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

Pbr028512.1

Organism

Pyrus bretschneideri

Taxonomic ID

225117

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Pyrus

Family

GRAS

Protein Properties

Length: 786aa MW: 84521.2 Da PI: 6.5518

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pbr028512.1	genome	CPETR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	419.4	3.1e-128	413	772	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaN 99 +lLl+cAeavs++++ +a+++L ++sel++p g++ qR+aayf eA++arl++s+ ++y++lp s+ +++++++ ++a+++f+ +sP++kfsh+taN Pbr028512.1 413 LTLLLKCAEAVSADNFDEATKILLEISELSTPFGTSAQRVAAYFSEAMSARLVSSCLGIYASLPRSSVPTTHTQKMVSAFQVFNGISPFIKFSHFTAN 510 579***************************************************************999*********************** PP GRAS 100 qaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvk 197 qaI ea+e+e+rvHi+D+di+qGlQWp L++ LasRp+gpp +R+Tg+g s e+le+tg+rL++fA++lg+pfef + va+++++l++e+L+v+ Pbr028512.1 511 QAIQEAFEREDRVHIVDLDIMQGLQWPGLFHILASRPGGPPYVRLTGLGT----SMEALEATGKRLSDFADKLGLPFEFFP-VAEKVANLDPERLNVS 603 **********************************************....***********************.7*********** PP GRAS 198 pgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreiv 295 ++Ea+aV++ h+l+d ++s +s +L+l+++l Pkvv+vveq+++h ++sFl rf+ea++yysalfdsl a++++eseer++vE++ll+rei+ Pbr028512.1 604 KREAVAVHWLQ--HSLYDVTGSDSS----TLWLLQRLAPKVVTVVEQDLSH-AGSFLGRFVEAIHYYSALFDSLGASYGEESEERHVVEQQLLSREIR 694 ******9..999999999888....******************.899*************************************** PP GRAS 296 nvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 nv+a g +r + + +++Wre++++ GF+ ++l +aa+qa+lll +++sdgy++ e++g+l lgWkd L+++SaWr Pbr028512.1 695 NVLAVGGPSRSGEVK-FHNWREKFQQTGFRGISLAGNAANQASLLLGMFPSDGYTLVEDNGTLKLGWKDLCLLTASAWR 772 *****888776.************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	62.276	386	752	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.1E-125	413	772	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: 786 aa Download sequence Send to blast
MNNTTTNSNS SSVEQQPPKM VRKRMASEIE VQTTLTSRTA GSDYFRLSRR GIINNSPPVQ 60 PVSQNPNASK VNSSMFYPNH STMLLPVPSS TNLAALTSPG GAFLSPTSPS PSPSSAAAAG 120 TWGPIDPLSF HRPPPVQPTT TTQTTTTPAV CGFSGLPLFP PEKTTPLNTS ITATTPSSVS 180 MEDGSSAATA WIDGIIKDLV HSSTNVSIPQ LIHNVREIIF PCNPSLAALL EYRLRSISEP 240 LPPPPLPLPV PSFNPTPIPD MRRRQQGGPG PGALKLNLDS GAIHDVAIFN PSTVENNDLY 300 LQSWSGGAGG GGVGLSLPQP NPTAAPITCN QTNPHHQSPS FNQAIHQTQD KQLENSSSSS 360 PAAESTTPTA APAPTTTAAT APPEPTTSAV SLLREKKEEI RQQKRDEEGL HLLTLLLKCA 420 EAVSADNFDE ATKILLEISE LSTPFGTSAQ RVAAYFSEAM SARLVSSCLG IYASLPRSSV 480 PTTHTQKMVS AFQVFNGISP FIKFSHFTAN QAIQEAFERE DRVHIVDLDI MQGLQWPGLF 540 HILASRPGGP PYVRLTGLGT SMEALEATGK RLSDFADKLG LPFEFFPVAE KVANLDPERL 600 NVSKREAVAV HWLQHSLYDV TGSDSSTLWL LQRLAPKVVT VVEQDLSHAG SFLGRFVEAI 660 HYYSALFDSL GASYGEESEE RHVVEQQLLS REIRNVLAVG GPSRSGEVKF HNWREKFQQT 720 GFRGISLAGN AANQASLLLG MFPSDGYTLV EDNGTLKLGW KDLCLLTASA WRPPFHAAAN 780 PNLHY*

Sequence ? help Back to Top

Protein Sequence Length: 786 aa Download sequence Send to blast

MNNTTTNSNS SSVEQQPPKM VRKRMASEIE VQTTLTSRTA GSDYFRLSRR GIINNSPPVQ  60
PVSQNPNASK VNSSMFYPNH STMLLPVPSS TNLAALTSPG GAFLSPTSPS PSPSSAAAAG  120
TWGPIDPLSF HRPPPVQPTT TTQTTTTPAV CGFSGLPLFP PEKTTPLNTS ITATTPSSVS  180
MEDGSSAATA WIDGIIKDLV HSSTNVSIPQ LIHNVREIIF PCNPSLAALL EYRLRSISEP  240
LPPPPLPLPV PSFNPTPIPD MRRRQQGGPG PGALKLNLDS GAIHDVAIFN PSTVENNDLY  300
LQSWSGGAGG GGVGLSLPQP NPTAAPITCN QTNPHHQSPS FNQAIHQTQD KQLENSSSSS  360
PAAESTTPTA APAPTTTAAT APPEPTTSAV SLLREKKEEI RQQKRDEEGL HLLTLLLKCA  420
EAVSADNFDE ATKILLEISE LSTPFGTSAQ RVAAYFSEAM SARLVSSCLG IYASLPRSSV  480
PTTHTQKMVS AFQVFNGISP FIKFSHFTAN QAIQEAFERE DRVHIVDLDI MQGLQWPGLF  540
HILASRPGGP PYVRLTGLGT SMEALEATGK RLSDFADKLG LPFEFFPVAE KVANLDPERL  600
NVSKREAVAV HWLQHSLYDV TGSDSSTLWL LQRLAPKVVT VVEQDLSHAG SFLGRFVEAI  660
HYYSALFDSL GASYGEESEE RHVVEQQLLS REIRNVLAVG GPSRSGEVKF HNWREKFQQT  720
GFRGISLAGN AANQASLLLG MFPSDGYTLV EDNGTLKLGW KDLCLLTASA WRPPFHAAAN  780
PNLHY*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	396	773	3	380	Protein SCARECROW
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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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pbr028512.1

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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009337846.1	0.0	PREDICTED: protein SCARECROW 2-like
Swissprot	Q2Z2E9	0.0	SCR_IPONI; Protein SCARECROW
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A498IKT2	0.0	A0A498IKT2_MALDO; Uncharacterized protein
STRING	XP_009337846.1	0.0	(Pyrus x bretschneideri)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF2068	34	89

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