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

Cotton_A_40750_BGI-A2_v1.0

Organism

Gossypium arboreum

Taxonomic ID

29729

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

GRAS

Protein Properties

Length: 456aa MW: 51139.7 Da PI: 5.2413

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cotton_A_40750_BGI-A2_v1.0	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	341	2e-104	67	455	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfs 85 + L+e A+a+++++ + q+l++ l+el+sp+gd+ q+l +yf++AL +r+++s++++y++l++ ++++ + +++ ++ f+ Cotton_A_40750_BGI-A2_v1.0 67 DILMETATAIADRNSGRFQQLIWMLNELSSPYGDTDQKLGSYFLQALFSRMTDSGERCYRTLASVSEKTCSFETTRKMALKFQ 149 679*********************************************************8777765553333333345 PP GRAS 86 evsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg............... 153 evsP+ +f+h+++N aI+ea+ege+++HiiD++ ++++QWp+Ll++La+R++++p+l++T++++ ++g Cotton_A_40750_BGI-A2_v1.0 150 EVSPWTTFGHVACNGAIMEAFEGESKLHIIDISSTYCTQWPTLLESLATRTDETPHLKLTTIVATKNGgvpgsstsgtaagsl 232 **************************************************************99889********99 PP GRAS 154 ..skeeleetgerLakfAeelgvpfefnvlvak.rledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvks 233 ++ ++e+++r++kfA+ +gvpf+fnv+++ +l +l+l++L++k++Eala+n+v lh++ +++++rd +++ +k+ Cotton_A_40750_BGI-A2_v1.0 233 aaVQDIMKEIENRMEKFARLMGVPFKFNVIHHGgDLCELDLSKLDIKEDEALAINCVGTLHSIR----AVDNRRDMMISNFKK 311 999999*******************97777*************************8....8888899**** PP GRAS 234 lsPkvvvvveqeadhnse....sFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetl 312 l+P++++vve+ead++ + +F+++f e+l+++ + f++l+++++r+s+er ++Er+ gr+iv++vac+ +e++er+e + Cotton_A_40750_BGI-A2_v1.0 312 LQPRIITVVEEEADLDVGvdgmEFVKGFQECLRWFRVYFEALDESFARTSNERLMLERA-AGRAIVELVACAPSESVERREPA 393 ********8874333344*********************************.******************* PP GRAS 313 ekWrerleeaGFkpvplsekaakqaklllrkvksdgyrve.eesgslvlgWkdrpLvsvSaWr 374 ++W++r++ +GF+p+ ls+++ +++++llr++k +g+++ ++++ ++l Wk++p+v++SaWr Cotton_A_40750_BGI-A2_v1.0 394 NRWSRRFHGSGFNPLVLSDEVCDDVRALLRRYK-EGWSMTqSSDAGIFLSWKGQPVVWASAWR 455 *****************************.77666615566777************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	47.817	39	435	IPR005202	Transcription factor GRAS
Pfam	PF03514	7.0E-102	67	455	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 456 aa Download sequence Send to blast
MDEEDFSASS SKQYYPYYPH PQPHPSATGT TTTTATSIHH AFETSEFSTL SPARDLTLDF 60 SGKWANDILM ETATAIADRN SGRFQQLIWM LNELSSPYGD TDQKLGSYFL QALFSRMTDS 120 GERCYRTLAS VSEKTCSFET TRKMALKFQE VSPWTTFGHV ACNGAIMEAF EGESKLHIID 180 ISSTYCTQWP TLLESLATRT DETPHLKLTT IVATKNGGVP GSSTSGTAAG SLAAVQDIMK 240 EIENRMEKFA RLMGVPFKFN VIHHGGDLCE LDLSKLDIKE DEALAINCVG TLHSIRAVDN 300 RRDMMISNFK KLQPRIITVV EEEADLDVGV DGMEFVKGFQ ECLRWFRVYF EALDESFART 360 SNERLMLERA AGRAIVELVA CAPSESVERR EPANRWSRRF HGSGFNPLVL SDEVCDDVRA 420 LLRRYKEGWS MTQSSDAGIF LSWKGQPVVW ASAWRP

Sequence ? help Back to Top

Protein Sequence Length: 456 aa Download sequence Send to blast

MDEEDFSASS SKQYYPYYPH PQPHPSATGT TTTTATSIHH AFETSEFSTL SPARDLTLDF  60
SGKWANDILM ETATAIADRN SGRFQQLIWM LNELSSPYGD TDQKLGSYFL QALFSRMTDS  120
GERCYRTLAS VSEKTCSFET TRKMALKFQE VSPWTTFGHV ACNGAIMEAF EGESKLHIID  180
ISSTYCTQWP TLLESLATRT DETPHLKLTT IVATKNGGVP GSSTSGTAAG SLAAVQDIMK  240
EIENRMEKFA RLMGVPFKFN VIHHGGDLCE LDLSKLDIKE DEALAINCVG TLHSIRAVDN  300
RRDMMISNFK KLQPRIITVV EEEADLDVGV DGMEFVKGFQ ECLRWFRVYF EALDESFART  360
SNERLMLERA AGRAIVELVA CAPSESVERR EPANRWSRRF HGSGFNPLVL SDEVCDDVRA  420
LLRRYKEGWS MTQSSDAGIF LSWKGQPVVW ASAWRP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_B	0.0	35	456	4	420	Protein SHORT-ROOT
5b3h_E	0.0	35	456	4	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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017636404.1	0.0	PREDICTED: protein SHORT-ROOT-like
Swissprot	Q9SZF7	0.0	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A1U8M3L3	0.0	A0A1U8M3L3_GOSHI; protein SHORT-ROOT-like
STRING	Gorai.008G083500.1	0.0	(Gossypium raimondii)

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]