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

Neem_7911_f_1

Organism

Azadirachta indica

Taxonomic ID

124943

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta

Family

GRAS

Protein Properties

Length: 511aa MW: 57413.2 Da PI: 6.427

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_7911_f_1	genome	NGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	348.3	1.2e-106	150	506	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlselaspdg.dpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfsh 95 l++lL+e A a+s ++l +a+++L +l ++asp+g + +R++ayf++A+a+r+ +s+ ++++ l +++ a+++f++vsP++kf+h Neem_7911_f_1 150 LITLLFESAVAISVDNLGEAHRMLLELTQMASPYGpSCAERVVAYFAKAMASRVINSWLGICSPLINHKSA-------HWAFQAFNNVSPFIKFAH 238 5789*****************************9999*******************877655554.......57899********* PP GRAS 96 ltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledlel 191 +t Nqa lea+++ +rvHiiD+di+qGlQWpaL++ La+R egpp++R+Tg+g s e l etg++L++fA++lg++fef++ +ak++ + ++ Neem_7911_f_1 239 FTSNQATLEAFHRRDRVHIIDLDIMQGLQWPALFHILATRMEGPPHVRMTGMGT----SMEILLETGKQLSNFAKRLGMSFEFHP-IAKKFGEADP 329 **************************************************....9**********************.7***** PP GRAS 192 eeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvEr 287 ++L+v++gE+laV++ h+l+d +++ + +++l+ +lsP+v+++veqe++h ++sFl+rf+ +l+yys+lfdsl a lp+++ r+ vE+ Neem_7911_f_1 330 SMLQVRRGETLAVHWLQ--HSLYDATGPDWK----TVRLLEELSPRVITLVEQEISH-GGSFLDRFVGSLHYYSTLFDSLGAYLPSDDPSRHRVEH 418 ************9..999999999888....******************.789******************************* PP GRAS 288 ellgreivnvvacegaerrerhetlekWrerle.eaGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaWr 374 ll rei n++a g +r + ++++Wr+ l + F +vp+s++ ++qa+l+l++++ +gy++ + +g+l+lgWkd +L+++S+W+ Neem_7911_f_1 419 CLLYREINNILAIGGPARSGED-KFRHWRSELAgRNSFVQVPMSSNSMAQAQLILNMFPpAHGYSLVQGDGTLMLGWKDTSLFTASSWT 506 *************77665.5*98852799*************************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	49.952	124	485	IPR005202	Transcription factor GRAS
Pfam	PF03514	4.2E-104	150	506	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 511 aa Download sequence Send to blast
MMKGGFEVVR GALEMIQPHE RWDYSSIGFP TPSPNSFPIP TSNVIDNRCA NLERNDLSEW 60 VEHVTKQLID DLPDANSDSL QADAMMVCEN NPIPSILGDL RTRKTMRRSY FEGNGEEFQW 120 VNELGNQTNV CENGSSNRVL TKVDEQGLSL ITLLFESAVA ISVDNLGEAH RMLLELTQMA 180 SPYGPSCAER VVAYFAKAMA SRVINSWLGI CSPLINHKSA HWAFQAFNNV SPFIKFAHFT 240 SNQATLEAFH RRDRVHIIDL DIMQGLQWPA LFHILATRME GPPHVRMTGM GTSMEILLET 300 GKQLSNFAKR LGMSFEFHPI AKKFGEADPS MLQVRRGETL AVHWLQHSLY DATGPDWKTV 360 RLLEELSPRV ITLVEQEISH GGSFLDRFVG SLHYYSTLFD SLGAYLPSDD PSRHRVEHCL 420 LYREINNILA IGGPARSGED KFRHWRSELA GRNSFVQVPM SSNSMAQAQL ILNMFPPAHG 480 YSLVQGDGTL MLGWKDTSLF TASSWTSHAS R

Sequence ? help Back to Top

Protein Sequence Length: 511 aa Download sequence Send to blast

MMKGGFEVVR GALEMIQPHE RWDYSSIGFP TPSPNSFPIP TSNVIDNRCA NLERNDLSEW  60
VEHVTKQLID DLPDANSDSL QADAMMVCEN NPIPSILGDL RTRKTMRRSY FEGNGEEFQW  120
VNELGNQTNV CENGSSNRVL TKVDEQGLSL ITLLFESAVA ISVDNLGEAH RMLLELTQMA  180
SPYGPSCAER VVAYFAKAMA SRVINSWLGI CSPLINHKSA HWAFQAFNNV SPFIKFAHFT  240
SNQATLEAFH RRDRVHIIDL DIMQGLQWPA LFHILATRME GPPHVRMTGM GTSMEILLET  300
GKQLSNFAKR LGMSFEFHPI AKKFGEADPS MLQVRRGETL AVHWLQHSLY DATGPDWKTV  360
RLLEELSPRV ITLVEQEISH GGSFLDRFVG SLHYYSTLFD SLGAYLPSDD PSRHRVEHCL  420
LYREINNILA IGGPARSGED KFRHWRSELA GRNSFVQVPM SSNSMAQAQL ILNMFPPAHG  480
YSLVQGDGTL MLGWKDTSLF TASSWTSHAS R

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	1e-141	142	506	11	379	Protein SCARECROW
5b3h_A	1e-141	142	506	10	378	Protein SCARECROW
5b3h_D	1e-141	142	506	10	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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021281121.1	0.0	protein SCARECROW-like
Swissprot	Q2Z2E9	1e-136	SCR_IPONI; Protein SCARECROW
Swissprot	Q9M384	1e-138	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A061DWK6	0.0	A0A061DWK6_THECC; GRAS family transcription factor
STRING	EOX94398	0.0	(Theobroma cacao)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM16005	11	15

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G54220.1	1e-140	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]