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

Gh_D13G0692

Organism

Gossypium hirsutum

Taxonomic ID

3635

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

Whirly

Protein Properties

Length: 232aa MW: 25899.2 Da PI: 10.0262

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_D13G0692	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	181.5	1.6e-56	92	202	1	111
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkveP 98 s+yk+kaal+v++++p+f+ ldsg++k++r+G++ll++a+a+++r+ydW++kq+f+ls+te+++l++l+ +esceffhdp++++s+eGkvrk+lkveP Gh_D13G0692 92 SIYKGKAALTVEPRAPEFVPLDSGAFKISREGFVLLQFAPAAGVRQYDWSRKQVFSLSVTEIGTLISLGLRESCEFFHDPFKGKSDEGKVRKVLKVEP 189 7*********************************************************************************************** PP Whirly 99 lpdGsGlfvnlsv 111 lpdGsG+f+nl Gh_D13G0692 190 LPDGSGHFFNLGW 202 ********965 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	9.5E-55	84	200	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	3.53E-55	86	232	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	1.4E-50	93	202	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: 232 aa Download sequence Send to blast
MLQLQLLSSP PLTPQTLNLN SISNPKLFPS FSSLNSSQTR SFKFNPLSKP SKFSLKCRQS 60 EYFDQKQRFD DSSSSTSPSS LGLPARFYVG HSIYKGKAAL TVEPRAPEFV PLDSGAFKIS 120 REGFVLLQFA PAAGVRQYDW SRKQVFSLSV TEIGTLISLG LRESCEFFHD PFKGKSDEGK 180 VRKVLKVEPL PDGSGHFFNL GWHAFANSTK PDDTSRANNA NPRYGGDYEW SR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1l3a_A	8e-79	86	231	37	219	p24: plant transcriptional regulator PBF-2
1l3a_B	8e-79	86	231	37	219	p24: plant transcriptional regulator PBF-2
1l3a_C	8e-79	86	231	37	219	p24: plant transcriptional regulator PBF-2
1l3a_D	8e-79	86	231	37	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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JX617609	9e-86	JX617609.1 Gossypium hirsutum clone NBRI_GE62797 microsatellite sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016705284.1	1e-155	PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic-like isoform X2
Swissprot	Q9M9S3	1e-105	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	A0A1U8KWY9	1e-154	A0A1U8KWY9_GOSHI; single-stranded DNA-binding protein WHY1, chloroplastic-like isoform X2
STRING	Gorai.013G077400.1	1e-133	(Gossypium raimondii)

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-101	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]