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

Sevir.5G421100.1.p

Organism

Setaria viridis

Taxonomic ID

4556

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria

Family

AP2

Protein Properties

Length: 699aa MW: 72818.4 Da PI: 6.9339

Description

AP2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sevir.5G421100.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	47.5	4.4e-15	272	331	1	55
AP2 1 sgykGVrwdkkrgrWvAeIrd.pse.ng..kr.krfslgkfgtaeeAakaaiaarkkleg 55 s y+GV++++++gr++A+++d + g ++ ++++lg ++ +e+Aa+a++ a++k++g Sevir.5G421100.1.p 272 SIYRGVTRHRWTGRYEAHLWDnSCRrEGqtRKgRQVYLGGYDKEEKAARAYDLAALKYWG 331 57*****************666664478446***********************98 PP
2	AP2	46.7	8e-15	374	425	1	55
AP2 1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 s y+GV+++++ grW A+I + +k +lg+f t eeAa+a++ a+ k++g Sevir.5G421100.1.p 374 SIYRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFSTQEEAAEAYDIAAIKFRG 425 57**************988532...5**********************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF00847	5.9E-12	272	331	IPR001471	AP2/ERF domain
SuperFamily	SSF54171	2.09E-17	272	341	IPR016177	DNA-binding domain
CDD	cd00018	1.98E-20	272	341	No hit	No description
SMART	SM00380	7.2E-30	273	345	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	8.2E-16	273	340	IPR001471	AP2/ERF domain
PROSITE profile	PS51032	19.23	273	339	IPR001471	AP2/ERF domain
PRINTS	PR00367	3.7E-6	274	285	IPR001471	AP2/ERF domain
SuperFamily	SSF54171	1.11E-17	374	435	IPR016177	DNA-binding domain
Pfam	PF00847	9.9E-10	374	425	IPR001471	AP2/ERF domain
CDD	cd00018	1.13E-22	374	435	No hit	No description
PROSITE profile	PS51032	19.045	375	433	IPR001471	AP2/ERF domain
SMART	SM00380	1.5E-33	375	439	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	5.1E-18	375	434	IPR001471	AP2/ERF domain
PRINTS	PR00367	3.7E-6	415	435	IPR001471	AP2/ERF domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000723	Biological Process	telomere maintenance
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0007389	Biological Process	pattern specification process
GO:0010073	Biological Process	meristem maintenance
GO:0010449	Biological Process	root meristem growth
GO:0019827	Biological Process	stem cell population maintenance
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 699 aa Download sequence Send to blast
MATVNNWLAF SLSPQDLPPS QTDSTLISAT ATDEVSGDVC FNIPQDWSMR GSELSALVAE 60 PKLEDFLGGI NFSEQHHKAN LNVIPSSSNA CYASSGASTG YHQLYHHQSS ALHFADSVMV 120 ASSAGVHDGG ASMLSAAATV NGGAGAASAN GGSIGLSMIK NWLRSQPAPP LPQPRVVAAA 180 EGAQAAQGLS LSMNMAGAQG AGMPLLAGER GRAPESVSTS AQGGAVAARK EDSGGSGGAG 240 ALVAVSTDTG GSGTVAETAA RKTVDTFGQR TSIYRGVTRH RWTGRYEAHL WDNSCRREGQ 300 TRKGRQVYLG GYDKEEKAAR AYDLAALKYW GPTTTTNFPV SNYEKELEEM KHMTRQEFVA 360 SLRRKSSGFS RGASIYRGVT RHHQHGRWQA RIGRVAGNKD LYLGTFSTQE EAAEAYDIAA 420 IKFRGLNAVT NFDMSRYDVK SILDSSALPI GSAAKRLKEA EAAASAQHAG VVSYDVGRIA 480 SHLGDGGALA AYGTHYHAAA AAWPTIAFQP SAAAAGLYHP YAQPMRGWCK QEQDHAVIAA 540 AHSLHELNHL NLGAAAGAHD FFSAGQAAMH GLGSIDNASL EHSTGSNSVV YNGVGDSNGG 600 AVGGGYMMPM SAAAATTTAM VSHEQVHARS HQGEHDEATK QAAQMGYESY LVNAEAAYGG 660 GRMPSWTPAS APAAASSNDN MAGVGHGGAQ LFSVWNDT*

