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_022868-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: 223aa MW: 24856.6 Da PI: 8.6123

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
NNU_022868-RA	genome	CAS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	99	4.8e-31	82	155	1	74
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesc 74 s+yk+kaal+v+++ +f+ ldsg++kl+++G++ll++a+a++ r+ydW++kq+f+ls+te+++l++l++k+sc NNU_022868-RA 82 SIYKGKAALTVEPKVLEFVPLDSGAFKLSKEGFVLLQFAPAVGLRQYDWSRKQVFSLSVTEIGTLINLGAKGSC 155 7************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	2.2E-33	74	155	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	7.85E-53	75	223	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	1.0E-26	83	156	IPR013742	Plant transcription factor
Gene3D	G3DSA:2.30.31.10	2.6E-14	156	204	IPR009044	ssDNA-binding transcriptional regulator

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0045910	Biological Process	negative regulation of DNA recombination
GO:0009570	Cellular Component	chloroplast stroma
GO:0003677	Molecular Function	DNA binding
GO:0003723	Molecular Function	RNA binding

Sequence ? help Back to Top
Protein Sequence Length: 223 aa Download sequence Send to blast
MHLVSHLLPP QNPKCSPIFS QVSLRNSYCI PELGRVSTKT PSVKCRHSEN FEQQRFTRPS 60 EDSFAPQSPE VLPPPRVFVG HSIYKGKAAL TVEPKVLEFV PLDSGAFKLS KEGFVLLQFA 120 PAVGLRQYDW SRKQVFSLSV TEIGTLINLG AKGSCVQNKL LNVDESIYIP ITKAELTVLV 180 SAFNFILPYL IGWHAFVDSI KPDDPGRVSN ASPNYQADLE WSR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1l3a_A	8e-71	75	222	36	219	p24: plant transcriptional regulator PBF-2
1l3a_B	8e-71	75	222	36	219	p24: plant transcriptional regulator PBF-2
1l3a_C	8e-71	75	222	36	219	p24: plant transcriptional regulator PBF-2
1l3a_D	8e-71	75	222	36	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_010242375.1	1e-156	PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic-like isoform X1
Swissprot	Q9M9S3	2e-81	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	A0A1U7YQL4	1e-155	A0A1U7YQL4_NELNU; single-stranded DNA-binding protein WHY1, chloroplastic-like isoform X1
STRING	XP_010242375.1	1e-156	(Nelumbo nucifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14410.1	8e-84	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]