
AMHGIAPRGN PRDAVISNFR RLRPRIVTII EEEADLVGEE EGFDDEFLRS FGECLRWFRV  420
CFESLEESFP RTSNERLMLE RVAGCAIVDL VACEPSGSTE RRETARKWSR RMRNGGLGPW  480
GIVMKWRMTS ELC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_B	0.0	62	481	3	425	Protein SHORT-ROOT
Search in ModeBase

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_013599072.1	0.0	PREDICTED: protein SHORT-ROOT
Swissprot	Q9SZF7	0.0	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A0D3DI67	0.0	A0A0D3DI67_BRAOL; 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]