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

Rsa1.0_01244.1_g00008.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

GRAS

Protein Properties

Length: 635aa MW: 69617.5 Da PI: 5.8505

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_01244.1_g00008.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	426.7	1.9e-130	273	632	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsev 87 +lLl+cAeavs+++le+a++lL ++s+l++p+g++ qR+aayf eA++arl++s+ ++y+alp++ ++++s + ++a+++f+ + Rsa1.0_01244.1_g00008.1 273 LTLLLQCAEAVSADNLEEANKLLLEISQLSTPYGTSAQRVAAYFSEAMSARLLNSCLGIYAALPSRWMPQTHSLKMVSAFQVFNGI 358 579********************************************************************************* PP GRAS 88 sPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelg 173 sP++kfsh+taNqaI ea+e+e++vHiiD+di+qGlQWp L++ LasRp+gpp++R+Tg+g s e+l++tg+rL++fA++lg Rsa1.0_01244.1_g00008.1 359 SPLVKFSHFTANQAIQEAFEKEDCVHIIDLDIMQGLQWPGLFHILASRPGGPPHVRLTGLGT----SMEALQATGKRLSDFADKLG 440 **********************************************************....**************** PP GRAS 174 vpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerfle 259 +pfef + +a+++ +l+ e+L+v+++Ea+aV++ h+l+d ++s ++ +L+l+++l Pkvv+vveq+++h ++sFl rf+e Rsa1.0_01244.1_g00008.1 441 LPFEFCP-LAEKVGNLDAERLNVRKREAVAVHWLQ--HSLYDVTGSDTH----TLWLLQRLAPKVVTVVEQDLSH-AGSFLGRFVE 518 ***.59********************9..999988888777....******************.899*** PP GRAS 260 aleyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk 345 a++yysalfdsl a++++eseer++vE++ll++ei+nv+a g +r + + +e+Wre+++++GFk ++l +aa+qa lll +++ Rsa1.0_01244.1_g00008.1 519 AIHYYSALFDSLGASYGEESEERHVVEQQLLSKEIRNVLAVGGPSRSGEVK-FESWREKMQQCGFKGISLAGNAATQATLLLGMFP 603 *****************************************888776.****************************** PP GRAS 346 sdgyrveeesgslvlgWkdrpLvsvSaWr 374 sdgy++ +++g+l lgWkd +L+++SaW+ Rsa1.0_01244.1_g00008.1 604 SDGYTLVDDNGTLKLGWKDLSLLTASAWT 632 **************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	61.608	246	612	IPR005202	Transcription factor GRAS
Pfam	PF03514	6.4E-128	273	632	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: 635 aa Download sequence Send to blast
MAESSGRTTS SDNTSTNRTV PPLPPPASAM VRKRLASEMS SSPSLNNNQR LPPPHRVSHL 60 PDSSSNYIIT PDSTTHPTPP VSVCGFSGLP VFPSDNNNRT TTAMSVQPME QQQQQQQQDS 120 SASSSSSPTV WVDAIIRDLI NSSASVSIPQ LIQNVRDIIF PCNPNLGALL EYRLRSLMLL 180 DPPPSSDPPP PFDSISQYHQ ISNNPSPPPL TQQQQPKPPP PPPVQQQERE NSPPPPETVT 240 TTTNTNTNTA EALRERKEEI KRQKQDEEGL HLLTLLLQCA EAVSADNLEE ANKLLLEISQ 300 LSTPYGTSAQ RVAAYFSEAM SARLLNSCLG IYAALPSRWM PQTHSLKMVS AFQVFNGISP 360 LVKFSHFTAN QAIQEAFEKE DCVHIIDLDI MQGLQWPGLF HILASRPGGP PHVRLTGLGT 420 SMEALQATGK RLSDFADKLG LPFEFCPLAE KVGNLDAERL NVRKREAVAV HWLQHSLYDV 480 TGSDTHTLWL LQRLAPKVVT VVEQDLSHAG SFLGRFVEAI HYYSALFDSL GASYGEESEE 540 RHVVEQQLLS KEIRNVLAVG GPSRSGEVKF ESWREKMQQC GFKGISLAGN AATQATLLLG 600 MFPSDGYTLV DDNGTLKLGW KDLSLLTASA WTPCS

Sequence ? help Back to Top

Protein Sequence Length: 635 aa Download sequence Send to blast

MAESSGRTTS SDNTSTNRTV PPLPPPASAM VRKRLASEMS SSPSLNNNQR LPPPHRVSHL  60
PDSSSNYIIT PDSTTHPTPP VSVCGFSGLP VFPSDNNNRT TTAMSVQPME QQQQQQQQDS  120
SASSSSSPTV WVDAIIRDLI NSSASVSIPQ LIQNVRDIIF PCNPNLGALL EYRLRSLMLL  180
DPPPSSDPPP PFDSISQYHQ ISNNPSPPPL TQQQQPKPPP PPPVQQQERE NSPPPPETVT  240
TTTNTNTNTA EALRERKEEI KRQKQDEEGL HLLTLLLQCA EAVSADNLEE ANKLLLEISQ  300
LSTPYGTSAQ RVAAYFSEAM SARLLNSCLG IYAALPSRWM PQTHSLKMVS AFQVFNGISP  360
LVKFSHFTAN QAIQEAFEKE DCVHIIDLDI MQGLQWPGLF HILASRPGGP PHVRLTGLGT  420
SMEALQATGK RLSDFADKLG LPFEFCPLAE KVGNLDAERL NVRKREAVAV HWLQHSLYDV  480
TGSDTHTLWL LQRLAPKVVT VVEQDLSHAG SFLGRFVEAI HYYSALFDSL GASYGEESEE  540
RHVVEQQLLS KEIRNVLAVG GPSRSGEVKF ESWREKMQQC GFKGISLAGN AATQATLLLG  600
MFPSDGYTLV DDNGTLKLGW KDLSLLTASA WTPCS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	256	635	3	382	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	Rsa1.0_01244.1_g00008.1

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	EF104551	0.0	EF104551.1 Brassica rapa clone scr_5 genomic sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018432923.1	0.0	PREDICTED: LOW QUALITY PROTEIN: protein SCARECROW
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A0D3DSZ2	0.0	A0A0D3DSZ2_BRAOL; Uncharacterized protein
STRING	Bo8g083500.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM8164	26	40

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]