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

17086

Common Name

SELMODRAFT_17085, SELMODRAFT_17086

Organism

Selaginella moellendorffii

Taxonomic ID

88036

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Lycopodiidae; Selaginellales; Selaginellaceae; Selaginella

Family

AP2

Protein Properties

Length: 157aa MW: 18354.4 Da PI: 10.2988

Description

AP2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
17086	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	24.4	7.5e-08	2	51	8	55
AP2 8 wdkkrgrWvAeIrd.pse.ngkr.krfslgkfgtaeeAakaaiaarkkleg 55 +++++ r++A+++d ++ g r ++ + g ++++e Aa+a++ a++k++g 17086 2 RHRWTRRYEAHLWDnSYKqPG-RdRKGRQGGYDSEENAARAYDLAALKYWG 51 7999********6555644.334444488****************98 PP
2	AP2	55	2e-17	94	145	1	55
AP2 1 sgykGVrwdkkrgrWvAeIrdpsengkr..krfslgkfgtaeeAakaaiaarkkleg 55 s ++GV+++++ grW A+I + k +lg+fgt+eeAa+a+++a+ k++g 17086 94 SVFRGVTRHHQHGRWQARIGRV-----AghKDLYLGTFGTEEEAAEAYDRAAIKYRG 145 689*************9885.....235***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF00847	2.8E-5	2	51	IPR001471	AP2/ERF domain
PROSITE profile	PS51032	15.185	2	59	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	2.3E-9	2	59	IPR001471	AP2/ERF domain
SuperFamily	SSF54171	3.27E-11	2	60	IPR016177	DNA-binding domain
SMART	SM00380	6.4E-10	2	65	IPR001471	AP2/ERF domain
Pfam	PF00847	1.1E-12	94	145	IPR001471	AP2/ERF domain
SuperFamily	SSF54171	2.48E-18	94	155	IPR016177	DNA-binding domain
CDD	cd00018	2.01E-20	94	155	No hit	No description
PROSITE profile	PS51032	18.228	95	153	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	2.0E-18	95	153	IPR001471	AP2/ERF domain
SMART	SM00380	7.1E-25	95	157	IPR001471	AP2/ERF domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
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: 157 aa Download sequence Send to blast
SRHRWTRRYE AHLWDNSYKQ PGRDRKGRQG GYDSEENAAR AYDLAALKYW GPNTIINFPL 60 GNYTKELEEM KHNTRQEYVA AIRRKSDGFS RGTSVFRGVT RHHQHGRWQA RIGRVAGHKD 120 LYLGTFGTEE EAAEAYDRAA IKYRGLKAIT NFEISRY

Functional Description ? help Back to Top
Source	Description
UniProt	Acts as positive regulator of adventitious (crown) root formation by promoting its initiation. Promotes adventitious root initiation through repression of cytokinin signaling by positively regulating the two-component response regulator RR1. Regulated by the auxin response factor and transcriptional activator ARF23/ARF1. {ECO:0000269\|PubMed:21481033}.
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}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin accumulation. {ECO:0000269\|PubMed:15454085}.
UniProt	INDUCTION: Induced by auxin. {ECO:0000269\|PubMed:21481033}.

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_002325046.2	7e-87	AP2-like ethylene-responsive transcription factor AIL5 isoform X2
Refseq	XP_020523524.1	2e-87	AP2-like ethylene-responsive transcription factor AIL5 isoform X2
Refseq	XP_021890465.1	2e-87	AP2-like ethylene-responsive transcription factor ANT, partial
Swissprot	Q5YGP8	1e-85	PLET1_ARATH; AP2-like ethylene-responsive transcription factor PLT1
Swissprot	Q84Z02	1e-85	CRL5_ORYSJ; AP2-like ethylene-responsive transcription factor CRL5
TrEMBL	D8RSY0	1e-112	D8RSY0_SELML; Uncharacterized protein (Fragment)
STRING	EFJ23833	1e-113	(Selaginella moellendorffii)
STRING	EFJ24417	1e-113	(Selaginella moellendorffii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP112	17	209

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G57390.1	1e-82	AINTEGUMENTA-like 5

Link Out ? help Back to Top
Phytozome	17086
Entrez Gene	9638168 \| 9657366

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] Kitomi Y, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling. Plant J., 2011. 67(3): p. 472-84 [PMID:21481033] Banks JA, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science, 2011. 332(6032): p. 960-3 [PMID:21551031] Li P,Xue H Structural characterization and expression pattern analysis of the rice PLT gene family. Acta Biochim. Biophys. Sin. (Shanghai), 2011. 43(9): p. 688-97 [PMID:21807632] 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] García-Cruz KV, et al. The MADS-box XAANTAL1 increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell-cycle components. Ann. Bot., 2018. [PMID:27474508] 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] Franssen HJ,Kulikova O,Willemsen V,Heidstra R Cis-regulatory PLETHORA promoter elements directing root and nodule expression are conserved between Arabidopsis thaliana and Medicago truncatula. Plant Signal Behav, 2017. 12(2): p. e1278102 [PMID:28067580] 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] Ercoli MF, et al. GIF Transcriptional Coregulators Control Root Meristem Homeostasis. Plant Cell, 2018. 30(2): p. 347-359 [PMID:29352064] Xu C, et al. Control of auxin-induced callus formation by bZIP59-LBD complex in Arabidopsis regeneration. Nat Plants, 2018. 4(2): p. 108-115 [PMID:29358751]