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

Achn342431

Organism

Actinidia chinensis

Taxonomic ID

3625

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Actinidiaceae; Actinidia

Family

GRAS

Protein Properties

Length: 1124aa MW: 122024 Da PI: 6.9472

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Achn342431	genome	IKGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	392.5	4.7e-120	750	1120	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlta 98 +lLl+cAeav+++++e+a+++L ++s+l++p g++ qR+aayf eA++arl++s+ +l ++lp ++ + ++++ ++a++lf+ +sP++kfsh+t+ Achn342431 750 LTLLLKCAEAVAADNFEEANNMLLEISQLSTPFGTSAQRVAAYFSEAMSARLLNSCLGLNATLPLIPALP-HTQKIVSAFQLFNGISPLVKFSHFTT 845 579**********************************************************9888874.6788999*************** PP GRAS 99 NqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLr 195 NqaI ea+e+e++vHiiD+di+qGlQWp L++ LasRp+gpp +R+Tg+g s e+le+tg+rL++fA++lg+pfef + +a+++ +l++e+L+ Achn342431 846 NQAIQEAFEREDKVHIIDLDIMQGLQWPGLFHILASRPGGPPFVRLTGLGT----SMEALEATGKRLSDFADKLGIPFEFFP-IADKVGNLDPERLN 937 ***********************************************....***********************.7********* PP GRAS 196 vkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgr 292 v++gEa+a+++ h+l+d ++s + +L+l+k+l Pkvv+vveq+++h ++sFl rf+ea++yysalfdsl +++++eseer++vE++ll+r Achn342431 938 VSEGEAVAIHWLQ--HSLYDVTGSHTR----TLWLLKRLAPKVVTVVEQDLSH-GGSFLGRFVEAIHYYSALFDSLGESYGEESEERHVVEQQLLSR 1027 ********9..999988888887....******************.789************************************ PP GRAS 293 eivnvvacegaerr.........erhetlekWrerleeaGF.kpvplsekaakqaklllrkvksdgyrve.eesgslvlgWkdrpLvsvSaWr 374 ei+nv+a g +rr e+ +l++Wre+le++GF k +++ +aa+qa lll +++s+gy+++ e++g+l lgWkd L+++SaWr Achn342431 1028 EIRNVLAVGGPSRRrtssleeeeEEVIKLNNWREKLEQCGFfKGISIAGNAATQATLLLGMFPSHGYTMQvEDNGTLKLGWKDLCLLTASAWR 1120 *****9987533333322133447899*****73789*********************88899999************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	58.372	723	1099	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.6E-117	750	1120	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 1124 aa Download sequence Send to blast
MARKRAACET IDQLQTEAGF HRTVTPAATN PLNHSTTMLM PASSATISSG TYFGMGPLVL 60 PHHHRTQPQG RAPPLPLPPP PPPPHQSQPQ PPSFCVFSGL PLFPPESTSR NTNVSPISSC 120 VAGSTSSGSG SMEDTEATAW IDGIIKDLIH TSTHVSIPQL IKNVREIILP CNPNLAALLE 180 YRLHSLTNMD PIPPNTTTTT GNFQQQQQPP SHKTSSRKEA RASGNLQQLR HRYHPNQLLQ 240 GADVLLNLDS NAALANLPFP LPAEYYSSPS HNVHGITNHY LNSVLTTTLV PTTPNPNIST 300 STGNGDHGQH LPNNVINPTN CPSSISPSIN HIIASGPAGQ YCGSSNPVMA RKRAACETID 360 QLQTEAGFHR TVTPAATNPL NHSTTMLMPA SSATISSGTY FGMGPLVLPH HHRTQPQGRA 420 PPLPLPPPPP PPHQSQPQPP SFCVFSGLPL FPPESTSRNT NVSPISSCVA GSTSSGSGSM 480 EDTEATAWID GIIKDLIHTS THVSIPQLIK NVREIILPCN PNLAALLEYR LHSLTNMDPI 540 PPNTTTTTTG NFQQQQQPPS HKTSSRKEAR ASGNMQQLRH RYHPNQLLQG ADVLLNLDSN 600 AALANLPFPL PAEYYSSPSH NVHGITNHYL NSVLTTTLVP TTPNPNISTS TGNGDHGQHL 660 PNNVINPTNC PSSISPSINH VRQSGRQQLC SQNQPQPQPQ PQPQVEKPQI DESPPPPVPD 720 QPATSAVSTA ITKKEEMQKK KRDEEGLRLL TLLLKCAEAV AADNFEEANN MLLEISQLST 780 PFGTSAQRVA AYFSEAMSAR LLNSCLGLNA TLPLIPALPH TQKIVSAFQL FNGISPLVKF 840 SHFTTNQAIQ EAFEREDKVH IIDLDIMQGL QWPGLFHILA SRPGGPPFVR LTGLGTSMEA 900 LEATGKRLSD FADKLGIPFE FFPIADKVGN LDPERLNVSE GEAVAIHWLQ HSLYDVTGSH 960 TRTLWLLKRL APKVVTVVEQ DLSHGGSFLG RFVEAIHYYS ALFDSLGESY GEESEERHVV 1020 EQQLLSREIR NVLAVGGPSR RRTSSLEEEE EEVIKLNNWR EKLEQCGFFK GISIAGNAAT 1080 QATLLLGMFP SHGYTMQVED NGTLKLGWKD LCLLTASAWR PLF*

