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

Thecc1EG003984t1

Common Name

TCM_003984

Organism

Theobroma cacao

Taxonomic ID

3641

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma

Family

GRAS

Protein Properties

Length: 512aa MW: 57336.1 Da PI: 6.2318

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thecc1EG003984t1	genome	CGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	355.7	6.8e-109	151	506	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlselaspdg.dpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilk 92 l++lLlecA a+s ++l +a+++L +l ++asp++ + +R++ayf++A+++r+ +s+ ++++ l ++ + ++++f++vsP++k Thecc1EG003984t1 151 LITLLLECAVAISVDNLGEAHRMLLELTQMASPYApSCAERVVAYFAKAMSSRVINSWLGICSPLINYKS-------VHCSFQAFNNVSPYVK 236 5789*****************************8999******************987654444.......4567899***** PP GRAS 93 fshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakr 185 f+h+t NqaIlea+++ +rvHiiD+di+qGlQWpaL++ La+R egpp++R+Tg+g+ s e l etg++L++fA++lg++fef++ +ak+ Thecc1EG003984t1 237 FAHFTSNQAILEALHRRDRVHIIDLDIMQGLQWPALFHILATRIEGPPHVRMTGMGN----SMELLVETGKQLSNFAKRLGMSFEFHP-IAKK 324 *****************************************************....***********************.7* PP GRAS 186 ledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpre 278 + ++++ + +v++gE+laV++ h+l+d +++ + +L+l+ +l P+v+++veq++ h ++sFl+rf+ +l+yys++fdsl a lp++ Thecc1EG003984t1 325 FGEIDITMVQVRRGETLAVHWLQ--HSLYDATGPEWK----TLRLFEQLAPRVITLVEQDLFH-GGSFLDRFVGSLHYYSTMFDSLGAYLPAD 410 ********************9..999988888888....*****************9.789********************** PP GRAS 279 seerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsv 370 + r+ +E+ ll rei n++a g +r + ++++Wr+ l + F +vp+s++ ++qa+l+l++++ +gy++ + +g+l lgWkd +L+++ Thecc1EG003984t1 411 DPSRHRIEHYLLYREINNILAIGGPARSGED-KFKHWRSELARNCFVQVPMSSNSMAQAQLILNMFPpAHGYSLVQGDGTLRLGWKDTSLFTA 502 **********************77665.5******************************************************** PP GRAS 371 SaWr 374 SaW+ Thecc1EG003984t1 503 SAWT 506 *6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	52.633	125	485	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.3E-106	151	506	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

Sequence ? help Back to Top
Protein Sequence Length: 512 aa Download sequence Send to blast
MMKGGFEVVH ATLDMIQPHE PIWDFASVGF PTTSVSSIPR QAVENRCSNL EGNELSEWVE 60 QVTKQLIDDL PAETETDSSL LADTSMVCED SFAPSPLGDF RARKTVRRSF LDGSGEENQW 120 SNEQGNQTNN FCENGVNGRG LSRLDEQGLS LITLLLECAV AISVDNLGEA HRMLLELTQM 180 ASPYAPSCAE RVVAYFAKAM SSRVINSWLG ICSPLINYKS VHCSFQAFNN VSPYVKFAHF 240 TSNQAILEAL HRRDRVHIID LDIMQGLQWP ALFHILATRI EGPPHVRMTG MGNSMELLVE 300 TGKQLSNFAK RLGMSFEFHP IAKKFGEIDI TMVQVRRGET LAVHWLQHSL YDATGPEWKT 360 LRLFEQLAPR VITLVEQDLF HGGSFLDRFV GSLHYYSTMF DSLGAYLPAD DPSRHRIEHY 420 LLYREINNIL AIGGPARSGE DKFKHWRSEL ARNCFVQVPM SSNSMAQAQL ILNMFPPAHG 480 YSLVQGDGTL RLGWKDTSLF TASAWTSRAS R*

Sequence ? help Back to Top

Protein Sequence Length: 512 aa Download sequence Send to blast

MMKGGFEVVH ATLDMIQPHE PIWDFASVGF PTTSVSSIPR QAVENRCSNL EGNELSEWVE  60
QVTKQLIDDL PAETETDSSL LADTSMVCED SFAPSPLGDF RARKTVRRSF LDGSGEENQW  120
SNEQGNQTNN FCENGVNGRG LSRLDEQGLS LITLLLECAV AISVDNLGEA HRMLLELTQM  180
ASPYAPSCAE RVVAYFAKAM SSRVINSWLG ICSPLINYKS VHCSFQAFNN VSPYVKFAHF  240
TSNQAILEAL HRRDRVHIID LDIMQGLQWP ALFHILATRI EGPPHVRMTG MGNSMELLVE  300
TGKQLSNFAK RLGMSFEFHP IAKKFGEIDI TMVQVRRGET LAVHWLQHSL YDATGPEWKT  360
LRLFEQLAPR VITLVEQDLF HGGSFLDRFV GSLHYYSTMF DSLGAYLPAD DPSRHRIEHY  420
LLYREINNIL AIGGPARSGE DKFKHWRSEL ARNCFVQVPM SSNSMAQAQL ILNMFPPAHG  480
YSLVQGDGTL RLGWKDTSLF TASAWTSRAS R*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	1e-145	143	509	11	382	Protein SCARECROW
5b3h_A	1e-145	143	509	10	381	Protein SCARECROW
5b3h_D	1e-145	143	509	10	381	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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_007050241.2	0.0	PREDICTED: protein SCARECROW
Swissprot	Q9M384	1e-141	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-143	GRAS family protein

Link Out ? help Back to Top
Phytozome	Thecc1EG003984t1
Entrez Gene	18613111

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] Motamayor JC, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol., 2013. 14(6): p. r53 [PMID:23731509] 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]