PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

GRAS

Protein Properties

Length: 491aa MW: 55281.9 Da PI: 4.9883

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10025470m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	344.2	2.1e-105	107	489	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfsh 95 ++lL+e A+a ++++ +++q+l++ l+el+sp+gd+ q+l +yf++AL r+++s++++y++l++ ++++ + +++ +++ f+evsP+ +f+h Ciclev10025470m 107 TDLLIETARASADKNSARVQQLMWMLNELSSPYGDTDQKLSSYFLQALFGRMTDSGERCYRTLSSASDKTCSFESTRKMVLKFQEVSPWTTFGH 200 579**********************************************************9988886665555555566******** PP GRAS 96 ltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg..........skeeleetgerLakfAeelgvpfefn 179 +++N aI+ea+ege+++Hi+D++ ++++QWp+Ll+aLa+R++++p+lR+T+v+ ++++ ++ ++e+g+r++kfA+ +gvpfefn Ciclev10025470m 201 VACNGAIMEAFEGESKLHIVDISNTYCTQWPTLLEALATRTDDTPHLRLTTVVTSKPVggsgagglaaVQKVMKEIGNRMEKFARLMGVPFEFN 294 **************************************************998899***9999********************* PP GRAS 180 vlvak.rledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse....sFlerflealeyysalf 268 v+++ ++ dl+l eL+v+++Eala+n++ +lh++ +++++rd +++ ++sl+P++++vve+e+d++ + +F+++f e+l+++ + f Ciclev10025470m 295 VIHHVgDFCDLNLTELDVRSDEALAINCIGALHTIA----AVDDRRDVLISNLRSLQPRIITVVEEEVDLDVGidgvEFVKGFQECLRWFRVYF 384 96666**************************8....888899*****************8875444555************* PP GRAS 269 dsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdg.yrveeesgslvlg 361 +sl+ ++ ++s+er ++Er+ gr+iv++vac+ +e++er+et+ +W rl+ aGF+p +s+++ +++++llr++k +g + ++ ++ ++l Ciclev10025470m 385 ESLDDSFTKTSNERLMLERA-AGRAIVDLVACQPSESTERRETATRWCGRLHGAGFSPFMFSDEVCDDVRALLRRYK-EGwSMAQCPDAGIFLS 476 ****************.****************************************************.66255568899999 PP GRAS 362 WkdrpLvsvSaWr 374 Wkd+++v++SaWr Ciclev10025470m 477 WKDHTVVWASAWR 489 ************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	49.774	80	469	IPR005202	Transcription factor GRAS
Pfam	PF03514	7.3E-103	107	489	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: 491 aa Download sequence Send to blast
MDTLFRLVNL QPDQSFNSSR TSSSSRSSKQ NNHYQTAEEE ECFNFFMDEE DFSSSSSKQH 60 YYPYHQPHHS TPTTTATTTT TSSTPPHQPN FDPTLDFSFE FSANWATDLL IETARASADK 120 NSARVQQLMW MLNELSSPYG DTDQKLSSYF LQALFGRMTD SGERCYRTLS SASDKTCSFE 180 STRKMVLKFQ EVSPWTTFGH VACNGAIMEA FEGESKLHIV DISNTYCTQW PTLLEALATR 240 TDDTPHLRLT TVVTSKPVGG SGAGGLAAVQ KVMKEIGNRM EKFARLMGVP FEFNVIHHVG 300 DFCDLNLTEL DVRSDEALAI NCIGALHTIA AVDDRRDVLI SNLRSLQPRI ITVVEEEVDL 360 DVGIDGVEFV KGFQECLRWF RVYFESLDDS FTKTSNERLM LERAAGRAIV DLVACQPSES 420 TERRETATRW CGRLHGAGFS PFMFSDEVCD DVRALLRRYK EGWSMAQCPD AGIFLSWKDH 480 TVVWASAWRP *

Sequence ? help Back to Top

Protein Sequence Length: 491 aa Download sequence Send to blast

MDTLFRLVNL QPDQSFNSSR TSSSSRSSKQ NNHYQTAEEE ECFNFFMDEE DFSSSSSKQH  60
YYPYHQPHHS TPTTTATTTT TSSTPPHQPN FDPTLDFSFE FSANWATDLL IETARASADK  120
NSARVQQLMW MLNELSSPYG DTDQKLSSYF LQALFGRMTD SGERCYRTLS SASDKTCSFE  180
STRKMVLKFQ EVSPWTTFGH VACNGAIMEA FEGESKLHIV DISNTYCTQW PTLLEALATR  240
TDDTPHLRLT TVVTSKPVGG SGAGGLAAVQ KVMKEIGNRM EKFARLMGVP FEFNVIHHVG  300
DFCDLNLTEL DVRSDEALAI NCIGALHTIA AVDDRRDVLI SNLRSLQPRI ITVVEEEVDL  360
DVGIDGVEFV KGFQECLRWF RVYFESLDDS FTKTSNERLM LERAAGRAIV DLVACQPSES  420
TERRETATRW CGRLHGAGFS PFMFSDEVCD DVRALLRRYK EGWSMAQCPD AGIFLSWKDH  480
TVVWASAWRP *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_B	0.0	63	490	2	420	Protein SHORT-ROOT
5b3h_E	0.0	63	490	2	420	Protein SHORT-ROOT
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in the procambium during embryogenesis. {ECO:0000269\|PubMed:10850497}.
Uniprot	TISSUE SPECIFICITY: Expressed in the stele and the quiescent center. Not detected in the ground tissue cell lineage. The SHR protein moves from the stele to a single layer of adjacent cells, where it enters the nucleus. {ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:11565032, ECO:0000269\|PubMed:15142972, ECO:0000269\|PubMed:15314023}.

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_006426117.1	0.0	protein SHORT-ROOT
Swissprot	Q9SZF7	0.0	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	V4SFK8	0.0	V4SFK8_9ROSI; Uncharacterized protein
STRING	XP_006426117.1	0.0	(Citrus clementina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6104	25	47

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	0.0	GRAS family protein

Link Out ? help Back to Top
Phytozome	Ciclev10025470m
Entrez Gene	18037577

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]