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_27.model.AmTr_v1.0_scaffold00086.29

Common Name

AMTR_s00086p00066190

Organism

Amborella trichopoda

Taxonomic ID

13333

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella

Family

GRAS

Protein Properties

Length: 406aa MW: 45594.6 Da PI: 5.3549

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00086.29	genome	TAGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	336.3	5.5e-103	31	404	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetsek 72 ++L+ecA a++++d +++q+lL+ l+el+sp+gd+ q+laa f++AL ++++s+ ++ + l + +++ + evm_27.model.AmTr_v1.0_scaffold00086.29 31 KVLVECAMAIETQDSTRTQHLLWVLNELSSPYGDTDQKLAAAFLQALFCKVTDSGRKTHRNLVAAAEKMY 100 78**********************************************************99999877 PP GRAS 73 nsseelaalklfsevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppsl 142 + +++ ++ f+evsP+ +f+h++aN a+ ea++ge+r+Hi+D++ ++++QWp+Ll+aLa+R++++p++ evm_27.model.AmTr_v1.0_scaffold00086.29 101 TFESTRRMMLRFQEVSPWTTFGHVAANGALIEAMNGENRIHIVDISGTYCTQWPTLLEALATRSDDTPHV 170 76666666666******************************************************* PP GRAS 143 RiTgvgspesg..skeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlql 210 RiT v s+ g ++ +e+g r++kfA+ +gvpf+f+ l++ ++e+l+ e+L++++gE+la+n++++l evm_27.model.AmTr_v1.0_scaffold00086.29 171 RITHVLSSV-GpaGHRVSREIGARMEKFARLMGVPFNFSSLHVAEIEALNHENLKLQEGEVLAINCIFSL 239 999844.357999*************************************************** PP GRAS 211 hrlldesvsleserdevLklvkslsPkvvvvveqeadhnse...sFlerflealeyysalfdsleaklpr 277 h++ + rd+ ++++++l P+v+++ve+e+d++s F++ + e+++++ a ++sl++++p+ evm_27.model.AmTr_v1.0_scaffold00086.29 240 HKVG------PTSRDTAVSALRRLDPRVLTLVEEEVDLDSDrgqGFAAWLGECVRFFRAYLESLDESFPK 303 8......444689****************9996543459********************* PP GRAS 278 eseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksd 347 +seer ++Er+ ++r++v++vac +e+rer+e+ + W +r++++GF+pv +s+++ +++++llr++ + evm_27.model.AmTr_v1.0_scaffold00086.29 304 ASEERLMLERA-MARAAVDLVACPADESRERRERSGWWARRMRACGFGPVGFSDDVLDDMRALLRRYR-E 371 *******.***************************************************9.6 PP GRAS 348 gyrve.....eesgslv.lgWkdrpLvsvSaWr 374 g+++ +e gs v l Wk++p+v++SaW+ evm_27.model.AmTr_v1.0_scaffold00086.29 372 GWSMGlgradDEAGSGVyLEWKEEPMVWASAWK 404 655544465555666666************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	49.919	3	379	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.9E-100	31	404	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0008356	Biological Process	asymmetric cell division
GO:0009956	Biological Process	radial pattern formation
GO:0045930	Biological Process	negative regulation of mitotic cell cycle
GO:0048366	Biological Process	leaf development
GO:0055072	Biological Process	iron ion homeostasis
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 406 aa Download sequence Send to blast
MDEEDFSSSS NPNPNPNFDP SQFSSPKWAL KVLVECAMAI ETQDSTRTQH LLWVLNELSS 60 PYGDTDQKLA AAFLQALFCK VTDSGRKTHR NLVAAAEKMY TFESTRRMML RFQEVSPWTT 120 FGHVAANGAL IEAMNGENRI HIVDISGTYC TQWPTLLEAL ATRSDDTPHV RITHVLSSVG 180 PAGHRVSREI GARMEKFARL MGVPFNFSSL HVAEIEALNH ENLKLQEGEV LAINCIFSLH 240 KVGPTSRDTA VSALRRLDPR VLTLVEEEVD LDSDRGQGFA AWLGECVRFF RAYLESLDES 300 FPKASEERLM LERAMARAAV DLVACPADES RERRERSGWW ARRMRACGFG PVGFSDDVLD 360 DMRALLRRYR EGWSMGLGRA DDEAGSGVYL EWKEEPMVWA SAWKP*

Sequence ? help Back to Top

Protein Sequence Length: 406 aa Download sequence Send to blast

MDEEDFSSSS NPNPNPNFDP SQFSSPKWAL KVLVECAMAI ETQDSTRTQH LLWVLNELSS  60
PYGDTDQKLA AAFLQALFCK VTDSGRKTHR NLVAAAEKMY TFESTRRMML RFQEVSPWTT  120
FGHVAANGAL IEAMNGENRI HIVDISGTYC TQWPTLLEAL ATRSDDTPHV RITHVLSSVG  180
PAGHRVSREI GARMEKFARL MGVPFNFSSL HVAEIEALNH ENLKLQEGEV LAINCIFSLH  240
KVGPTSRDTA VSALRRLDPR VLTLVEEEVD LDSDRGQGFA AWLGECVRFF RAYLESLDES  300
FPKASEERLM LERAMARAAV DLVACPADES RERRERSGWW ARRMRACGFG PVGFSDDVLD  360
DMRALLRRYR EGWSMGLGRA DDEAGSGVYL EWKEEPMVWA SAWKP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_B	1e-150	5	405	65	474	Protein SHORT-ROOT
5b3h_B	1e-151	5	405	11	420	Protein SHORT-ROOT
5b3h_E	1e-151	5	405	11	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}.

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_006841098.2	0.0	protein SHORT-ROOT
Swissprot	Q9SZF7	1e-150	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	W1P4D6	0.0	W1P4D6_AMBTC; Uncharacterized protein
STRING	ERN02773	0.0	(Amborella trichopoda)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP2755	13	32

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	1e-124	GRAS family protein

Link Out ? help Back to Top
Phytozome	evm_27.model.AmTr_v1.0_scaffold00086.29

Publications ? help Back to Top
Amborella Genome Project The Amborella genome and the evolution of flowering plants. Science, 2013. 342(6165): p. 1241089 [PMID:24357323] 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]