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

RrC1334_p5

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

Whirly

Protein Properties

Length: 233aa MW: 25347.6 Da PI: 9.6474

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1334_p5	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	107.2	1.4e-33	92	165	1	74
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesc 74 s+yk+kaal+v++++p+f++ldsg++kl+++G+lll++a+a+++r+ydW+kkq+f+ls+ e+++lv+l+++esc RrC1334_p5 92 SIYKGKAALTVEPRAPEFVSLDSGAFKLSKDGFLLLQFAPAAGVRQYDWSKKQVFSLSVSEIGTLVSLGPRESC 165 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	5.9E-36	82	165	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	2.59E-57	86	233	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	3.9E-29	93	166	IPR013742	Plant transcription factor
Gene3D	G3DSA:2.30.31.10	4.5E-15	166	215	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:0045910	Biological Process	negative regulation of DNA recombination
GO:0009508	Cellular Component	plastid chromosome
GO:0009570	Cellular Component	chloroplast stroma
GO:0003697	Molecular Function	single-stranded DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0003723	Molecular Function	RNA binding
GO:0042162	Molecular Function	telomeric DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 233 aa Download sequence Send to blast
MSQLLSSPLM AASYNPFASP RFLSSSSSVL VPGGGGGLAV KWHGLASKPA RTVNLSVKSR 60 QTDYFEKQRF GDSSSSSQNG EGGPARFYVG HSIYKGKAAL TVEPRAPEFV SLDSGAFKLS 120 KDGFLLLQFA PAAGVRQYDW SKKQVFSLSV SEIGTLVSLG PRESCVQNKL LNVDESIYIP 180 ITRAEFTVLV SAFNFVLPYL IGWHAFANSI KPEETIRTNN ASSNYGGDYE WNR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koo_A	7e-80	80	211	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B	7e-80	80	211	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C	7e-80	80	211	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D	7e-80	80	211	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}.

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	1e-103	AF332452.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBank	AF370156	1e-103	AF370156.1 Arabidopsis thaliana putative DNA-binding protein p24 (At1g14410) mRNA, complete cds.
GenBank	AY059097	1e-103	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	XP_018447906.1	1e-144	PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic
Swissprot	Q9M9S3	1e-127	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	A0A3N6U4Y7	1e-150	A0A3N6U4Y7_BRACR; Uncharacterized protein
STRING	Bra016702.1-P	1e-140	(Brassica rapa)
STRING	Bo8g066030.1	1e-139	(Brassica oleracea)

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-121	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]