PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja

Family

GRAS

Protein Properties

Length: 477aa MW: 54005.6 Da PI: 5.4661

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.01G194200.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	356	5.9e-109	102	473	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilk 92 + Lle A+av+++++++ q+l++ l+el+sp+gd+ q+la+yf++A +r+++ ++++y++l++ ++++ + +++ + + f+evsP+ + Glyma.01G194200.1.p 102 DILLETARAVADKNTTRLQQLMWMLNELSSPYGDTDQKLASYFLQAFFSRISQAGDRTYRTLASASEKTCSFESTRKTVLKFQEVSPWTT 191 689*********************************************************8887775554444455555***** PP GRAS 93 fshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlv 182 f+h++ N aIlea+ege ++HiiD++ ++++QWp+L++aLa+R++++p+lR+T v+ ++++ ++ ++e+g r++kfA+ +gvpf+fnv++ Glyma.01G194200.1.p 192 FGHVASNGAILEALEGEPKLHIIDISNTYCTQWPTLFEALATRNDDTPHLRLTSVVTADATAQKLMKEIGARMEKFARLMGVPFKFNVVH 281 *****************************************************9999***********************96 PP GRAS 183 ak.rledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse....sFlerflealeyysal 267 + +l+dl++++L++k++Eala+n+v lh++ ++ ++rd+v++ +++l+P++v++ve+ead++ + +F+++f e+l+++ + Glyma.01G194200.1.p 282 HVgQLSDLDFSMLDIKEDEALAINCVNTLHSIA----AVGNHRDAVISSLRRLKPRIVTLVEEEADLDVGlegfEFVKGFEECLRWFRVY 367 656*************************8....888899*****************99865556679*********** PP GRAS 268 fdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdg.yrveeesg 356 f++l++++pr+s+er +Er+ gr++v++vac+ ae++er+et+++W +r++ G+++v++se++ +++++llr++ +g + +++++ Glyma.01G194200.1.p 368 FEALDESFPRTSNERLLLERA-AGRAVVDLVACSAAESVERRETAARWARRMHGGGLNTVAFSEEVCDDVRALLRRYR-EGwAMTQCSDA 455 *****************.****************************************************.66255668899 PP GRAS 357 slvlgWkdrpLvsvSaWr 374 ++l+Wk++p+v++SaWr Glyma.01G194200.1.p 456 GIFLTWKEQPVVWASAWR 473 999************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	51.32	74	453	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.0E-106	102	473	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
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:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 477 aa Download sequence Send to blast
MDTTLFRVVS SFQHQHQPDH DQSLNNSTTS SSSRSSRQQQ NYPYPQEDEE CFNFFMDEED 60 LSSSSSKHYC PYQPHPPSTT TIHHSFSPTP CDFEFSGKWA QDILLETARA VADKNTTRLQ 120 QLMWMLNELS SPYGDTDQKL ASYFLQAFFS RISQAGDRTY RTLASASEKT CSFESTRKTV 180 LKFQEVSPWT TFGHVASNGA ILEALEGEPK LHIIDISNTY CTQWPTLFEA LATRNDDTPH 240 LRLTSVVTAD ATAQKLMKEI GARMEKFARL MGVPFKFNVV HHVGQLSDLD FSMLDIKEDE 300 ALAINCVNTL HSIAAVGNHR DAVISSLRRL KPRIVTLVEE EADLDVGLEG FEFVKGFEEC 360 LRWFRVYFEA LDESFPRTSN ERLLLERAAG RAVVDLVACS AAESVERRET AARWARRMHG 420 GGLNTVAFSE EVCDDVRALL RRYREGWAMT QCSDAGIFLT WKEQPVVWAS AWRALT*

Sequence ? help Back to Top

Protein Sequence Length: 477 aa Download sequence Send to blast

MDTTLFRVVS SFQHQHQPDH DQSLNNSTTS SSSRSSRQQQ NYPYPQEDEE CFNFFMDEED  60
LSSSSSKHYC PYQPHPPSTT TIHHSFSPTP CDFEFSGKWA QDILLETARA VADKNTTRLQ  120
QLMWMLNELS SPYGDTDQKL ASYFLQAFFS RISQAGDRTY RTLASASEKT CSFESTRKTV  180
LKFQEVSPWT TFGHVASNGA ILEALEGEPK LHIIDISNTY CTQWPTLFEA LATRNDDTPH  240
LRLTSVVTAD ATAQKLMKEI GARMEKFARL MGVPFKFNVV HHVGQLSDLD FSMLDIKEDE  300
ALAINCVNTL HSIAAVGNHR DAVISSLRRL KPRIVTLVEE EADLDVGLEG FEFVKGFEEC  360
LRWFRVYFEA LDESFPRTSN ERLLLERAAG RAVVDLVACS AAESVERRET AARWARRMHG  420
GGLNTVAFSE EVCDDVRALL RRYREGWAMT QCSDAGIFLT WKEQPVVWAS AWRALT*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_B	0.0	77	473	2	419	Protein SHORT-ROOT
5b3h_E	0.0	77	473	2	419	Protein SHORT-ROOT
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in the procambium during embryogenesis. {ECO:0000269\|PubMed:10850497}.
Uniprot	TISSUE SPECIFICITY: Expressed in the stele and the quiescent center. Not detected in the ground tissue cell lineage. The SHR protein moves from the stele to a single layer of adjacent cells, where it enters the nucleus. {ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:11565032, ECO:0000269\|PubMed:15142972, ECO:0000269\|PubMed:15314023}.

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Glyma.01G194200.1.p

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	AC235306	0.0	AC235306.1 Glycine max strain Williams 82 clone GM_WBb0068C17, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003517347.1	0.0	protein SHORT-ROOT
Swissprot	Q9SZF7	0.0	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	I1J9E7	0.0	I1J9E7_SOYBN; Uncharacterized protein
STRING	GLYMA01G40180.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF1297	34	106
Representative plant	OGRP2755	13	32

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

Link Out ? help Back to Top
Phytozome	Glyma.01G194200.1.p
Entrez Gene	100820459

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]