PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Picea

Family

GRAS

Protein Properties

Length: 741aa MW: 81871.9 Da PI: 5.7913

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MA_140003g0010	genome	ConGenIE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	390.2	2.2e-119	377	737	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetsekn.sseelaalklfsevsPilkfsh 95 +lLl+cAea+s ++ ++a ++L +lse ++p+g+p+qR+aayf+e++aarl++s +l+ l+ s+ + + + l+a+++f+ ++P++kfsh MA_140003g0010 377 LSLLLQCAEAISMDKIQQAYSILPQLSEFSTPYGNPLQRVAAYFAEGMAARLHNSYLGLCCPLEISRPQLVSiNHNFLTAFQTFNSICPFVKFSH 471 689*******************************************************999888877666688999************* PP GRAS 96 ltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledle 190 +t NqaIlea++ge++vHiiDfdi+qGlQWpaL++ La+Rp+g p++RiTg+g s e+le+tg+rL++fA++l++pfef++ va++l +l+ MA_140003g0010 472 FTSNQAILEAFNGESQVHIIDFDIMQGLQWPALFHILAARPGGCPHVRITGLGT----SMEALEATGKRLSSFAHTLKLPFEFHP-VAEKLGQLD 561 **************************************************....***********************.7**** PP GRAS 191 leeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikv 285 + Lrv++g+alaV++ + h+l+d ++s + +L+l+++l+Pkv+++veq++++ ++Fl+rf+eal+yysa+fd+l a + +++ er++v MA_140003g0010 562 PAVLRVRSGDALAVHWLH--HSLYDVTGSDTC----TLRLLQRLNPKVITMVEQDLNT-VGPFLNRFVEALHYYSAMFDALGACFNEDNMERHSV 649 *************9..999988888887....*****************9.889***************************** PP GRAS 286 ErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 E++ll+ ei+n++a g +r+ + + +++Wr +l+++GF++++++ +a qa+lll+++ +gy++ ee g l lgWkd +L+++SaW+ MA_140003g0010 650 EQQLLSHEIRNILAVGGPARTGEPK-FQNWRTQLQSCGFQQISMRGNASVQAELLLNMFCCEGYSLVEEGGILKLGWKDLSLYTASAWT 737 ***************999887.************************************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	60.374	350	717	IPR005202	Transcription factor GRAS
Pfam	PF03514	7.8E-117	377	737	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 741 aa Download sequence Send to blast
MCECPSYYNL ITAGDFNSTE DDQNRVGFSD ADGLEVIASN KKMKNLIGSS SAQEEASSVF 60 HSPNSWPGDL NTLQTIFNAS SSVCNPCSSP SWEGSQTRLA VPYISTGSAD FLIPADPDAS 120 SHGMFWGESS GRLLDMQFMN KNGSGRRIDS SVVDPKLDEI LMPTMPHAES LISPSRRFEP 180 FSALESHGSL NYMSSNIRAV QMILDNNQSI NRRSGMVKEA VGFVVASEKP VLDNTSGYES 240 LCQGWRHAPT TMMKKREFNA DHEGLSTQSD SGQSFLECNL MERQAIMDSS ESDHQGNESA 300 GFHLQSKAKR PCHVSYGECS SQSDQQGFTT LHQGQFQDSC QAQRKTNTET NHQGCKKTLN 360 ASSNAYDLTD AQGLHLLSLL LQCAEAISMD KIQQAYSILP QLSEFSTPYG NPLQRVAAYF 420 AEGMAARLHN SYLGLCCPLE ISRPQLVSIN HNFLTAFQTF NSICPFVKFS HFTSNQAILE 480 AFNGESQVHI IDFDIMQGLQ WPALFHILAA RPGGCPHVRI TGLGTSMEAL EATGKRLSSF 540 AHTLKLPFEF HPVAEKLGQL DPAVLRVRSG DALAVHWLHH SLYDVTGSDT CTLRLLQRLN 600 PKVITMVEQD LNTVGPFLNR FVEALHYYSA MFDALGACFN EDNMERHSVE QQLLSHEIRN 660 ILAVGGPART GEPKFQNWRT QLQSCGFQQI SMRGNASVQA ELLLNMFCCE GYSLVEEGGI 720 LKLGWKDLSL YTASAWTSWT S

