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

Sphfalx0001s0307.1.p

Organism

Sphagnum fallax

Taxonomic ID

53036

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Bryophyta; Sphagnophytina; Sphagnopsida; Sphagnales; Sphagnaceae; Sphagnum

Family

GRAS

Protein Properties

Length: 600aa MW: 67792.9 Da PI: 5.3752

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sphfalx0001s0307.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	342.2	8.5e-105	214	587	3	374
GRAS 3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPil 91 +lLlecA+a++++d+ ++q+l++ l+elasp+gd qRla+yf++AL r+++++ ++ ++l++ ++++++ +++ ++ +++e+sP+ Sphfalx0001s0307.1.p 214 NLLLECARAIATSDTPRVQNLMWVLNELASPYGDYDQRLASYFLQALFCRITNTGARCHSILSAAAEKTHTFESVRKMILTYQEASPWT 302 69**********************************************************9999998887777788889**** PP GRAS 92 kfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg.skeeleetgerLakfAeelgvpfefn 179 +f+h++ N a++ea+ege ++Hi+D++++ ++QWp L++aLa+R+eg+p+lR+T ++ ++++ e ++++ rL++fA+ +gvpfef+ Sphfalx0001s0307.1.p 303 TFGHVAGNGAMMEAFEGEMKIHIVDISVTFCTQWPMLFEALATRAEGTPHLRLTIIVISKQEsAMEVMRQIMTRLERFARLMGVPFEFT 391 **************************************************999877667999********************* PP GRAS 180 vlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsles..erdevLklvkslsPkvvvvveqeadh.nsesFlerflealeyys 265 ++ +le+le+ eL+++++Eala+n+++ lh++++ + ++ +rd vL ++k+ +Pk++++ve e+d+ +s++F++ f eal+yys Sphfalx0001s0307.1.p 392 LIQKPQLETLEIAELKLREDEALAINCIHTLHHVPETIPDDKNhsPRDIVLYTFKDANPKIITIVEDEVDLvSSPDFFTYFREALRYYS 480 8777***************************76655555669*********************9************* PP GRAS 266 alfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveee 354 lf+sle+++pr+s++r ++Er +r+ vn++ac +e ++r+e ++W r++++G+ p+s+++++++++ll+++k +g+ + ++ Sphfalx0001s0307.1.p 481 LLFESLEESFPRASNDRLTLERT-CARNMVNLLACDPSENEQRQEPGSRWATRFQTVGLLRSPFSDDVVDDVRALLKRYK-EGWGLASD 567 *******************.7999************************************************.99** PP GRAS 355 sgslvlgWkdrpLvsvSaWr 374 + l+l+Wk++ +++S+W+ Sphfalx0001s0307.1.p 568 ESGLFLTWKRQVAIFASSWK 587 *****************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	53.545	186	568	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.9E-102	214	587	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 600 aa Download sequence Send to blast
MDKFSSEQVE YPEIEQVRDL NSIGTTATSS MRSDEAEASR NIFDNTRRST VTHPGEYIQQ 60 HHGFTVLGLQ DQQQRTAGSS YGVASTSTQR PQFSNLRSVD HDPAAARHEM NIPLFKLEES 120 FELRSAARHP QHDTWTEHQS HHERQQQWEQ DLSSQRIAAT KQEIINDSTL ALSGFTSFLN 180 PIGAAQQQAS SSAAQPAAAS TSSGDDGDQH WAPNLLLECA RAIATSDTPR VQNLMWVLNE 240 LASPYGDYDQ RLASYFLQAL FCRITNTGAR CHSILSAAAE KTHTFESVRK MILTYQEASP 300 WTTFGHVAGN GAMMEAFEGE MKIHIVDISV TFCTQWPMLF EALATRAEGT PHLRLTIIVI 360 SKQESAMEVM RQIMTRLERF ARLMGVPFEF TLIQKPQLET LEIAELKLRE DEALAINCIH 420 TLHHVPETIP DDKNHSPRDI VLYTFKDANP KIITIVEDEV DLVSSPDFFT YFREALRYYS 480 LLFESLEESF PRASNDRLTL ERTCARNMVN LLACDPSENE QRQEPGSRWA TRFQTVGLLR 540 SPFSDDVVDD VRALLKRYKE GWGLASDESG LFLTWKRQVA IFASSWKPNL EASHNPTRS*

Sequence ? help Back to Top

Protein Sequence Length: 600 aa Download sequence Send to blast

MDKFSSEQVE YPEIEQVRDL NSIGTTATSS MRSDEAEASR NIFDNTRRST VTHPGEYIQQ  60
HHGFTVLGLQ DQQQRTAGSS YGVASTSTQR PQFSNLRSVD HDPAAARHEM NIPLFKLEES  120
FELRSAARHP QHDTWTEHQS HHERQQQWEQ DLSSQRIAAT KQEIINDSTL ALSGFTSFLN  180
PIGAAQQQAS SSAAQPAAAS TSSGDDGDQH WAPNLLLECA RAIATSDTPR VQNLMWVLNE  240
LASPYGDYDQ RLASYFLQAL FCRITNTGAR CHSILSAAAE KTHTFESVRK MILTYQEASP  300
WTTFGHVAGN GAMMEAFEGE MKIHIVDISV TFCTQWPMLF EALATRAEGT PHLRLTIIVI  360
SKQESAMEVM RQIMTRLERF ARLMGVPFEF TLIQKPQLET LEIAELKLRE DEALAINCIH  420
TLHHVPETIP DDKNHSPRDI VLYTFKDANP KIITIVEDEV DLVSSPDFFT YFREALRYYS  480
LLFESLEESF PRASNDRLTL ERTCARNMVN LLACDPSENE QRQEPGSRWA TRFQTVGLLR  540
SPFSDDVVDD VRALLKRYKE GWGLASDESG LFLTWKRQVA IFASSWKPNL EASHNPTRS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_B	1e-136	208	588	29	420	Protein SHORT-ROOT
5b3h_E	1e-136	208	588	29	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}.

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_024379763.1	0.0	protein SHORT-ROOT-like
Swissprot	Q9SZF7	1e-135	SHR_ARATH; Protein SHORT-ROOT
TrEMBL	A0A2K1KCY7	0.0	A0A2K1KCY7_PHYPA; Uncharacterized protein
STRING	PP1S97_39V6.1	0.0	(Physcomitrella patens)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G37650.1	1e-137	GRAS family protein

Link Out ? help Back to Top
Phytozome	Sphfalx0001s0307.1.p

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]