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

Tp57577_TGAC_v2_mRNA25048

Organism

Trifolium pratense

Taxonomic ID

57577

Taxonomic Lineage

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

Family

GRAS

Protein Properties

Length: 527aa MW: 60498 Da PI: 4.8302

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp57577_TGAC_v2_mRNA25048	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	344.5	1.7e-105	152	525	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfse 86 + L+e A+a+s+++++++q+l++ l+el+sp+gd q+l +yf++AL +r+++ ++++yk+l+ ++++ + +++ ++l f+e Tp57577_TGAC_v2_mRNA25048 152 NILIETARAISDNNTNRIQQLMWMLNELSSPYGDMEQKLSSYFLQALFSRMNDAGDRTYKTLTFASEKTCSFDSTRKMLLKFQE 235 689*********************************************************9999886666666566666* PP GRAS 87 vsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg..skeeleetgerLakf 168 vsP+ +f+h++ N aIlea+eg+ ++HiiD++ ++++QWp+Ll+aLa+R++++p+lR+T+v+ + sg ++ ++e+g r++kf Tp57577_TGAC_v2_mRNA25048 236 VSPWTTFGHVASNGAILEALEGNPKLHIIDISNTYCTQWPTLLEALATRSDDTPHLRLTTVVTAVSGgsVQKVMKEIGTRMEKF 319 *************************************************************9998999999******* PP GRAS 169 AeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh...n 249 A+ +gvpf+f++ + ++l +l+l++++++++Eala+n+v +lh++ + ++rd++++l+++l+P+v++vve+ead Tp57577_TGAC_v2_mRNA25048 320 ARLMGVPFKFKI-IFSDLRELNLSDFDIQEDEALAINCVNSLHSIS----GVGNHRDNLISLLRGLEPRVMTVVEEEADFevcF 398 *******9.7999************************8....77778999***************9873345 PP GRAS 250 sesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplseka 333 s++F+e+f e+l+++ + f++le++++r+s e+ ++Ere gr+iv++vac +e++er+et+++Wr+rl+ GF++v++s+++ Tp57577_TGAC_v2_mRNA25048 399 SSDFVEGFGECLRWFRVYFEALEESFSRTSCEKLMLERE-AGRSIVDLVACDAFESVERRETASRWRRRLHGGGFNTVSFSDEV 481 89*********************************.**************************************** PP GRAS 334 akqaklllrkvksdgyrve....eesgslvlgWkdrpLvsvSaWr 374 +++++llr++ +g+++ ++++ ++l Wk++p+v++S+Wr Tp57577_TGAC_v2_mRNA25048 482 CDDVRALLRRYR-EGWSMTqcssSSDDGIFLSWKEKPVVWASVWR 525 ********.77666545555689999************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	50.497	124	502	IPR005202	Transcription factor GRAS
Pfam	PF03514	5.9E-103	152	525	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 527 aa Download sequence Send to blast
MDTLFRLVNF HQQPQYQPDP SLNSTTTLTT SSSSRSSRQT TPTTTYYYNH QLQQEEDEEC 60 FNNFYYMDHN NNNNEEDLSS SSSKQNYYNN YSYDQTHHHH VSPTTITTTT NTYTTFNTIN 120 TPTNTDINYS YSPSQDYFNN FDFSGNNSWS QNILIETARA ISDNNTNRIQ QLMWMLNELS 180 SPYGDMEQKL SSYFLQALFS RMNDAGDRTY KTLTFASEKT CSFDSTRKML LKFQEVSPWT 240 TFGHVASNGA ILEALEGNPK LHIIDISNTY CTQWPTLLEA LATRSDDTPH LRLTTVVTAV 300 SGGSVQKVMK EIGTRMEKFA RLMGVPFKFK IIFSDLRELN LSDFDIQEDE ALAINCVNSL 360 HSISGVGNHR DNLISLLRGL EPRVMTVVEE EADFEVCFSS DFVEGFGECL RWFRVYFEAL 420 EESFSRTSCE KLMLEREAGR SIVDLVACDA FESVERRETA SRWRRRLHGG GFNTVSFSDE 480 VCDDVRALLR RYREGWSMTQ CSSSSDDGIF LSWKEKPVVW ASVWRP*

Sequence ? help Back to Top

Protein Sequence Length: 527 aa Download sequence Send to blast

MDTLFRLVNF HQQPQYQPDP SLNSTTTLTT SSSSRSSRQT TPTTTYYYNH QLQQEEDEEC  60
FNNFYYMDHN NNNNEEDLSS SSSKQNYYNN YSYDQTHHHH VSPTTITTTT NTYTTFNTIN  120
TPTNTDINYS YSPSQDYFNN FDFSGNNSWS QNILIETARA ISDNNTNRIQ QLMWMLNELS  180
SPYGDMEQKL SSYFLQALFS RMNDAGDRTY KTLTFASEKT CSFDSTRKML LKFQEVSPWT  240
TFGHVASNGA ILEALEGNPK LHIIDISNTY CTQWPTLLEA LATRSDDTPH LRLTTVVTAV  300
SGGSVQKVMK EIGTRMEKFA RLMGVPFKFK IIFSDLRELN LSDFDIQEDE ALAINCVNSL  360
HSISGVGNHR DNLISLLRGL EPRVMTVVEE EADFEVCFSS DFVEGFGECL RWFRVYFEAL  420
EESFSRTSCE KLMLEREAGR SIVDLVACDA FESVERRETA SRWRRRLHGG GFNTVSFSDE  480
VCDDVRALLR RYREGWSMTQ CSSSSDDGIF LSWKEKPVVW ASVWRP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_B	0.0	140	526	77	474	Protein SHORT-ROOT
5b3h_B	0.0	140	526	23	420	Protein SHORT-ROOT
5b3h_E	0.0	140	526	23	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp57577_TGAC_v2_mRNA25048

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_003608528.1	0.0	protein SHORT-ROOT
Swissprot	Q9SZF7	0.0	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A2Z6NNE7	0.0	A0A2Z6NNE7_TRISU; Uncharacterized protein
STRING	AES90725	0.0	(Medicago truncatula)

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-173	GRAS family protein

Link Out ? help Back to Top
Phytozome	Tp57577_TGAC_v2_mRNA25048

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]