Sequence ? help Back to Top

Protein Sequence Length: 741 aa Download sequence Send to blast

MCECPSYYNL ITAGDFNSTE DDQNRVGFSD ADGLEVIASN KKMKNLIGSS SAQEEASSVF  60
HSPNSWPGDL NTLQTIFNAS SSVCNPCSSP SWEGSQTRLA VPYISTGSAD FLIPADPDAS  120
SHGMFWGESS GRLLDMQFMN KNGSGRRIDS SVVDPKLDEI LMPTMPHAES LISPSRRFEP  180
FSALESHGSL NYMSSNIRAV QMILDNNQSI NRRSGMVKEA VGFVVASEKP VLDNTSGYES  240
LCQGWRHAPT TMMKKREFNA DHEGLSTQSD SGQSFLECNL MERQAIMDSS ESDHQGNESA  300
GFHLQSKAKR PCHVSYGECS SQSDQQGFTT LHQGQFQDSC QAQRKTNTET NHQGCKKTLN  360
ASSNAYDLTD AQGLHLLSLL LQCAEAISMD KIQQAYSILP QLSEFSTPYG NPLQRVAAYF  420
AEGMAARLHN SYLGLCCPLE ISRPQLVSIN HNFLTAFQTF NSICPFVKFS HFTSNQAILE  480
AFNGESQVHI IDFDIMQGLQ WPALFHILAA RPGGCPHVRI TGLGTSMEAL EATGKRLSSF  540
AHTLKLPFEF HPVAEKLGQL DPAVLRVRSG DALAVHWLHH SLYDVTGSDT CTLRLLQRLN  600
PKVITMVEQD LNTVGPFLNR FVEALHYYSA MFDALGACFN EDNMERHSVE QQLLSHEIRN  660
ILAVGGPART GEPKFQNWRT QLQSCGFQQI SMRGNASVQA ELLLNMFCCE GYSLVEEGGI  720
LKLGWKDLSL YTASAWTSWT S

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	1e-166	370	737	13	379	Protein SCARECROW
5b3h_A	1e-166	370	737	12	378	Protein SCARECROW
5b3h_D	1e-166	370	737	12	378	Protein SCARECROW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Putative transcription factor involved in asymmetric cell division (By similarity). Required for differentiation of endodermis and graviresponses. {ECO:0000250, ECO:0000269\|PubMed:16339910}.
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 cell division but not differentiation of the ground tissue. Also required for normal shoot gravitropism. Regulates the radial organization of the shoot axial organs. Binds to the promoter of MGP, NUC, RLK and SCL3. Restricts SHR movment and sequesters it into the nucleus of the endodermis. {ECO:0000269\|PubMed:10631180, ECO:0000269\|PubMed:12569126, ECO:0000269\|PubMed:15142972, ECO:0000269\|PubMed:15314023, ECO:0000269\|PubMed:16640459, ECO:0000269\|PubMed:17446396, ECO:0000269\|PubMed:22921914, ECO:0000269\|PubMed:24302889, ECO:0000269\|PubMed:8819871, ECO:0000269\|PubMed:9375406, ECO:0000269\|PubMed:9670559}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by SHR and by itself. {ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:11565032, ECO:0000269\|PubMed:15314023}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	KM264390	0.0	KM264390.1 Pinus radiata SCL3 (SCL3) mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021897229.1	1e-166	protein SCARECROW
Swissprot	Q2Z2E9	1e-161	SCR_IPONI; Protein SCARECROW
Swissprot	Q9M384	1e-162	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A0B4U7W6	1e-176	A0A0B4U7W6_PINRA; SCR
STRING	evm.model.supercontig_1018.1	1e-165	(Carica papaya)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP2183	14	37

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G54220.1	1e-164	GRAS family protein

Publications ? help Back to Top
Liu YG, et al. Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning. Proc. Natl. Acad. Sci. U.S.A., 1999. 96(11): p. 6535-40 [PMID:10339623] Ticconi CA, et al. ER-resident proteins PDR2 and LPR1 mediate the developmental response of root meristems to phosphate availability. Proc. Natl. Acad. Sci. U.S.A., 2009. 106(33): p. 14174-9 [PMID:19666499] 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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] 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] Reyes-Hernández BJ, et al. The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana. New Phytol., 2014. 202(4): p. 1223-36 [PMID:24635769] 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] Ron M, et al. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol., 2014. 166(2): p. 455-69 [PMID:24868032] 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] 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] 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] Madmon O, et al. Expression of MAX2 under SCARECROW promoter enhances the strigolactone/MAX2 dependent response of Arabidopsis roots to low-phosphate conditions. Planta, 2016. 243(6): p. 1419-27 [PMID:26919985] 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] Benfey PN Defining the Path from Stem Cells to Differentiated Tissue. Curr. Top. Dev. Biol., 2016. 116: p. 35-43 [PMID:26970612] 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] Choi JW,Lim J Control of Asymmetric Cell Divisions during Root Ground Tissue Maturation. Mol. Cells, 2016. 39(7): p. 524-9 [PMID:27306644] 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] Goh T, et al. Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor. Development, 2016. 143(18): p. 3363-71 [PMID:27510971] 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] 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] Bruno L, et al. In Arabidopsis thaliana Cadmium Impact on the Growth of Primary Root by Altering SCR Expression and Auxin-Cytokinin Cross-Talk. Front Plant Sci, 2017. 8: p. 1323 [PMID:28798767] Mira MM, et al. Expression of Arabidopsis class 1 phytoglobin (AtPgb1) delays death and degradation of the root apical meristem during severe PEG-induced water deficit. J. Exp. Bot., 2017. 68(20): p. 5653-5668 [PMID:29059380] 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] Ercoli MF, et al. GIF Transcriptional Coregulators Control Root Meristem Homeostasis. Plant Cell, 2018. 30(2): p. 347-359 [PMID:29352064] Shimotohno A,Heidstra R,Blilou I,Scheres B Root stem cell niche organizer specification by molecular convergence of PLETHORA and SCARECROW transcription factor modules. Genes Dev., 2018. 32(15-16): p. 1085-1100 [PMID:30018102]