Sequence ? help Back to Top

Protein Sequence Length: 1124 aa Download sequence Send to blast

MARKRAACET IDQLQTEAGF HRTVTPAATN PLNHSTTMLM PASSATISSG TYFGMGPLVL  60
PHHHRTQPQG RAPPLPLPPP PPPPHQSQPQ PPSFCVFSGL PLFPPESTSR NTNVSPISSC  120
VAGSTSSGSG SMEDTEATAW IDGIIKDLIH TSTHVSIPQL IKNVREIILP CNPNLAALLE  180
YRLHSLTNMD PIPPNTTTTT GNFQQQQQPP SHKTSSRKEA RASGNLQQLR HRYHPNQLLQ  240
GADVLLNLDS NAALANLPFP LPAEYYSSPS HNVHGITNHY LNSVLTTTLV PTTPNPNIST  300
STGNGDHGQH LPNNVINPTN CPSSISPSIN HIIASGPAGQ YCGSSNPVMA RKRAACETID  360
QLQTEAGFHR TVTPAATNPL NHSTTMLMPA SSATISSGTY FGMGPLVLPH HHRTQPQGRA  420
PPLPLPPPPP PPHQSQPQPP SFCVFSGLPL FPPESTSRNT NVSPISSCVA GSTSSGSGSM  480
EDTEATAWID GIIKDLIHTS THVSIPQLIK NVREIILPCN PNLAALLEYR LHSLTNMDPI  540
PPNTTTTTTG NFQQQQQPPS HKTSSRKEAR ASGNMQQLRH RYHPNQLLQG ADVLLNLDSN  600
AALANLPFPL PAEYYSSPSH NVHGITNHYL NSVLTTTLVP TTPNPNISTS TGNGDHGQHL  660
PNNVINPTNC PSSISPSINH VRQSGRQQLC SQNQPQPQPQ PQPQVEKPQI DESPPPPVPD  720
QPATSAVSTA ITKKEEMQKK KRDEEGLRLL TLLLKCAEAV AADNFEEANN MLLEISQLST  780
PFGTSAQRVA AYFSEAMSAR LLNSCLGLNA TLPLIPALPH TQKIVSAFQL FNGISPLVKF  840
SHFTTNQAIQ EAFEREDKVH IIDLDIMQGL QWPGLFHILA SRPGGPPFVR LTGLGTSMEA  900
LEATGKRLSD FADKLGIPFE FFPIADKVGN LDPERLNVSE GEAVAIHWLQ HSLYDVTGSH  960
TRTLWLLKRL APKVVTVVEQ DLSHGGSFLG RFVEAIHYYS ALFDSLGESY GEESEERHVV  1020
EQQLLSREIR NVLAVGGPSR RRTSSLEEEE EEVIKLNNWR EKLEQCGFFK GISIAGNAAT  1080
QATLLLGMFP SHGYTMQVED NGTLKLGWKD LCLLTASAWR PLF*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	733	1121	3	380	Protein SCARECROW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Putative transcription factor involved in asymmetric cell division (By similarity). Required for differentiation of endodermis and graviresponses. {ECO:0000250, ECO:0000269\|PubMed:16339910}.
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 cell division but not differentiation of the ground tissue. Also required for normal shoot gravitropism. Regulates the radial organization of the shoot axial organs. Binds to the promoter of MGP, NUC, RLK and SCL3. Restricts SHR movment and sequesters it into the nucleus of the endodermis. {ECO:0000269\|PubMed:10631180, ECO:0000269\|PubMed:12569126, ECO:0000269\|PubMed:15142972, ECO:0000269\|PubMed:15314023, ECO:0000269\|PubMed:16640459, ECO:0000269\|PubMed:17446396, ECO:0000269\|PubMed:22921914, ECO:0000269\|PubMed:24302889, ECO:0000269\|PubMed:8819871, ECO:0000269\|PubMed:9375406, ECO:0000269\|PubMed:9670559}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by SHR and by itself. {ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:11565032, ECO:0000269\|PubMed:15314023}.

