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

892081

Common Name

ARALYDRAFT_892081

Organism

Arabidopsis lyrata

Taxonomic ID

81972

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

AP2

Protein Properties

Length: 569aa MW: 62478.4 Da PI: 6.6118

Description

AP2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
892081	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	47.9	3.4e-15	189	248	1	55
AP2 1 sgykGVrwdkkrgrWvAeIrd.pse.ng..kr.krfslgkfgtaeeAakaaiaarkkleg 55 s y+GV++++++gr++A+++d + g ++ ++++lg ++ +e+Aa+a++ a++k++g 892081 189 SIYRGVTRHRWTGRYEAHLWDnSCRrEGqsRKgRQVYLGGYDKEEKAARAYDLAALKYWG 248 57*****************666664477446***********************98 PP
2	AP2	47	6.3e-15	293	342	3	55
AP2 3 ykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 y+GV+++++ grW A+I + +k +lg+f t+eeAa+a++ a+ k++g 892081 293 YRGVTRHHQHGRWQARIGRVAG---NKDLYLGTFSTEEEAAEAYDIAAIKFRG 342 9*************988532...5**********************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00018	2.08E-22	189	258	No hit	No description
SuperFamily	SSF54171	2.94E-17	189	257	IPR016177	DNA-binding domain
Pfam	PF00847	3.3E-12	189	248	IPR001471	AP2/ERF domain
PROSITE profile	PS51032	19.322	190	256	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	5.5E-16	190	256	IPR001471	AP2/ERF domain
SMART	SM00380	6.2E-30	190	262	IPR001471	AP2/ERF domain
PRINTS	PR00367	5.1E-6	191	202	IPR001471	AP2/ERF domain
SuperFamily	SSF54171	9.15E-18	291	351	IPR016177	DNA-binding domain
CDD	cd00018	2.78E-24	291	352	No hit	No description
PROSITE profile	PS51032	19.506	292	350	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	4.7E-18	292	350	IPR001471	AP2/ERF domain
SMART	SM00380	1.5E-32	292	356	IPR001471	AP2/ERF domain
Pfam	PF00847	1.5E-9	293	342	IPR001471	AP2/ERF domain
PRINTS	PR00367	5.1E-6	332	352	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:0005634	Cellular Component	nucleus
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: 569 aa Download sequence Send to blast
MNSNNWLAFP LSPTHSSLPP HIHSSQTSHF NLGLVNDNID NPFQNQEWNM INPHGGGGEG 60 GEVPKVADFL GVSKSGDHHP DHNLVPYNDI HQTNDSDYYF QTNSLLPTVV TCASNAPNNY 120 ELQESAHNLQ SLTLSMGSTG AAAAEADTVK ASPAETSADN SSSTTNTSGG AIVEATPRRT 180 LETFGQRTSI YRGVTRHRWT GRYEAHLWDN SCRREGQSRK GRQVYLGGYD KEEKAARAYD 240 LAALKYWGPS TTTNFPITNY EKEVEEMKNM TRQEFVASIR RKSSGFSRGA SMYRGVTRHH 300 QHGRWQARIG RVAGNKDLYL GTFSTEEEAA EAYDIAAIKF RGLNAVTNFE INRYDVKAIL 360 ESNTLPIGGG AAKRLKEAQA LESSRKREEM IALGSNFHQY GAASGSSSVA SSSRLQLQPY 420 PLSIQQPFEH LHHHQPLLTL QNNNDISQYH DSYSYIQTQL HLHQQQTNNY LQSSSHSTQL 480 YNAYLQSNPG LLHGFISDNN NTSGFLGNNG IGIGSTSTVG SSAEEEFPAV KVDYDMPPSG 540 GATGYGGWNT GESVQGMNPG GVFTMWNE*

Sequence ? help Back to Top

Protein Sequence Length: 569 aa Download sequence Send to blast

MNSNNWLAFP LSPTHSSLPP HIHSSQTSHF NLGLVNDNID NPFQNQEWNM INPHGGGGEG  60
GEVPKVADFL GVSKSGDHHP DHNLVPYNDI HQTNDSDYYF QTNSLLPTVV TCASNAPNNY  120
ELQESAHNLQ SLTLSMGSTG AAAAEADTVK ASPAETSADN SSSTTNTSGG AIVEATPRRT  180
LETFGQRTSI YRGVTRHRWT GRYEAHLWDN SCRREGQSRK GRQVYLGGYD KEEKAARAYD  240
LAALKYWGPS TTTNFPITNY EKEVEEMKNM TRQEFVASIR RKSSGFSRGA SMYRGVTRHH  300
QHGRWQARIG RVAGNKDLYL GTFSTEEEAA EAYDIAAIKF RGLNAVTNFE INRYDVKAIL  360
ESNTLPIGGG AAKRLKEAQA LESSRKREEM IALGSNFHQY GAASGSSSVA SSSRLQLQPY  420
PLSIQQPFEH LHHHQPLLTL QNNNDISQYH DSYSYIQTQL HLHQQQTNNY LQSSSHSTQL  480
YNAYLQSNPG LLHGFISDNN NTSGFLGNNG IGIGSTSTVG SSAEEEFPAV KVDYDMPPSG  540
GATGYGGWNT GESVQGMNPG GVFTMWNE*

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	892081

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	AY506550	0.0	AY506550.1 Arabidopsis thaliana PLETHORA2 (PLT2) mRNA, complete cds.
GenBank	BT020277	0.0	BT020277.1 Arabidopsis thaliana At1g51190 mRNA, complete cds.
GenBank	BT020460	0.0	BT020460.1 Arabidopsis thaliana At1g51190 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002891621.1	0.0	AP2-like ethylene-responsive transcription factor PLT2
Refseq	XP_020870613.1	0.0	AP2-like ethylene-responsive transcription factor PLT2
Swissprot	Q5YGP7	0.0	PLET2_ARATH; AP2-like ethylene-responsive transcription factor PLT2
TrEMBL	D7KHN8	0.0	D7KHN8_ARALL; AP2/EREBP transcription factor
STRING	scaffold_104875.1	0.0	(Arabidopsis lyrata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3015	27	67

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G51190.1	0.0	AP2 family protein

Link Out ? help Back to Top
Phytozome	892081
Entrez Gene	9330361

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]