PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Protein Features |

3D Structure |

Function |

Orthologous Group |

Publication

Basic Information? help Back to Top

TF ID

Niben101Scf00991g02005.1

Organism

Nicotiana benthamiana

Taxonomic ID

4100

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana

Family

GRAS

Protein Properties

Length: 468aa MW: 53355.3 Da PI: 5.7466

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Niben101Scf00991g02005.1	genome	BTI	-

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	83.6	3.4e-26	133	240	3	110
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsev 87 + Lle +a+++++ +++q+l++ l+el+sp+gd+ q+la+yf++AL +r+++s++++y++l + ++++ + +++ + + f+ev Niben101Scf00991g02005.1 133 DILLETSRAIADKNSTRVQQLMWMLNELSSPYGDTEQKLASYFLQALFSRMTDSGESCYRTLVSASDKTCSFESTRKLVLKFQEV 217 6799********************************************************8888876555555455555 PP GRAS 88 sPilkfshltaNqaIleavegee 110 sP+ +f+h++ N aI+ea+ege+ Niben101Scf00991g02005.1 218 SPWTTFGHVASNGAIMEAFEGER 240 ******************985 PP
2	GRAS	181.6	5.5e-56	246	467	155	374
GRAS 155 keeleetgerLakfAeelgvpfefnvlvak.rledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkv 238 ++ ++e+g+r++kfA+ +gvpf+fnv+++ +l++l++ +L++k++Ea+aVn++ +lh++ ++ ++rd +++l+++l+P++ Niben101Scf00991g02005.1 246 QKVMKEIGSRMEKFARLMGVPFKFNVIHHMgNLSELDIGALDIKEDEAVAVNCIGALHSVS----PTGNRRDYLISLFRRLQPRI 326 6889********************96656*************************8....7888899********* PP GRAS 239 vvvveqeadhnse....sFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerl 319 +++ve+ead++ +F+++f e+l++ + f+sl++++p++s+er ++Er+ gr+iv+++ac +e+ er+et +kW++rl Niben101Scf00991g02005.1 327 ITIVEEEADLDVRadglDFVKGFQECLRWIRVYFESLDESFPKTSNERLMLERQ-AGRSIVDLLACPPSESMERRETGAKWSHRL 410 ***98854435559********************************.************************** PP GRAS 320 eeaGFkpvplsekaakqaklllrkvksdgyrveee...sgslvlgWkdrpLvsvSaWr 374 ++ GF+p+ +s+++ +++++llr++k +g+++ ++ s+ ++l W+++++v++SaW+ Niben101Scf00991g02005.1 411 HAGGFSPILYSDEVCDDVRALLRRYK-EGWTMTQSggdSAGIFLSWNEQSVVWASAWK 467 **********************.8888886645488899************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	20.779	105	445	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.2E-23	133	240	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.9E-53	246	467	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 468 aa Download sequence Send to blast
MDTLFRLVSF QQQQQSDQSF NSSRTSSSSR SSNKQNTYST YNYPSQHNQE DEECFNFFMD 60 EDDFSSNSSS KHNNYPPTYH YQHHHQQQFS NTPTPTTTSS TPTQSHQYYD HFSPARDLNL 120 EFGSSFSGKW ATDILLETSR AIADKNSTRV QQLMWMLNEL SSPYGDTEQK LASYFLQALF 180 SRMTDSGESC YRTLVSASDK TCSFESTRKL VLKFQEVSPW TTFGHVASNG AIMEAFEGER 240 GTAAVQKVMK EIGSRMEKFA RLMGVPFKFN VIHHMGNLSE LDIGALDIKE DEAVAVNCIG 300 ALHSVSPTGN RRDYLISLFR RLQPRIITIV EEEADLDVRA DGLDFVKGFQ ECLRWIRVYF 360 ESLDESFPKT SNERLMLERQ AGRSIVDLLA CPPSESMERR ETGAKWSHRL HAGGFSPILY 420 SDEVCDDVRA LLRRYKEGWT MTQSGGDSAG IFLSWNEQSV VWASAWKP

