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

Tp1g12780

Organism

Thellungiella parvula

Taxonomic ID

98039

Taxonomic Lineage

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

Family

Whirly

Protein Properties

Length: 269aa MW: 29685.7 Da PI: 9.7305

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp1g12780	genome	thellungiella	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	227.3	1.2e-70	92	230	1	139
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkvePlp 100 s+yk+kaal+v++++p+f+aldsg++kl+++G+lll++a+a ++r+ydW+kkq+f+ls+te+++lv+l+++esceffhdp +++s+eGkvrk+lkvePlp Tp1g12780 92 SIYKGKAALTVEPRAPEFVALDSGAFKLSKDGFLLLQFAPASGVRQYDWSKKQVFSLSVTEIGTLVSLGPRESCEFFHDPNKGKSDEGKVRKVLKVEPLP 191 7************************************************************************************************* PP Whirly 101 dGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139 dGsG+f+nlsv+n+l++++es+++P+++aefav++s+++ Tp1g12780 192 DGSGHFFNLSVQNKLLNVDESIYIPITRAEFAVMISAFN 230 **********************************996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	1.6E-79	81	252	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	2.59E-80	86	269	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	6.3E-61	93	227	IPR013742	Plant transcription factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006281	Biological Process	DNA repair
GO:0032211	Biological Process	negative regulation of telomere maintenance via telomerase
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0009507	Cellular Component	chloroplast
GO:0009508	Cellular Component	plastid chromosome
GO:0003697	Molecular Function	single-stranded DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0042162	Molecular Function	telomeric DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 269 aa Download sequence Send to blast
MSQLLSSSPM AVIFNPFTSP RFLSSSSVLV AGGFAVKRHG IASKPTTTMK LSVKSRQTDY 60 FEKQRFGDSS SSPSYSSQNA EGLPARFYVG HSIYKGKAAL TVEPRAPEFV ALDSGAFKLS 120 KDGFLLLQFA PASGVRQYDW SKKQVFSLSV TEIGTLVSLG PRESCEFFHD PNKGKSDEGK 180 VRKVLKVEPL PDGSGHFFNL SVQNKLLNVD ESIYIPITRA EFAVMISAFN FVLPYLIGWH 240 AFANSIKPED TTRINNASPN YGGDYEWNR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koo_A	1e-118	80	247	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B	1e-118	80	247	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C	1e-118	80	247	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D	1e-118	80	247	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
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Functional Description ? help Back to Top
Source	Description
UniProt	Single-stranded DNA-binding protein that functions in both chloroplasts and nucleus. In chloroplasts, maintains plastid genome stability by preventing break-induced and short homology-dependent illegitimate recombinations. In nucleus, modulates telomere length homeostasis by inhibiting the action of the telomerase at the extreme termini of chromosomes. Is recruited to a distal element upstream of the kinesin KP1 to mediate the transcriptional repression of KP1. Is required for full salicylic acid-dependent plant disease resistance responses. Can bind double-stranded DNA in vivo. {ECO:0000269\|PubMed:14960277, ECO:0000269\|PubMed:17217467, ECO:0000269\|PubMed:19666500, ECO:0000269\|PubMed:19669906, ECO:0000269\|PubMed:20551348, ECO:0000269\|PubMed:21911368}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp1g12780

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By salicylic acid (SA) and infection by H.parasitica. {ECO:0000269\|PubMed:14960277, ECO:0000269\|PubMed:19669906}.

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	AF332452	0.0	AF332452.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBank	AF370156	0.0	AF370156.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBank	AY059097	0.0	AY059097.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_172893.1	1e-170	ssDNA-binding transcriptional regulator
Swissprot	Q9M9S3	1e-171	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	A0A1J3G7D2	1e-170	A0A1J3G7D2_NOCCA; Single-stranded DNA-binding protein WHY1, chloroplastic (Fragment)
STRING	AT1G14410.1	1e-169	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5023	27	52

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14410.1	1e-169	ssDNA-binding transcriptional regulator

Publications ? help Back to Top
Lepage É,Zampini É,Brisson N Plastid genome instability leads to reactive oxygen species production and plastid-to-nucleus retrograde signaling in Arabidopsis. Plant Physiol., 2013. 163(2): p. 867-81 [PMID:23969600] Carella P,Wilson DC,Cameron RK Some things get better with age: differences in salicylic acid accumulation and defense signaling in young and mature Arabidopsis. Front Plant Sci, 2014. 5: p. 775 [PMID:25620972] Zampini É,Lepage É,Tremblay-Belzile S,Truche S,Brisson N Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans. Genome Res., 2015. 25(5): p. 645-54 [PMID:25800675] Ren Y,Li Y,Jiang Y,Wu B,Miao Y Phosphorylation of WHIRLY1 by CIPK14 Shifts Its Localization and Dual Functions in Arabidopsis. Mol Plant, 2017. 10(5): p. 749-763 [PMID:28412544] Karpinska B,Alomrani SO,Foyer CH Inhibitor-induced oxidation of the nucleus and cytosol in Arabidopsis thaliana: implications for organelle to nucleus retrograde signalling. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 2018. [PMID:28808105] Huang D,Lin W,Deng B,Ren Y,Miao Y Dual-Located WHIRLY1 Interacting with LHCA1 Alters Photochemical Activities of Photosystem I and Is Involved in Light Adaptation in Arabidopsis. Int J Mol Sci, 2018. [PMID:29112140] Guan Z,Wang W,Yu X,Lin W,Miao Y Comparative Proteomic Analysis of Coregulation of CIPK14 and WHIRLY1/3 Mediated Pale Yellowing of Leaves in Arabidopsis. Int J Mol Sci, 2018. [PMID:30065159]