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

Neem_38953_f_1

Organism

Azadirachta indica

Taxonomic ID

124943

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta

Family

GRAS

Protein Properties

Length: 448aa MW: 50279.9 Da PI: 6.1986

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_38953_f_1	genome	NGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	314.8	1.9e-96	89	447	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlt 97 +lL ecA+a+s++d +++++lL+ l+elasp+gd q+la+yf++AL + ++s++++yk+l++ ++++++ +++ + f+evsP+ +f+h++ Neem_38953_f_1 89 KLLKECARAISDKDSSKIHHLLWMLNELASPYGDCDQKLASYFLQALFCKATESGQRCYKTLTSVAERSHSFDSARKLILKFQEVSPWTTFGHVA 183 7999********************************************************9999996555555455555********** PP GRAS 98 aNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvl.vakrledlel 191 N aIlea+ege+++HiiD++ + ++QWp+Ll+aLa+R++++p+l++T+v+ ++ + ++e+g+r++kfA+ +gvpfefnv+ +rl++l+ Neem_38953_f_1 184 SNGAILEALEGETKLHIIDISNTLCTQWPTLLEALATRNDETPHLKLTVVVT-ATIVRSVMKEIGQRMEKFARLMGVPFEFNVItGLNRLAELTK 277 ************************************************.556999********************94456*** PP GRAS 192 eeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse..sFlerflealeyysalfdsleaklpreseerik 284 e+L v+++Ea+aVn++ +l r+ ++er +v+++++sl+Pk+v+vve+ead++s+ +F++ f e+l++y+ f++le++++++s+er + Neem_38953_f_1 278 ETLGVREDEAVAVNCIGALRRVS------AEERASVIQMFQSLRPKLVTVVEEEADLTSSryDFVKCFEECLRFYTLYFEMLEESFSPTSNERLM 366 *****************97......344789*****************9665459**************************** PP GRAS 285 vErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrve....eesgslvlgWkdrpLvsvSaWr 374 +Ere +r+iv r+e+ +W+e+l+eaGF+p +s+++++++k+ll+++ g+ + ++ ++l+Wk++p+v++SaW+ Neem_38953_f_1 367 LERE-CSRSIV-----------RRRERGTQWSEKLKEAGFSPFGFSDDVVDDVKALLKRYR-AGWALVlpqgTDDSGIYLTWKEEPVVWASAWK 447 .556654...........3566778****************************.66666655767788899************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	46.505	61	424	IPR005202	Transcription factor GRAS
Pfam	PF03514	6.6E-94	89	447	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 448 aa Download sequence Send to blast
MDITLFTTLK GTTTPTAEAA THSQYFFSTS NHQQLSNGDH IALDMQSNNN NNSNIQPQNS 60 SCHTSTSRSS DSGDPCAATS AGGNKWASKL LKECARAISD KDSSKIHHLL WMLNELASPY 120 GDCDQKLASY FLQALFCKAT ESGQRCYKTL TSVAERSHSF DSARKLILKF QEVSPWTTFG 180 HVASNGAILE ALEGETKLHI IDISNTLCTQ WPTLLEALAT RNDETPHLKL TVVVTATIVR 240 SVMKEIGQRM EKFARLMGVP FEFNVITGLN RLAELTKETL GVREDEAVAV NCIGALRRVS 300 AEERASVIQM FQSLRPKLVT VVEEEADLTS SRYDFVKCFE ECLRFYTLYF EMLEESFSPT 360 SNERLMLERE CSRSIVRRRE RGTQWSEKLK EAGFSPFGFS DDVVDDVKAL LKRYRAGWAL 420 VLPQGTDDSG IYLTWKEEPV VWASAWKP

Sequence ? help Back to Top

Protein Sequence Length: 448 aa Download sequence Send to blast

MDITLFTTLK GTTTPTAEAA THSQYFFSTS NHQQLSNGDH IALDMQSNNN NNSNIQPQNS  60
SCHTSTSRSS DSGDPCAATS AGGNKWASKL LKECARAISD KDSSKIHHLL WMLNELASPY  120
GDCDQKLASY FLQALFCKAT ESGQRCYKTL TSVAERSHSF DSARKLILKF QEVSPWTTFG  180
HVASNGAILE ALEGETKLHI IDISNTLCTQ WPTLLEALAT RNDETPHLKL TVVVTATIVR  240
SVMKEIGQRM EKFARLMGVP FEFNVITGLN RLAELTKETL GVREDEAVAV NCIGALRRVS  300
AEERASVIQM FQSLRPKLVT VVEEEADLTS SRYDFVKCFE ECLRFYTLYF EMLEESFSPT  360
SNERLMLERE CSRSIVRRRE RGTQWSEKLK EAGFSPFGFS DDVVDDVKAL LKRYRAGWAL  420
VLPQGTDDSG IYLTWKEEPV VWASAWKP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_B	1e-149	59	448	5	420	Protein SHORT-ROOT
5b3h_E	1e-149	59	448	5	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_006442965.1	0.0	protein SHORT-ROOT
Refseq	XP_006478752.1	0.0	protein SHORT-ROOT-like
Swissprot	Q9SZF7	1e-149	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A2H5QBD5	0.0	A0A2H5QBD5_CITUN; Uncharacterized protein
STRING	XP_006478752.1	0.0	(Citrus sinensis)
STRING	XP_006442965.1	0.0	(Citrus clementina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM16273	8	14

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	1e-144	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]