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

Dca15260.1

Organism

Dianthus caryophyllus

Taxonomic ID

3570

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Caryophyllaceae; Caryophylleae; Dianthus

Family

Whirly

Protein Properties

Length: 114aa MW: 12718.6 Da PI: 9.8134

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Dca15260.1	genome	DCA	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	69.3	6.8e-22	48	100	1	53
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkq 53 s+yk+kaal++++++p+f+ l+sg+lk++r+G +ll++a+a+++r+ydW++kq Dca15260.1 48 SIYKGKAALTIDPRAPEFTPLESGALKISREGYILLQFAPAAGVRQYDWSRKQ 100 7***************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	1.1E-25	38	100	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	1.18E-22	41	100	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	6.8E-20	49	100	IPR013742	Plant transcription factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 114 aa Download sequence Send to blast
MLRLLKFDVN EVAVYGDLGS LPELPKAYND LKIAIRHGST PRVYVGHSIY KGKAALTIDP 60 RAPEFTPLES GALKISREGY ILLQFAPAAG VRQYDWSRKQ GDTRRQYGNL PSVD

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koq_A	4e-33	39	113	5	81	Single-stranded DNA-binding protein WHY3, 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 the nucleus, is recruited to a distal element upstream of the kinesin KP1 to mediate the transcriptional repression of KP1. Can bind double-stranded DNA in vivo. {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). {ECO:0000269\|PubMed:19669906}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010683246.1	1e-32	PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic
Swissprot	Q66GR6	1e-31	WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBL	A0A061ECB4	2e-30	A0A061ECB4_THECC; SsDNA-binding transcriptional regulator isoform 3
TrEMBL	A0A0D2SAE1	2e-30	A0A0D2SAE1_GOSRA; Uncharacterized protein
TrEMBL	A0A0D2VAT4	2e-30	A0A0D2VAT4_GOSRA; Uncharacterized protein
TrEMBL	A0A0K9Q7Z7	3e-31	A0A0K9Q7Z7_SPIOL; Uncharacterized protein (Fragment)
TrEMBL	A0A2R6RFA1	2e-30	A0A2R6RFA1_ACTCH; Single-stranded DNA-binding protein
STRING	XP_010683246.1	5e-32	(Beta vulgaris)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02740.2	5e-34	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] 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] 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]