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

evm.model.supercontig_1018.1

Organism

Carica papaya

Taxonomic ID

3649

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Caricaceae; Carica

Family

GRAS

Protein Properties

Length: 787aa MW: 85708.9 Da PI: 5.7926

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm.model.supercontig_1018.1	genome	ASGPB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	422.4	3.7e-129	416	775	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalk 82 +lLl+cAeavs+++le+a+++L ++sel++p+g++ qR+aayf eA++arl++s+ ++y+alp+ + ++++ + ++a++ evm.model.supercontig_1018.1 416 LTLLLQCAEAVSAENLEEANRMLLEISELSTPYGTSAQRVAAYFSEAMSARLVSSCLGIYAALPSISMPQTHAHKMVSAFQ 496 579****************************************************************9******* PP GRAS 83 lfsevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetge 163 +f+ +sP++kfsh+taNqaI ea+e+eervHiiD+di+qGlQWp L++ LasRp+gpp +R+Tg+g s e+le+tg+ evm.model.supercontig_1018.1 497 VFNGISPFVKFSHFTANQAIQEAFEREERVHIIDLDIMQGLQWPGLFHILASRPGGPPYVRLTGLGT----SMEALEATGK 573 ***************************************************************....****** PP GRAS 164 rLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveq 244 rL++fA++lg+pfef + va+++ +l++++L++++ Ea+aV++ h+l+d ++s ++ +L+l+++l Pkvv+vveq evm.model.supercontig_1018.1 574 RLSDFAHKLGLPFEFCP-VAEKVGNLDPDRLNISKTEAVAVHWLQ--HSLYDVTGSDTN----TLWLLQRLAPKVVTVVEQ 647 *************.7*********************9..999999999999....************** PP GRAS 245 eadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFk 325 +++h +++Fl rf+ea++yysalfdsl a++++eseer++vE++ll+rei+nv+a g +r +++ +++Wre+l+++GFk evm.model.supercontig_1018.1 648 DLSH-AGPFLGRFVEAIHYYSALFDSLGASYGEESEERHVVEQQLLSREIRNVLAVGGPSRSGEMK-FHNWREKLQQCGFK 726 .89*************************************************999887.********** PP GRAS 326 pvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 ++l +aa+qa lll +++sdgy++ e++g+l lgWkd L+++SaWr evm.model.supercontig_1018.1 727 GISLAGNAATQATLLLGMFPSDGYTLVEDNGTLKLGWKDLCLLTASAWR 775 **********************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	62.353	389	755	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.3E-126	416	775	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008356	Biological Process	asymmetric cell division
GO:0009630	Biological Process	gravitropism
GO:0009956	Biological Process	radial pattern formation
GO:0048366	Biological Process	leaf development
GO:0051457	Biological Process	maintenance of protein location in nucleus
GO:0090610	Biological Process	bundle sheath cell fate specification
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 787 aa Download sequence Send to blast
MAAFGLVGND DGDDDRSNGS SGQNNNHPSS ITCSGSNSKD CSTPSDGKMV RKRMASEMGV 60 HNPEYQRISR RSSFLLPASS IDGNEKSPTP NSSSNYSTMN IMNMGFNPSC TLTSGSASLS 120 TNCNNTTNFT CLDSLSDSPQ IPSVCGFSGL PLFPPEKNPN SSATASVVSN TSAAPLISVP 180 TAMEDASATA WIDSIIKDLL HSSTTVSIPQ LIQNVREIIY PCNPNLAALF EYRLRSLIDP 240 LDRRRKETFP LQPPVGSLYR PPAYAHQQQQ SSGIFDNVPN FTLPDSSAML NQYSSWGLSP 300 AFPIHSGTDA NNQQYPRPQI ITTSGASSAL YTPGLSLNQA VPQPVPVEIQ PQTRRQAQVQ 360 PQEQEPEQEN SSPAETVSST PPTTSKPTSA TTATVKIDKK EELRQQKRDE EGLHLLTLLL 420 QCAEAVSAEN LEEANRMLLE ISELSTPYGT SAQRVAAYFS EAMSARLVSS CLGIYAALPS 480 ISMPQTHAHK MVSAFQVFNG ISPFVKFSHF TANQAIQEAF EREERVHIID LDIMQGLQWP 540 GLFHILASRP GGPPYVRLTG LGTSMEALEA TGKRLSDFAH KLGLPFEFCP VAEKVGNLDP 600 DRLNISKTEA VAVHWLQHSL YDVTGSDTNT LWLLQRLAPK VVTVVEQDLS HAGPFLGRFV 660 EAIHYYSALF DSLGASYGEE SEERHVVEQQ LLSREIRNVL AVGGPSRSGE MKFHNWREKL 720 QQCGFKGISL AGNAATQATL LLGMFPSDGY TLVEDNGTLK LGWKDLCLLT ASAWRPFHAN 780 PTPHNSX

Sequence ? help Back to Top

Protein Sequence Length: 787 aa Download sequence Send to blast

MAAFGLVGND DGDDDRSNGS SGQNNNHPSS ITCSGSNSKD CSTPSDGKMV RKRMASEMGV  60
HNPEYQRISR RSSFLLPASS IDGNEKSPTP NSSSNYSTMN IMNMGFNPSC TLTSGSASLS  120
TNCNNTTNFT CLDSLSDSPQ IPSVCGFSGL PLFPPEKNPN SSATASVVSN TSAAPLISVP  180
TAMEDASATA WIDSIIKDLL HSSTTVSIPQ LIQNVREIIY PCNPNLAALF EYRLRSLIDP  240
LDRRRKETFP LQPPVGSLYR PPAYAHQQQQ SSGIFDNVPN FTLPDSSAML NQYSSWGLSP  300
AFPIHSGTDA NNQQYPRPQI ITTSGASSAL YTPGLSLNQA VPQPVPVEIQ PQTRRQAQVQ  360
PQEQEPEQEN SSPAETVSST PPTTSKPTSA TTATVKIDKK EELRQQKRDE EGLHLLTLLL  420
QCAEAVSAEN LEEANRMLLE ISELSTPYGT SAQRVAAYFS EAMSARLVSS CLGIYAALPS  480
ISMPQTHAHK MVSAFQVFNG ISPFVKFSHF TANQAIQEAF EREERVHIID LDIMQGLQWP  540
GLFHILASRP GGPPYVRLTG LGTSMEALEA TGKRLSDFAH KLGLPFEFCP VAEKVGNLDP  600
DRLNISKTEA VAVHWLQHSL YDVTGSDTNT LWLLQRLAPK VVTVVEQDLS HAGPFLGRFV  660
EAIHYYSALF DSLGASYGEE SEERHVVEQQ LLSREIRNVL AVGGPSRSGE MKFHNWREKL  720
QQCGFKGISL AGNAATQATL LLGMFPSDGY TLVEDNGTLK LGWKDLCLLT ASAWRPFHAN  780
PTPHNSX

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	399	776	3	380	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	evm.model.supercontig_1018.1

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021897229.1	0.0	protein SCARECROW
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A061EF07	0.0	A0A061EF07_THECC; GRAS family transcription factor isoform 1
TrEMBL	A0A061ELM0	0.0	A0A061ELM0_THECC; GRAS family transcription factor isoform 2
STRING	evm.model.supercontig_1018.1	0.0	(Carica papaya)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8164	26	40
Representative plant	OGRP2183	14	37

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G54220.1	0.0	GRAS family protein

Link Out ? help Back to Top
Phytozome	evm.model.supercontig_1018.1

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]