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_012090957.1	0.0	protein SCARECROW
Swissprot	Q2Z2E9	0.0	SCR_IPONI; Protein SCARECROW
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A2R6R8L1	0.0	A0A2R6R8L1_ACTCH; Protein SCARECROW like
STRING	cassava4.1_001986m	0.0	(Manihot esculenta)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA8258	24	30

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G54220.1	0.0	GRAS family protein

Publications ? help Back to Top
Liu YG, et al. Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning. Proc. Natl. Acad. Sci. U.S.A., 1999. 96(11): p. 6535-40 [PMID:10339623] Ticconi CA, et al. ER-resident proteins PDR2 and LPR1 mediate the developmental response of root meristems to phosphate availability. Proc. Natl. Acad. Sci. U.S.A., 2009. 106(33): p. 14174-9 [PMID:19666499] Moubayidin L, et al. Spatial coordination between stem cell activity and cell differentiation in the root meristem. Dev. Cell, 2013. 26(4): p. 405-15 [PMID:23987513] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] 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] Reyes-Hernández BJ, et al. The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana. New Phytol., 2014. 202(4): p. 1223-36 [PMID:24635769] 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] Ron M, et al. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol., 2014. 166(2): p. 455-69 [PMID:24868032] 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] 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] Moubayidin L, et al. A SCARECROW-based regulatory circuit controls Arabidopsis thaliana meristem size from the root endodermis. Planta, 2016. 243(5): p. 1159-68 [PMID:26848984] Madmon O, et al. Expression of MAX2 under SCARECROW promoter enhances the strigolactone/MAX2 dependent response of Arabidopsis roots to low-phosphate conditions. Planta, 2016. 243(6): p. 1419-27 [PMID:26919985] 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] Benfey PN Defining the Path from Stem Cells to Differentiated Tissue. Curr. Top. Dev. Biol., 2016. 116: p. 35-43 [PMID:26970612] 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] Choi JW,Lim J Control of Asymmetric Cell Divisions during Root Ground Tissue Maturation. Mol. Cells, 2016. 39(7): p. 524-9 [PMID:27306644] 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] Goh T, et al. Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor. Development, 2016. 143(18): p. 3363-71 [PMID:27510971] 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] 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] Bruno L, et al. In Arabidopsis thaliana Cadmium Impact on the Growth of Primary Root by Altering SCR Expression and Auxin-Cytokinin Cross-Talk. Front Plant Sci, 2017. 8: p. 1323 [PMID:28798767] Mira MM, et al. Expression of Arabidopsis class 1 phytoglobin (AtPgb1) delays death and degradation of the root apical meristem during severe PEG-induced water deficit. J. Exp. Bot., 2017. 68(20): p. 5653-5668 [PMID:29059380] 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] Ercoli MF, et al. GIF Transcriptional Coregulators Control Root Meristem Homeostasis. Plant Cell, 2018. 30(2): p. 347-359 [PMID:29352064] Shimotohno A,Heidstra R,Blilou I,Scheres B Root stem cell niche organizer specification by molecular convergence of PLETHORA and SCARECROW transcription factor modules. Genes Dev., 2018. 32(15-16): p. 1085-1100 [PMID:30018102]