PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Cannabaceae; Humulus

Family

Whirly

Protein Properties

Length: 277aa MW: 30560.6 Da PI: 9.5729

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
HL.SW.v1.0.G017088.1	genome	HOPBASE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	217.4	1.4e-67	99	237	1	139
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGk 89 s+yk+kaal+v++++p+f+aldsg++k++++G++ll++a+a+++r ydW++kq+f+ls+te+++lv+l++ +sceffhdp+++ s+eG+ HL.SW.v1.0.G017088.1 99 SIYKGKAALTVEPKAPEFTALDSGAFKISKEGFVLLQFAPAAGVRVYDWSRKQVFSLSVTEIGNLVSLGATGSCEFFHDPFKGRSEEGQ 187 7************************************************************************************** PP Whirly 90 vrkalkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139 vrk lkvePlpdGsG+f+nlsv+n+l++ +es+++Pv++aefavl+s+++ HL.SW.v1.0.G017088.1 188 VRKMLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEFAVLNSAFN 237 ********************************************9996 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-76	88	258	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	2.82E-77	93	276	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	2.9E-60	100	234	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: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: 277 aa Download sequence Send to blast
MMRPYSLSSS SSLTVTPQNP KLSPAHSFFL PPLPGTTAFS FSSNPTYIRK GLSLKCRQSE 60 YFDQQKFATT NAQYDNSSFA PQTPSRADQL PARFYVGHSI YKGKAALTVE PKAPEFTALD 120 SGAFKISKEG FVLLQFAPAA GVRVYDWSRK QVFSLSVTEI GNLVSLGATG SCEFFHDPFK 180 GRSEEGQVRK MLKVEPLPDG SGHFFNLSVQ NKLINLDESI YIPVTRAEFA VLNSAFNFIL 240 PHLLGWSAFA NSIKPEEVSR GNNASPKYGG DYEWKR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1l3a_A	1e-103	93	274	37	218	p24: plant transcriptional regulator PBF-2
1l3a_B	1e-103	93	274	37	218	p24: plant transcriptional regulator PBF-2
1l3a_C	1e-103	93	274	37	218	p24: plant transcriptional regulator PBF-2
1l3a_D	1e-103	93	274	37	218	p24: plant transcriptional regulator PBF-2
4koo_A	1e-103	87	254	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B	1e-103	87	254	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C	1e-103	87	254	2	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D	1e-103	87	254	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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024021369.1	1e-143	single-stranded DNA-binding protein WHY1, chloroplastic-like
Swissprot	Q9M9S3	1e-125	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	D9ZJE7	1e-132	D9ZJE7_MALDO; WHY domain class transcription factor
STRING	XP_004297331.1	1e-134	(Fragaria vesca)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF6416	32	51

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14410.1	1e-127	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]