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

NNU_000760-RA

Organism

Nelumbo nucifera

Taxonomic ID

4432

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; stem eudicotyledons; Proteales; Nelumbonaceae; Nelumbo

Family

Whirly

Protein Properties

Length: 231aa MW: 25911.6 Da PI: 9.3538

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
NNU_000760-RA	genome	CAS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	95.4	6.1e-30	84	152	1	69
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdla 69 s+yk+kaal+v++++p+f ldsg++kl+++G++ll++a+a+++r+ydW++kq+f+ls+te+++l++l+ NNU_000760-RA 84 SIYKGKAALTVEPKAPEFIPLDSGAFKLSKEGFVLLQFAPAVGVRQYDWSRKQVFSLSVTEIGTLINLG 152 7*****************************************************************997 PP
2	Whirly	26.8	8.8e-09	146	181	104	139
Whirly 104 GlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139 G+++nl v+n+l + +es+++P++kaef+vl+s+++ NNU_000760-RA 146 GTLINLGVQNKLSNIDESIYIPITKAEFTVLISAFN 181 789******************************996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	2.4E-34	73	152	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	4.63E-55	77	222	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	1.2E-26	85	151	IPR013742	Plant transcription factor
Gene3D	G3DSA:2.30.31.10	6.2E-16	153	201	IPR009044	ssDNA-binding transcriptional regulator

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: 231 aa Download sequence Send to blast
MHILSHRLPL QNPRCPLRFS EDSLRTSCFT SILPPVSAKT FKDLSVKCRR SEYFEQQRFT 60 RPSEDSSTSQ SPGALPPRVF VGHSIYKGKA ALTVEPKAPE FIPLDSGAFK LSKEGFVLLQ 120 FAPAVGVRQY DWSRKQVFSL SVTEIGTLIN LGVQNKLSNI DESIYIPITK AEFTVLISAF 180 NFILPYLIGW HAFADSTKPN DPGRVSNANL KYGADLEWSR YEQRPASPVE V

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1l3a_A	2e-70	49	219	12	219	p24: plant transcriptional regulator PBF-2
1l3a_B	2e-70	49	219	12	219	p24: plant transcriptional regulator PBF-2
1l3a_C	2e-70	49	219	12	219	p24: plant transcriptional regulator PBF-2
1l3a_D	2e-70	49	219	12	219	p24: plant transcriptional regulator PBF-2
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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}.

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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010256524.1	1e-153	PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic-like
Swissprot	Q9M9S3	2e-84	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	A0A1U7ZWB6	1e-152	A0A1U7ZWB6_NELNU; single-stranded DNA-binding protein WHY1, chloroplastic-like
STRING	XP_010256524.1	1e-153	(Nelumbo nucifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14410.1	8e-87	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]