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

XP_016494518.1

Organism

Nicotiana tabacum

Taxonomic ID

4097

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana

Family

GRAS

Protein Properties

Length: 508aa MW: 57067.8 Da PI: 6.439

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_016494518.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	353.1	4.4e-108	149	503	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdg.dpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfsh 95 ++ LlecA a+s ++l +a+++L +l +++sp+g + +R++ yf++A+a+r+ +s+ ++++ l ++ + a+++f+++sP++kf+h XP_016494518.1 149 ITHLLECAVAISVDNLGEAHRMLLELTQMSSPYGpSCAERVVVYFAKAMASRVINSWLGICSPLINYKS-------VHCAFQVFNNISPFIKFAH 236 678*****************************9999******************986644443.......457899********* PP GRAS 96 ltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledle 190 +t NqaIlea+++ +rvHiiD di+qGlQWpaL++ La+R egpp++ +Tg+g s e l etg++L++fA++lg++fef++ + k++ +l+ XP_016494518.1 237 FTSNQAILEAFHRRDRVHIIDVDIMQGLQWPALFHILATRIEGPPHVTMTGMGT----SMELLIETGKQLSSFAKHLGMSFEFHP-IGKKIGELD 326 **************************************************....9**********************.7**** PP GRAS 191 leeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikv 285 + +L++++gEa+a+++ h+l+d +++ + +++l++++sP+v+++veqe+ + ++sFl+rf+ +l+yys++fdsl a l+++++ r++v XP_016494518.1 327 ITMLQIRRGEAIAIHWLQ--HSLYDATGPDWK----TMRLLQEVSPRVITLVEQEIPL-GGSFLDRFVGSLHYYSTIFDSLGAFLHSDDSSRHNV 414 *************9..999999999888....******************.789***************************** PP GRAS 286 ErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaWr 374 E+ ll rei n++a g +r+ + ++++Wr+ l++ GF +vp+s++a++qa+l+l++++ ++gy++ + +g+l lgWkd +L+++SaW+ XP_016494518.1 415 EHGLLYREINNILAIGGPARNGE-DKFKHWRSELSRNGFMQVPMSTNAMAQAQLILNMFPpVHGYSLVQGDGTLKLGWKDTSLYTASAWT 503 ***************7665.55*************************************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	52.388	122	482	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.5E-105	149	503	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 508 aa Download sequence Send to blast
MLKGGSEVIH QHGALDSMQQ SNEHWDCASL VGFPGITSAP NYPSKPITDR GNNPERNELS 60 QWVEHVTRQL IEDFPENETE AMTYQDNIVP ALLGELRPKK VARRNSSESM EQQHQWNSHD 120 LARDENNMNI NETGTKGMNG LDDQGLNLIT HLLECAVAIS VDNLGEAHRM LLELTQMSSP 180 YGPSCAERVV VYFAKAMASR VINSWLGICS PLINYKSVHC AFQVFNNISP FIKFAHFTSN 240 QAILEAFHRR DRVHIIDVDI MQGLQWPALF HILATRIEGP PHVTMTGMGT SMELLIETGK 300 QLSSFAKHLG MSFEFHPIGK KIGELDITML QIRRGEAIAI HWLQHSLYDA TGPDWKTMRL 360 LQEVSPRVIT LVEQEIPLGG SFLDRFVGSL HYYSTIFDSL GAFLHSDDSS RHNVEHGLLY 420 REINNILAIG GPARNGEDKF KHWRSELSRN GFMQVPMSTN AMAQAQLILN MFPPVHGYSL 480 VQGDGTLKLG WKDTSLYTAS AWTSPNSR

Sequence ? help Back to Top

Protein Sequence Length: 508 aa Download sequence Send to blast

MLKGGSEVIH QHGALDSMQQ SNEHWDCASL VGFPGITSAP NYPSKPITDR GNNPERNELS  60
QWVEHVTRQL IEDFPENETE AMTYQDNIVP ALLGELRPKK VARRNSSESM EQQHQWNSHD  120
LARDENNMNI NETGTKGMNG LDDQGLNLIT HLLECAVAIS VDNLGEAHRM LLELTQMSSP  180
YGPSCAERVV VYFAKAMASR VINSWLGICS PLINYKSVHC AFQVFNNISP FIKFAHFTSN  240
QAILEAFHRR DRVHIIDVDI MQGLQWPALF HILATRIEGP PHVTMTGMGT SMELLIETGK  300
QLSSFAKHLG MSFEFHPIGK KIGELDITML QIRRGEAIAI HWLQHSLYDA TGPDWKTMRL  360
LQEVSPRVIT LVEQEIPLGG SFLDRFVGSL HYYSTIFDSL GAFLHSDDSS RHNVEHGLLY  420
REINNILAIG GPARNGEDKF KHWRSELSRN GFMQVPMSTN AMAQAQLILN MFPPVHGYSL  480
VQGDGTLKLG WKDTSLYTAS AWTSPNSR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	1e-145	142	503	13	379	Protein SCARECROW
5b3h_A	1e-145	142	503	12	378	Protein SCARECROW
5b3h_D	1e-145	142	503	12	378	Protein SCARECROW
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 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}.

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	HG975448	0.0	HG975448.1 Solanum pennellii chromosome ch09, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016494518.1	0.0	PREDICTED: protein SCARECROW-like
Swissprot	Q9M384	1e-142	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A1S4C0B4	0.0	A0A1S4C0B4_TOBAC; protein SCARECROW-like
STRING	XP_009608328.1	0.0	(Nicotiana tomentosiformis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA12291	20	23

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G54220.1	1e-144	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]