PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna

Family

GRAS

Protein Properties

Length: 328aa MW: 36953.5 Da PI: 6.0765

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Vradi0332s00260.1	genome	SNU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	213.6	1e-65	2	228	27	263
GRAS 27 lselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalkl.fsevsPilkfshltaNqaIleavegeervHiiDf 117 l+elasp+gd q+la+yf++AL r ++s++++yk+l++ ++++++ +++ l f+evsP+ +f+h++ N aIlea+ege ++HiiD+ Vradi0332s00260.1 2 LNELASPYGDCDQKLASYFLQALFCRATDSGERCYKTLSSVAEKNHSFDSARRLI-LkFQEVSPWTTFGHVASNGAILEALEGEPKLHIIDL 92 899*********************************99999844444333344.26****************************** PP GRAS 118 disqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlq 209 + + ++QWp+Ll+aLa+R++++p+l++T+v+ ++e+g+r++kfA+ +gvpfefnv+ + l dl+ e L+v+++Ea+aVn+v + Vradi0332s00260.1 93 SNTLCTQWPTLLEALATRNDETPHLKLTVVAL----AGSVMKEVGQRMEKFARLMGVPFEFNVI--NGLRDLTKEGLEVQEDEAIAVNCVGA 178 ****************************....99********************96..99******************** PP GRAS 210 lhrlldesvsleserdevLklvkslsPkvvvvveqeadh..nsesFlerflealey 263 l r+ +e+ r+++++++ksl Pkvv+vve+ead ++e+F++ f e+l++ Vradi0332s00260.1 179 LRRVE-----VEE-RENLIRVFKSLGPKVVTVVEEEADFcsSREDFVKCFEECLNF 228 97.....444.789******************8767789******987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	34.537	1	327	IPR005202	Transcription factor GRAS
Pfam	PF03514	3.5E-63	2	228	IPR005202	Transcription factor GRAS
ProDom	PD010361	9.0E-31	260	327	IPR002675	Ribosomal protein L38e
Pfam	PF01781	2.3E-32	260	327	IPR002675	Ribosomal protein L38e

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006412	Biological Process	translation
GO:0005840	Cellular Component	ribosome
GO:0003735	Molecular Function	structural constituent of ribosome

Sequence ? help Back to Top
Protein Sequence Length: 328 aa Download sequence Send to blast
MLNELASPYG DCDQKLASYF LQALFCRATD SGERCYKTLS SVAEKNHSFD SARRLILKFQ 60 EVSPWTTFGH VASNGAILEA LEGEPKLHII DLSNTLCTQW PTLLEALATR NDETPHLKLT 120 VVALAGSVMK EVGQRMEKFA RLMGVPFEFN VINGLRDLTK EGLEVQEDEA IAVNCVGALR 180 RVEVEERENL IRVFKSLGPK VVTVVEEEAD FCSSREDFVK CFEECLNFSN SSSIVQYPLC 240 DRFALYELMQ TSGVWCLVQP KQIHEIKDFL LTARRKDARS VKIKRSKDVV KFKVRCSTYL 300 YTLCVFDSEK ADKLKQSLPP GLSVQDV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_B	1e-90	2	228	113	361	Protein SHORT-ROOT
5b3h_B	3e-91	2	228	59	307	Protein SHORT-ROOT
5b3h_E	3e-91	2	228	59	307	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Vradi0332s00260.1

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	AP015040	0.0	AP015040.1 Vigna angularis var. angularis DNA, chromosome 7, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_014521903.1	1e-163	protein SHORT-ROOT
Swissprot	Q9SZF7	8e-91	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A1S3VU42	1e-161	A0A1S3VU42_VIGRR; protein SHORT-ROOT
STRING	XP_007150451.1	1e-155	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF1297	34	106

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	1e-91	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]