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

WALNUT_00019348-RA

Organism

Juglans regia

Taxonomic ID

51240

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Juglandaceae; Juglans

Family

GRAS

Protein Properties

Length: 491aa MW: 55614.3 Da PI: 5.4876

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
WALNUT_00019348-RA	genome	JHU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	354.3	1.9e-108	110	490	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkf 93 e Lle A+a+++++ +++q+l + l+el+sp+gd+ q+laa+f++AL +r+++s++++y++l++ ++++ + +++ +++ f+evsP+ +f WALNUT_00019348-RA 110 EILLETARAIAEKNSTRVQHLTWMLNELSSPYGDTDQKLAAHFLQALFSRMTDSGDRCYRTLASASEKTCSFESTRKMVLKFQEVSPWTTF 200 689*********************************************************8887776555555555556****** PP GRAS 94 shltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg........skeeleetgerLakfAeelgvpf 176 +h+++N aI+ea+ege ++Hi+Df+ ++++QWp+Ll+aLa+R++++p+lR+T+v++ +s+ ++ ++e+g+r++kfA+ +gvpf WALNUT_00019348-RA 201 GHVACNGAIMEAFEGEPKLHIVDFSNTYCTQWPTLLEALATRSDETPHLRLTTVVATKSSgstggvaaVQKVMKEIGSRMEKFARLMGVPF 291 **************************************************998877899999999****************** PP GRAS 177 efnvlvak.rledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse....sFlerfleale 262 +fnv+++ +l+dl++e+L++k +Eala+n+v lh++ +++++rd +++++++l+P++v+vve+ead++ + +F+++f e+l+ WALNUT_00019348-RA 292 KFNVIHHGgDLSDLNTEKLDLKDDEALAINCVGTLHSIT----PVRNRRDYLISAFRRLQPRIVTVVEEEADLDVGvdglEFVKGFEECLR 378 97777*************************8....888999*****************8885444555******* PP GRAS 263 yysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrve. 352 ++ + f++l++++pr+s+er ++Ere gr+iv++vac +e++er+e++ W++rl+++GF+pv++s+++ +++++llr++k +g+++ WALNUT_00019348-RA 379 WFRVYFEALDESFPRTSNERLMLERE-AGRAIVDLVACPPSESVERRESAVCWSRRLHACGFGPVSYSDEVCDDVRALLRRYK-EGWSMTq 467 **********************.****************************************************.5544442 PP GRAS 353 .eesgslvlgWkdrpLvsvSaWr 374 ++ + ++l Wkd+p+v++S+Wr WALNUT_00019348-RA 468 cSDVAGIFLSWKDQPVVWASSWR 490 26677888************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	50.119	82	469	IPR005202	Transcription factor GRAS
Pfam	PF03514	6.6E-106	110	490	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 491 aa Download sequence Send to blast
MDTLFRLVNL QSDQSYNSSR TSSSSRSSRQ NHHYQQEDEE CFNLFMDEED FSSSSSKHYY 60 PYQPHPNSST TTPPTATPTT TTTNISTPTE FSFSPALDFN FEFSGKWAHE ILLETARAIA 120 EKNSTRVQHL TWMLNELSSP YGDTDQKLAA HFLQALFSRM TDSGDRCYRT LASASEKTCS 180 FESTRKMVLK FQEVSPWTTF GHVACNGAIM EAFEGEPKLH IVDFSNTYCT QWPTLLEALA 240 TRSDETPHLR LTTVVATKSS GSTGGVAAVQ KVMKEIGSRM EKFARLMGVP FKFNVIHHGG 300 DLSDLNTEKL DLKDDEALAI NCVGTLHSIT PVRNRRDYLI SAFRRLQPRI VTVVEEEADL 360 DVGVDGLEFV KGFEECLRWF RVYFEALDES FPRTSNERLM LEREAGRAIV DLVACPPSES 420 VERRESAVCW SRRLHACGFG PVSYSDEVCD DVRALLRRYK EGWSMTQCSD VAGIFLSWKD 480 QPVVWASSWR P

Sequence ? help Back to Top

Protein Sequence Length: 491 aa Download sequence Send to blast

MDTLFRLVNL QSDQSYNSSR TSSSSRSSRQ NHHYQQEDEE CFNLFMDEED FSSSSSKHYY  60
PYQPHPNSST TTPPTATPTT TTTNISTPTE FSFSPALDFN FEFSGKWAHE ILLETARAIA  120
EKNSTRVQHL TWMLNELSSP YGDTDQKLAA HFLQALFSRM TDSGDRCYRT LASASEKTCS  180
FESTRKMVLK FQEVSPWTTF GHVACNGAIM EAFEGEPKLH IVDFSNTYCT QWPTLLEALA  240
TRSDETPHLR LTTVVATKSS GSTGGVAAVQ KVMKEIGSRM EKFARLMGVP FKFNVIHHGG  300
DLSDLNTEKL DLKDDEALAI NCVGTLHSIT PVRNRRDYLI SAFRRLQPRI VTVVEEEADL  360
DVGVDGLEFV KGFEECLRWF RVYFEALDES FPRTSNERLM LEREAGRAIV DLVACPPSES  420
VERRESAVCW SRRLHACGFG PVSYSDEVCD DVRALLRRYK EGWSMTQCSD VAGIFLSWKD  480
QPVVWASSWR P

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_B	0.0	78	491	2	420	Protein SHORT-ROOT
5b3h_E	0.0	78	491	2	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_018835769.1	0.0	PREDICTED: protein SHORT-ROOT-like
Swissprot	Q9SZF7	0.0	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A2I4FVU2	0.0	A0A2I4FVU2_JUGRE; protein SHORT-ROOT-like
STRING	VIT_07s0129g00030.t01	0.0	(Vitis vinifera)

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	0.0	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]