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

evm.model.supercontig_9.323

Organism

Carica papaya

Taxonomic ID

3649

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Caricaceae; Carica

Family

GRAS

Protein Properties

Length: 499aa MW: 56099.9 Da PI: 6.1757

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm.model.supercontig_9.323	genome	ASGPB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	309.7	6.6e-95	109	497	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklf 84 elL ecA+a+s++d +++++lL+ l+elasp+gdp q+la++f++AL + ++s+++++k+l++ +++++ +++ + f evm.model.supercontig_9.323 109 ELLKECARAISDKDSAKIHHLLWMLNELASPYGDPDQKLASHFLQALFCKATESGHRCFKTLTSVAEKSHCFDSARKLILKF 190 7899*********************************************************9999985554444444445 PP GRAS 85 sevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLa 166 +evsP+ +f+h++ N aIlea++ge ++HiiD++ + ++QWp+Ll++La+R++++p+lR+T+v+ ++ + +++e+++r++ evm.model.supercontig_9.323 191 QEVSPWTTFGHVASNGAILEALDGEMKLHIIDISNTLCTQWPTLLESLATRNDETPHLRLTVVVT-SNILRSMMKEIRQRME 271 ***************************************************************.66799******* PP GRAS 167 kfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh 248 kfA+ +gvpfefnv+ ++l+ e+L v+ +Ea+aVn++ +l+++ +++ r+ ++kl+kslsPk+v+vve+ead evm.model.supercontig_9.323 272 KFARLMGVPFEFNVI-----TKLTKENLGVRDDEAIAVNCIGSLKKVG-----IDK-RTGLIKLFKSLSPKIVTVVEEEADF 342 **********5.....88999*****************98.....555.999***************999 PP GRAS 249 ..nsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegae.....rrerhetlekWrerlee.a 322 ++ +F++ f e+l++y+ fd+le++++++s+er ++Ere +r++v v+aceg+e +er+e+ ++W+er+++ evm.model.supercontig_9.323 343 ssSKDDFMKCFEECLRFYTLYFDMLEESFAATSNERLMLERE-CSRSLVRVLACEGDEeeeeeEEERMERGRQWSERFGKeG 423 545569********************************.89*****99862222246799999***8758 PP GRAS 323 GFkpvplsekaakqaklllrkvksdgyrveee.......................sgslvlgWkdrpLvsvSaWr 374 GFk +s+++++++k+ll+++ g+++ ++ s ++l Wk++p+v++SaW+ evm.model.supercontig_9.323 424 GFKGTGFSDDVVDDVKALLKRYR-GGWSLVNNnnnnggdnggddssnsssssscfSSGIYLAWKEEPVVWASAWK 497 9******************.556666444678888999999999999999999999************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	43.724	81	455	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.3E-92	109	497	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 499 aa Download sequence Send to blast
MDRTLLTTLP KSKEYSTFMF PYSSSNSINT QSQSSYGGSH DHQHHHLHHP YQHHHHQQLA 60 PTQDMQNTNT ITAAAAAANI IGMNNSSCHS TSRSSSEFCT EPGQRWASEL LKECARAISD 120 KDSAKIHHLL WMLNELASPY GDPDQKLASH FLQALFCKAT ESGHRCFKTL TSVAEKSHCF 180 DSARKLILKF QEVSPWTTFG HVASNGAILE ALDGEMKLHI IDISNTLCTQ WPTLLESLAT 240 RNDETPHLRL TVVVTSNILR SMMKEIRQRM EKFARLMGVP FEFNVITKLT KENLGVRDDE 300 AIAVNCIGSL KKVGIDKRTG LIKLFKSLSP KIVTVVEEEA DFSSSKDDFM KCFEECLRFY 360 TLYFDMLEES FAATSNERLM LERECSRSLV RVLACEGDEE EEEEEEERME RGRQWSERFG 420 KEGGFKGTGF SDDVVDDVKA LLKRYRGGWS LVNNNNNNGG DNGGDDSSNS SSSSSCFSSG 480 IYLAWKEEPV VWASAWKP*

Sequence ? help Back to Top

Protein Sequence Length: 499 aa Download sequence Send to blast

MDRTLLTTLP KSKEYSTFMF PYSSSNSINT QSQSSYGGSH DHQHHHLHHP YQHHHHQQLA  60
PTQDMQNTNT ITAAAAAANI IGMNNSSCHS TSRSSSEFCT EPGQRWASEL LKECARAISD  120
KDSAKIHHLL WMLNELASPY GDPDQKLASH FLQALFCKAT ESGHRCFKTL TSVAEKSHCF  180
DSARKLILKF QEVSPWTTFG HVASNGAILE ALDGEMKLHI IDISNTLCTQ WPTLLESLAT  240
RNDETPHLRL TVVVTSNILR SMMKEIRQRM EKFARLMGVP FEFNVITKLT KENLGVRDDE  300
AIAVNCIGSL KKVGIDKRTG LIKLFKSLSP KIVTVVEEEA DFSSSKDDFM KCFEECLRFY  360
TLYFDMLEES FAATSNERLM LERECSRSLV RVLACEGDEE EEEEEEERME RGRQWSERFG  420
KEGGFKGTGF SDDVVDDVKA LLKRYRGGWS LVNNNNNNGG DNGGDDSSNS SSSSSCFSSG  480
IYLAWKEEPV VWASAWKP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_B	1e-141	84	498	64	474	Protein SHORT-ROOT
5b3h_B	1e-142	84	498	10	420	Protein SHORT-ROOT
5b3h_E	1e-142	84	498	10	420	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	evm.model.supercontig_9.323

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021906989.1	0.0	protein SHORT-ROOT-like
Swissprot	Q9SZF7	1e-141	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A061EK79	0.0	A0A061EK79_THECC; GRAS family transcription factor
STRING	evm.model.supercontig_9.323	0.0	(Carica papaya)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM16273	8	14
Representative plant	OGRP2755	13	32

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	1e-128	GRAS family protein

Link Out ? help Back to Top
Phytozome	evm.model.supercontig_9.323

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]