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

Csa09g062690.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

GRAS

Protein Properties

Length: 816aa MW: 88988.7 Da PI: 6.317

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa09g062690.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	425.8	3.4e-130	453	812	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshl 96 +lLl+cAeavs+++le+a++lL ++s+l++p+g++ qR+aayf eA++arl++s+ ++y+alp++ ++++s + ++a+++f+ +sP++kfsh+ Csa09g062690.1 453 LTLLLQCAEAVSADNLEEANKLLLEISQLSTPYGTSAQRVAAYFSEAMSARLLNSCLGIYAALPSRWMPQTHSLKMVSAFQVFNGISPLVKFSHF 547 579****************************************************************************************** PP GRAS 97 taNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledlel 191 taNqaI ea+e+e+ vHiiD+di+qGlQWp L++ LasRp+gpp++R+Tg+g s e+l++tg+rL++fA++lg+pfef + +a+++ +l++ Csa09g062690.1 548 TANQAIQEAFEKEDSVHIIDLDIMQGLQWPGLFHILASRPGGPPHVRLTGLGT----SMEALQATGKRLSDFADKLGLPFEFCP-LAEKVGNLDT 637 *************************************************....***********************.59**** PP GRAS 192 eeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvE 286 e+L+v+++Ea+aV++ h+l+d ++s ++ +L+l+++l Pkvv+vveq+++h ++sFl rf+ea++yysalfdsl a++++eseer++vE Csa09g062690.1 638 ERLNVRKREAVAVHWLQ--HSLYDVTGSDAH----TLWLLQRLAPKVVTVVEQDLSH-AGSFLGRFVEAIHYYSALFDSLGASYGEESEERHVVE 725 ************9..999988888888....******************.899****************************** PP GRAS 287 rellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 ++ll++ei+nv+a g +r + + +e+Wre+++++GFk ++l +aa+qa lll +++sdgy++ +++g+l lgWkd +L+++SaW+ Csa09g062690.1 726 QQLLSKEIRNVLAVGGPSRSGEVK-FESWREKMQQCGFKGISLAGNAATQATLLLGMFPSDGYTLVDDNGTLKLGWKDLSLLTASAWT 812 **************888776.************************************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	61.608	426	792	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.2E-127	453	812	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 816 aa Download sequence Send to blast
MADSGDFNGG QPPHSPLRTT SSGSSSSNNR SGAPPPPPLV MVRKRLASEM SSNPDYNNPS 60 RPPRRASHLL DSNYNTLSPQ QQQQQPPSLA AATAVASQPN PPLSVCGFSG LPVFPSDRGG 120 GRNAMSVQPM EQDSSSSSAS PTVWVDAIIR DLIHSSTSVS IPQLIQNVRD IIFPCNPNLG 180 ALLEXPFFFI GDLMVRKRLA SEMSSNPDYN NPSRPPRRAS HLLDSNYNTV PPQQQQQQPP 240 SLAAATAVAS QPNPPLSVCG FSGLPVFPSD RGGGRNAMSV QPMEQDSSSS SASPTVWVDA 300 IIRDLIHSST SVSIPQLIQN VRDIIFPCNP NLGALLEYRL RSLMLLDPSS SSDPSPQSFE 360 PLYQISNNPS PPVTQHQQQH QHQQQQQQQQ QHKTPPPPPI QQQERENSST DAPPQPETVT 420 TTTATVTNTA EALRERKEEI KRQKQDEEGL HLLTLLLQCA EAVSADNLEE ANKLLLEISQ 480 LSTPYGTSAQ RVAAYFSEAM SARLLNSCLG IYAALPSRWM PQTHSLKMVS AFQVFNGISP 540 LVKFSHFTAN QAIQEAFEKE DSVHIIDLDI MQGLQWPGLF HILASRPGGP PHVRLTGLGT 600 SMEALQATGK RLSDFADKLG LPFEFCPLAE KVGNLDTERL NVRKREAVAV HWLQHSLYDV 660 TGSDAHTLWL LQRLAPKVVT VVEQDLSHAG SFLGRFVEAI HYYSALFDSL GASYGEESEE 720 RHVVEQQLLS KEIRNVLAVG GPSRSGEVKF ESWREKMQQC GFKGISLAGN AATQATLLLG 780 MFPSDGYTLV DDNGTLKLGW KDLSLLTASA WTPRS*

Sequence ? help Back to Top

Protein Sequence Length: 816 aa Download sequence Send to blast

MADSGDFNGG QPPHSPLRTT SSGSSSSNNR SGAPPPPPLV MVRKRLASEM SSNPDYNNPS  60
RPPRRASHLL DSNYNTLSPQ QQQQQPPSLA AATAVASQPN PPLSVCGFSG LPVFPSDRGG  120
GRNAMSVQPM EQDSSSSSAS PTVWVDAIIR DLIHSSTSVS IPQLIQNVRD IIFPCNPNLG  180
ALLEXPFFFI GDLMVRKRLA SEMSSNPDYN NPSRPPRRAS HLLDSNYNTV PPQQQQQQPP  240
SLAAATAVAS QPNPPLSVCG FSGLPVFPSD RGGGRNAMSV QPMEQDSSSS SASPTVWVDA  300
IIRDLIHSST SVSIPQLIQN VRDIIFPCNP NLGALLEYRL RSLMLLDPSS SSDPSPQSFE  360
PLYQISNNPS PPVTQHQQQH QHQQQQQQQQ QHKTPPPPPI QQQERENSST DAPPQPETVT  420
TTTATVTNTA EALRERKEEI KRQKQDEEGL HLLTLLLQCA EAVSADNLEE ANKLLLEISQ  480
LSTPYGTSAQ RVAAYFSEAM SARLLNSCLG IYAALPSRWM PQTHSLKMVS AFQVFNGISP  540
LVKFSHFTAN QAIQEAFEKE DSVHIIDLDI MQGLQWPGLF HILASRPGGP PHVRLTGLGT  600
SMEALQATGK RLSDFADKLG LPFEFCPLAE KVGNLDTERL NVRKREAVAV HWLQHSLYDV  660
TGSDAHTLWL LQRLAPKVVT VVEQDLSHAG SFLGRFVEAI HYYSALFDSL GASYGEESEE  720
RHVVEQQLLS KEIRNVLAVG GPSRSGEVKF ESWREKMQQC GFKGISLAGN AATQATLLLG  780
MFPSDGYTLV DDNGTLKLGW KDLSLLTASA WTPRS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	436	815	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	Csa09g062690.1

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	AY056315	0.0	AY056315.1 Arabidopsis thaliana putative SCARECROW1 protein (At3g54220) mRNA, complete cds.
GenBank	AY080840	0.0	AY080840.1 Arabidopsis thaliana putative SCARECROW1 protein (At3g54220) mRNA, complete cds.
GenBank	AY113991	0.0	AY113991.1 Arabidopsis thaliana putative SCARECROW1 protein (At3g54220) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010427091.1	0.0	PREDICTED: protein SCARECROW-like
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A178V8F9	0.0	A0A178V8F9_ARATH; SGR1
STRING	XP_010427091.1	0.0	(Camelina sativa)

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]