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

Gh_A10G2319

Organism

Gossypium hirsutum

Taxonomic ID

3635

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: 476aa MW: 53508.5 Da PI: 6.7526

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_A10G2319	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	314.3	2.6e-96	104	475	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaNq 100 +lL ecA+a+s++d +++++lL+ l+elasp+gd q+la+yf++AL + ++s+++++k+l+ +++++ +++ + f+evsP+ +f+h++aN Gh_A10G2319 104 RLLKECARAISDKDSSKIHHLLWMLNELASPYGDCDQKLASYFLQALFCKATESGQRCFKTLTLVAEKSHCFDSARKLILKFQEVSPWTTFGHVAANG 201 7899********************************************************9999985554444444445************* PP GRAS 101 aIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvl.vakrledleleeLrvk 197 aIle ++ge ++HiiD++ + ++QWp+Ll+aLa+R++++p+l++T+v+ ++ + ++e+ +r++kfA+ +gvpfefnv+ ++l +l+ e L v Gh_A10G2319 202 AILEVLDGEPKLHIIDISNTLCTQWPTLLEALATRNDDTPHLKLTVVVT-ANIVRSVMKEISQRMEKFARLMGVPFEFNVVsGLNHLGQLTKEVLGVV 298 *********************************************.667999********************855679******** PP GRAS 198 pgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse..sFlerflealeyysalfdsleaklpreseerikvErellgre 293 ++Ea+aVn++ +l r++ +e r +v+ +++sl Pkvv+vve+ead +s+ +F++ f e+l++y++ f++le+++ ++s+e+ ++Ere +r Gh_A10G2319 299 EEEAVAVNCMGALRRVP-----VEG-RAAVIGMFRSLGPKVVTVVEEEADFSSTryDFVKCFEECLRFYTVYFEMLEESFTPTSNEKLMLERE-CSRG 389 ************9.....444.889****************99555449********************************.89 PP GRAS 294 ivnvvacegae....rrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrve...eesgslvlgWkdrpLvsvSaWr 374 iv v+ac ++ rer+e+ ++W+erl+ea F++v +s+++++++k+ll+++k g+ + +++ l+l+Wk++p+v++SaW+ Gh_A10G2319 390 IVRVLACDDDQdsegERERRERGSQWSERLKEA-FSSVGFSDDVVDDVKALLKRYK-PGWALAqpyQNETGLYLTWKEEPVVWASAWK 475 *****87764445689*********98.******************.8888885556688999************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	44.847	76	453	IPR005202	Transcription factor GRAS
Pfam	PF03514	9.2E-94	104	475	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 476 aa Download sequence Send to blast
MKLSSAKISK ESKGASPSHG GHHKNSFHSK RQSHHSILPL QPVDQLEQWS SVAVDMYNNS 60 SSSNNNNNHH HQPQTSHTST SRSSDYSAGG DREPSAVGNK WASRLLKECA RAISDKDSSK 120 IHHLLWMLNE LASPYGDCDQ KLASYFLQAL FCKATESGQR CFKTLTLVAE KSHCFDSARK 180 LILKFQEVSP WTTFGHVAAN GAILEVLDGE PKLHIIDISN TLCTQWPTLL EALATRNDDT 240 PHLKLTVVVT ANIVRSVMKE ISQRMEKFAR LMGVPFEFNV VSGLNHLGQL TKEVLGVVEE 300 EAVAVNCMGA LRRVPVEGRA AVIGMFRSLG PKVVTVVEEE ADFSSTRYDF VKCFEECLRF 360 YTVYFEMLEE SFTPTSNEKL MLERECSRGI VRVLACDDDQ DSEGERERRE RGSQWSERLK 420 EAFSSVGFSD DVVDDVKALL KRYKPGWALA QPYQNETGLY LTWKEEPVVW ASAWKP

Sequence ? help Back to Top

Protein Sequence Length: 476 aa Download sequence Send to blast

MKLSSAKISK ESKGASPSHG GHHKNSFHSK RQSHHSILPL QPVDQLEQWS SVAVDMYNNS  60
SSSNNNNNHH HQPQTSHTST SRSSDYSAGG DREPSAVGNK WASRLLKECA RAISDKDSSK  120
IHHLLWMLNE LASPYGDCDQ KLASYFLQAL FCKATESGQR CFKTLTLVAE KSHCFDSARK  180
LILKFQEVSP WTTFGHVAAN GAILEVLDGE PKLHIIDISN TLCTQWPTLL EALATRNDDT  240
PHLKLTVVVT ANIVRSVMKE ISQRMEKFAR LMGVPFEFNV VSGLNHLGQL TKEVLGVVEE  300
EAVAVNCMGA LRRVPVEGRA AVIGMFRSLG PKVVTVVEEE ADFSSTRYDF VKCFEECLRF  360
YTVYFEMLEE SFTPTSNEKL MLERECSRGI VRVLACDDDQ DSEGERERRE RGSQWSERLK  420
EAFSSVGFSD DVVDDVKALL KRYKPGWALA QPYQNETGLY LTWKEEPVVW ASAWKP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_B	1e-147	65	476	4	420	Protein SHORT-ROOT
5b3h_E	1e-147	65	476	4	420	Protein SHORT-ROOT
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Ghi.11914	0.0	stem

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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016677723.1	0.0	PREDICTED: protein SHORT-ROOT-like
Swissprot	Q9SZF7	1e-146	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A1U8IMU1	0.0	A0A1U8IMU1_GOSHI; protein SHORT-ROOT-like
STRING	Gorai.011G140100.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM16273	8	14

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	1e-127	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]