Sequence ? help Back to Top

Protein Sequence Length: 699 aa Download sequence Send to blast

MATVNNWLAF SLSPQDLPPS QTDSTLISAT ATDEVSGDVC FNIPQDWSMR GSELSALVAE  60
PKLEDFLGGI NFSEQHHKAN LNVIPSSSNA CYASSGASTG YHQLYHHQSS ALHFADSVMV  120
ASSAGVHDGG ASMLSAAATV NGGAGAASAN GGSIGLSMIK NWLRSQPAPP LPQPRVVAAA  180
EGAQAAQGLS LSMNMAGAQG AGMPLLAGER GRAPESVSTS AQGGAVAARK EDSGGSGGAG  240
ALVAVSTDTG GSGTVAETAA RKTVDTFGQR TSIYRGVTRH RWTGRYEAHL WDNSCRREGQ  300
TRKGRQVYLG GYDKEEKAAR AYDLAALKYW GPTTTTNFPV SNYEKELEEM KHMTRQEFVA  360
SLRRKSSGFS RGASIYRGVT RHHQHGRWQA RIGRVAGNKD LYLGTFSTQE EAAEAYDIAA  420
IKFRGLNAVT NFDMSRYDVK SILDSSALPI GSAAKRLKEA EAAASAQHAG VVSYDVGRIA  480
SHLGDGGALA AYGTHYHAAA AAWPTIAFQP SAAAAGLYHP YAQPMRGWCK QEQDHAVIAA  540
AHSLHELNHL NLGAAAGAHD FFSAGQAAMH GLGSIDNASL EHSTGSNSVV YNGVGDSNGG  600
AVGGGYMMPM SAAAATTTAM VSHEQVHARS HQGEHDEATK QAAQMGYESY LVNAEAAYGG  660
GRMPSWTPAS APAAASSNDN MAGVGHGGAQ LFSVWNDT*

Functional Description ? help Back to Top
Source	Description
UniProt	Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). Master regulator of basal/root fate. Essential for root quiescent center (QC) and columella specification, stem cell activity, as well as for establishment of the stem cell niche during embryogenesis. Modulates the root polar auxin transport by regulating the distribution of PIN genes. Essential role in respecifying pattern and polarity in damaged roots. Direct target of the transcriptional corepressor TPL. Expression levels and patterns regulated post-transcriptionally by root meristem growth factors (RGFs). {ECO:0000250, ECO:0000269\|PubMed:15454085, ECO:0000269\|PubMed:15635403, ECO:0000269\|PubMed:16424342, ECO:0000269\|PubMed:20190735}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sevir.5G421100.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin accumulation. {ECO:0000269\|PubMed:15454085}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK240892	0.0	AK240892.1 Oryza sativa Japonica Group cDNA, clone: J065030K10, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_022682077.1	0.0	AP2-like ethylene-responsive transcription factor BBM2
Swissprot	Q5YGP7	1e-135	PLET2_ARATH; AP2-like ethylene-responsive transcription factor PLT2
TrEMBL	A0A368REM7	0.0	A0A368REM7_SETIT; Uncharacterized protein
STRING	Si000593m	0.0	(Setaria italica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP1569	37	110

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G51190.1	1e-124	AP2 family protein

Link Out ? help Back to Top
Phytozome	Sevir.5G421100.1.p

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Lee DK,Sieburth LE The bps signal: embryonic arrest from an auxin-independent mechanism in bypass triple mutants. Plant Signal Behav, 2012. 7(6): p. 698-700 [PMID:22580686] Hong LW,Yan DW,Liu WC,Chen HG,Lu YT TIME FOR COFFEE controls root meristem size by changes in auxin accumulation in Arabidopsis. J. Exp. Bot., 2014. 65(1): p. 275-86 [PMID:24277277] 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] Zhao Q, et al. Sulfur nutrient availability regulates root elongation by affecting root indole-3-acetic acid levels and the stem cell niche. J Integr Plant Biol, 2014. 56(12): p. 1151-63 [PMID:24831283] Huang JB, et al. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell, 2014. 26(9): p. 3501-18 [PMID:25217509] Yang S, et al. The Arabidopsis SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA Targets Directly to PINs and Is Required for Root Stem Cell Niche Maintenance. Plant Cell, 2015. 27(6): p. 1670-80 [PMID:25991732] 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] Shinohara H,Mori A,Yasue N,Sumida K,Matsubayashi Y Identification of three LRR-RKs involved in perception of root meristem growth factor in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(14): p. 3897-902 [PMID:27001831] Ou Y, et al. RGF1 INSENSITIVE 1 to 5, a group of LRR receptor-like kinases, are essential for the perception of root meristem growth factor 1 in Arabidopsis thaliana. Cell Res., 2016. 26(6): p. 686-98 [PMID:27229312] Santuari L, et al. The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots. Plant Cell, 2016. 28(12): p. 2937-2951 [PMID:27920338] Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis . J Integr Plant Biol, 2017. 59(1): p. 30-43 [PMID:28074634] Du Y,Scheres B PLETHORA transcription factors orchestrate de novo organ patterning during Arabidopsis lateral root outgrowth. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(44): p. 11709-11714 [PMID:29078398] 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]