Sequence ? help Back to Top

Protein Sequence Length: 468 aa Download sequence Send to blast

MDTLFRLVSF QQQQQSDQSF NSSRTSSSSR SSNKQNTYST YNYPSQHNQE DEECFNFFMD  60
EDDFSSNSSS KHNNYPPTYH YQHHHQQQFS NTPTPTTTSS TPTQSHQYYD HFSPARDLNL  120
EFGSSFSGKW ATDILLETSR AIADKNSTRV QQLMWMLNEL SSPYGDTEQK LASYFLQALF  180
SRMTDSGESC YRTLVSASDK TCSFESTRKL VLKFQEVSPW TTFGHVASNG AIMEAFEGER  240
GTAAVQKVMK EIGSRMEKFA RLMGVPFKFN VIHHMGNLSE LDIGALDIKE DEAVAVNCIG  300
ALHSVSPTGN RRDYLISLFR RLQPRIITIV EEEADLDVRA DGLDFVKGFQ ECLRWIRVYF  360
ESLDESFPKT SNERLMLERQ AGRSIVDLLA CPPSESMERR ETGAKWSHRL HAGGFSPILY  420
SDEVCDDVRA LLRRYKEGWT MTQSGGDSAG IFLSWNEQSV VWASAWKP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_B	1e-162	122	468	78	474	Protein SHORT-ROOT
5b3h_B	1e-163	122	468	24	420	Protein SHORT-ROOT
5b3h_E	1e-163	122	468	24	420	Protein SHORT-ROOT
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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 both cell division and cell specification. Regulates the radial organization of the shoot axial organs and is required for normal shoot gravitropism. Directly controls the transcription of SCR, and when associated with SCR, of MGP, RLK, TRI, NUC and SCL3. {ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:12569126, ECO:0000269\|PubMed:15314023, ECO:0000269\|PubMed:16640459, ECO:0000269\|PubMed:17446396, ECO:0000269\|PubMed:9670559}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016479900.1	0.0	PREDICTED: protein SHORT-ROOT-like
Refseq	XP_016479901.1	0.0	PREDICTED: protein SHORT-ROOT-like
Swissprot	Q9SZF7	1e-174	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A1S4ATK6	0.0	A0A1S4ATK6_TOBAC; protein SHORT-ROOT-like
STRING	XP_009618165.1	0.0	(Nicotiana tomentosiformis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA2031	24	64

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	1e-168	GRAS family protein

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Muraro D, et al. Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(2): p. 857-62 [PMID:24381155] 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] 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] Ahrazem O, et al. Ectopic expression of a stress-inducible glycosyltransferase from saffron enhances salt and oxidative stress tolerance in Arabidopsis while alters anchor root formation. Plant Sci., 2015. 234: p. 60-73 [PMID:25804810] 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] Miguel A,Milhinhos A,Novák O,Jones B,Miguel CM The SHORT-ROOT-like gene PtSHR2B is involved in Populus phellogen activity. J. Exp. Bot., 2016. 67(5): p. 1545-55 [PMID:26709311] 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] Kim ES, et al. HAWAIIAN SKIRT regulates the quiescent center-independent meristem activity in Arabidopsis roots. Physiol Plant, 2016. 157(2): p. 221-33 [PMID:26968317] 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] 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] 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] 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] Henry S, et al. SHR overexpression induces the formation of supernumerary cell layers with cortex cell identity in rice. Dev. Biol., 2017. 425(1): p. 1-7 [PMID:28263767] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] 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] Yu Q, et al. Cell-Fate Specification in Arabidopsis Roots Requires Coordinative Action of Lineage Instruction and Positional Reprogramming. Plant Physiol., 2017. 175(2): p. 816-827 [PMID:28821591] Spiegelman Z,Lee CM,Gallagher KL KinG Is a Plant-Specific Kinesin That Regulates Both Intra- and Intercellular Movement of SHORT-ROOT. Plant Physiol., 2018. 176(1): p. 392-405 [PMID:29122988] 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]