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

Pta006481

Organism

Pinus taeda

Taxonomic ID

3352

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pinus; Pinus

Family

GRAS

Protein Properties

Length: 502aa MW: 57391.7 Da PI: 6.1274

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PUT-157a-Pinus_taeda-64601	PU_ref	plantGDB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	356	5.8e-109	135	499	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaNqaI 102 +lLlecA+a+++++++++q+lL+ l+el+sp+gd q+la+yf++A +++++++++y +l + ++++++ +++ ++ f+e sP+ +f+h++aN aI Pta006481 135 NLLLECARAIAENEKSRTQHLLWMLNELSSPYGDCEQKLASYFLQAFFCKITDTGPRCYTTLCSAAEKTYSFDSTRKMILKFQESSPWTTFGHVAANGAI 234 79********************************************************998888887776666666667*************** PP GRAS 103 leavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg.skeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpgEa 201 le++ege ++Hi+D++ + ++QWp+Ll+aLa+R++++p+lR+T+v+ +++ + ++e+g+r++kfA+ +gvpfef+v++ ++l++l++ +L+++p+Ea Pta006481 235 LESFEGEMKLHIVDLSNTFCTQWPTLLEALATRSDDTPHLRLTTVVTSKEAtAMKVMKEIGQRMEKFARLMGVPFEFSVIHQHHLHKLNVGALKIRPDEA 334 ****************************************9997777899*********************9999************* PP GRAS 202 laVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvace 301 la+n++++l+r+ ++ rd++L+++ s++Pk+v+vve e+d+++e+F + f+e+l+++s +fdsle++++r+s+er ++Er +r+ivn++ace Pta006481 335 LAINCIHSLQRVN------KNGRDSILSTFYSMNPKIVTVVEDEVDLTHEDFGDCFSECLRFFSLFFDSLEESFSRTSNERLMLERT-SARSIVNILACE 427 ********7......66799***********************************************************.9******* PP GRAS 302 gaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 +e er+e+ ++W rl+eaGF +++s+++++++++ll+++k +g+ ++s+ l+l+Wk++ +++SaW+ Pta006481 428 DSEVYERREKGAQWAWRLKEAGFIHAAFSDDVVDDVRALLKRYK-EGWGHCSNSDGLFLTWKEQCAIWASAWK 499 ****************************************.9999999******************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	50.597	107	480	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.0E-106	135	499	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 502 aa Download sequence Send to blast
MDRLFTSRLA DYQSEHPLSC FNSNKNCEDA DTPRHIDSYN NHLSQFVLPS RRDKSRQCNS 60 FMEDEDFSFK QFLPFKEMFN SNQTGKGTTG PNQFSGTRAT SSRSSEVPDP SLFSELNPNF 120 PEEFGPAGSR RWASNLLLEC ARAIAENEKS RTQHLLWMLN ELSSPYGDCE QKLASYFLQA 180 FFCKITDTGP RCYTTLCSAA EKTYSFDSTR KMILKFQESS PWTTFGHVAA NGAILESFEG 240 EMKLHIVDLS NTFCTQWPTL LEALATRSDD TPHLRLTTVV TSKEATAMKV MKEIGQRMEK 300 FARLMGVPFE FSVIHQHHLH KLNVGALKIR PDEALAINCI HSLQRVNKNG RDSILSTFYS 360 MNPKIVTVVE DEVDLTHEDF GDCFSECLRF FSLFFDSLEE SFSRTSNERL MLERTSARSI 420 VNILACEDSE VYERREKGAQ WAWRLKEAGF IHAAFSDDVV DDVRALLKRY KEGWGHCSNS 480 DGLFLTWKEQ CAIWASAWKP CL

Sequence ? help Back to Top

Protein Sequence Length: 502 aa Download sequence Send to blast

MDRLFTSRLA DYQSEHPLSC FNSNKNCEDA DTPRHIDSYN NHLSQFVLPS RRDKSRQCNS  60
FMEDEDFSFK QFLPFKEMFN SNQTGKGTTG PNQFSGTRAT SSRSSEVPDP SLFSELNPNF  120
PEEFGPAGSR RWASNLLLEC ARAIAENEKS RTQHLLWMLN ELSSPYGDCE QKLASYFLQA  180
FFCKITDTGP RCYTTLCSAA EKTYSFDSTR KMILKFQESS PWTTFGHVAA NGAILESFEG  240
EMKLHIVDLS NTFCTQWPTL LEALATRSDD TPHLRLTTVV TSKEATAMKV MKEIGQRMEK  300
FARLMGVPFE FSVIHQHHLH KLNVGALKIR PDEALAINCI HSLQRVNKNG RDSILSTFYS  360
MNPKIVTVVE DEVDLTHEDF GDCFSECLRF FSLFFDSLEE SFSRTSNERL MLERTSARSI  420
VNILACEDSE VYERREKGAQ WAWRLKEAGF IHAAFSDDVV DDVRALLKRY KEGWGHCSNS  480
DGLFLTWKEQ CAIWASAWKP CL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_B	1e-160	109	500	11	420	Protein SHORT-ROOT
5b3h_E	1e-160	109	500	11	420	Protein SHORT-ROOT
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	47	54	LPSRRDKS

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pta.15468	0.0	root

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_010274383.1	1e-176	PREDICTED: protein SHORT-ROOT-like
Swissprot	Q9SZF7	1e-159	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	B4XI11	0.0	B4XI11_PINRA; Short-root
STRING	XP_010274383.1	1e-176	(Nelumbo nucifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	1e-154	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]