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

Csa12g003740.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina

Family

GRAS

Protein Properties

Length: 531aa MW: 59363.1 Da PI: 5.354

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa12g003740.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	389.1	5.1e-119	144	528	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalkl..fsevsPilkfsh 95 ++Lle+A+a+s++d+++aq++L++l+el+sp+gd+ q+la+yf++AL +r+++s++++y+++ + +++ek+ s e + ++ f+evsP+ +f+h Csa12g003740.1 144 SVLLEAARAFSDKDTARAQQILWTLNELSSPYGDTEQKLASYFLQALFNRMTGSGERCYRTMVTAAATEKTCSFESTRKTVlkFQEVSPWATFGH 238 78**********************************************************999999988655544444468******** PP GRAS 96 ltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg......skeeleetgerLakfAeelgvpfefnvlvak 184 ++aN aIleav+ge ++Hi+D++ + ++QWp+Ll+aLa+R++++p+lR+T+v+ ++++ s+++++e+g+r++kfA+ +gvpf+fn++++ Csa12g003740.1 239 VAANGAILEAVDGEAKIHIVDISSTFCTQWPTLLEALATRSDDTPHLRLTTVVVANKFvndqtaSHRMMKEIGNRMEKFARLMGVPFKFNIIHHV 333 *************************************************999889999999**********************9666 PP GRAS 185 .rledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh.nse......sFlerflealeyysalfdsl 271 +l++++l+eL+vk++E+la+n+v ++h + + ++rd+v++ +++l+P++v+vve+ead+ ++e +Fl++f e+l+++ ++f+s+ Csa12g003740.1 334 gDLSEFDLNELDVKEDEVLAINCVGAMHGIA----PRGNPRDAVISNFRRLRPRIVTVVEEEADLiGEEeggfddEFLRGFGECLRWFRVCFESW 424 6*************************8....888899********************7766899999**************** PP GRAS 272 eaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdg..yrveeesgslv.lgWk 363 e+++pr+s+er ++Er+ gr++v++vace ++++er+et++kW++r+++ GF++v +s+++a+++++llr++k +g +v++++++ + l+W+ Csa12g003740.1 425 EESFPRTSNERLMLERA-AGRAVVDLVACEPSDSTERRETARKWSRRMRNGGFGAVGYSDEVADDVRALLRRYK-EGvwSMVQCSDAAGIfLCWR 517 *************.****************************************************.4444788876665555 PP GRAS 364 drpLvsvSaWr 374 d+p+v++SaWr Csa12g003740.1 518 DQPVVWASAWR 528 ********8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	51.732	116	506	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.7E-116	144	528	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 531 aa Download sequence Send to blast
MDTLFRLVSL QQQQQSDSII TNQSSLSRTS TTTTGSPQTA YHYNFPQNDV AEECFNFFMD 60 EEDLSSSSSH HNHHHTNPNT YYSPFTTPTQ YHPATSSTPS STAAAAALAS PYSSSGHHND 120 PSAFSIPQTP PSFDFSANAK WADSVLLEAA RAFSDKDTAR AQQILWTLNE LSSPYGDTEQ 180 KLASYFLQAL FNRMTGSGER CYRTMVTAAA TEKTCSFEST RKTVLKFQEV SPWATFGHVA 240 ANGAILEAVD GEAKIHIVDI SSTFCTQWPT LLEALATRSD DTPHLRLTTV VVANKFVNDQ 300 TASHRMMKEI GNRMEKFARL MGVPFKFNII HHVGDLSEFD LNELDVKEDE VLAINCVGAM 360 HGIAPRGNPR DAVISNFRRL RPRIVTVVEE EADLIGEEEG GFDDEFLRGF GECLRWFRVC 420 FESWEESFPR TSNERLMLER AAGRAVVDLV ACEPSDSTER RETARKWSRR MRNGGFGAVG 480 YSDEVADDVR ALLRRYKEGV WSMVQCSDAA GIFLCWRDQP VVWASAWRPT *

Sequence ? help Back to Top

Protein Sequence Length: 531 aa Download sequence Send to blast

MDTLFRLVSL QQQQQSDSII TNQSSLSRTS TTTTGSPQTA YHYNFPQNDV AEECFNFFMD  60
EEDLSSSSSH HNHHHTNPNT YYSPFTTPTQ YHPATSSTPS STAAAAALAS PYSSSGHHND  120
PSAFSIPQTP PSFDFSANAK WADSVLLEAA RAFSDKDTAR AQQILWTLNE LSSPYGDTEQ  180
KLASYFLQAL FNRMTGSGER CYRTMVTAAA TEKTCSFEST RKTVLKFQEV SPWATFGHVA  240
ANGAILEAVD GEAKIHIVDI SSTFCTQWPT LLEALATRSD DTPHLRLTTV VVANKFVNDQ  300
TASHRMMKEI GNRMEKFARL MGVPFKFNII HHVGDLSEFD LNELDVKEDE VLAINCVGAM  360
HGIAPRGNPR DAVISNFRRL RPRIVTVVEE EADLIGEEEG GFDDEFLRGF GECLRWFRVC  420
FESWEESFPR TSNERLMLER AAGRAVVDLV ACEPSDSTER RETARKWSRR MRNGGFGAVG  480
YSDEVADDVR ALLRRYKEGV WSMVQCSDAA GIFLCWRDQP VVWASAWRPT *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_B	0.0	59	530	3	475	Protein SHORT-ROOT
Search in ModeBase

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	Csa12g003740.1

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	AF233752	0.0	AF233752.1 Arabidopsis thaliana short-root protein (shr) gene, complete cds.
GenBank	AL035605	0.0	AL035605.1 Arabidopsis thaliana DNA chromosome 4, BAC clone F19F18 (ESSA project).
GenBank	AL161591	0.0	AL161591.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 87.
GenBank	BT033026	0.0	BT033026.1 Arabidopsis thaliana unknown protein (At4g37650) mRNA, complete cds.
GenBank	CP002687	0.0	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010446640.1	0.0	PREDICTED: protein SHORT-ROOT-like
Swissprot	Q9SZF7	0.0	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A0D3DI67	0.0	A0A0D3DI67_BRAOL; Uncharacterized protein
STRING	XP_010446640.1	0.0	(Camelina sativa)

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

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]