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

GSBRNA2T00057787001

Common Name

GSBRNA2T00057787001, GSBRNA2T00087190001

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

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

Family

Whirly

Protein Properties

Length: 153aa MW: 16763.3 Da PI: 10.7128

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00057787001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	74.5	1.6e-23	91	145	1	55
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsf 55 s+yk+kaa++v++++p+f++ldsg++kl+++G+lll++a+a+++r+ydW+kkq++ GSBRNA2T00057787001 91 SIYKGKAAVTVEPRAPEFVSLDSGAFKLSKDGSLLLQFAPAAGVRQYDWSKKQVW 145 7****************************************************85 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	4.5E-25	82	145	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	8.63E-23	85	146	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	9.2E-20	92	144	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: 153 aa Download sequence Send to blast
MSQLLSSPLV ALSYNPFASP RFLSSSSSVL VATGGLAVKR HVLASKPTKT VKLTVKSRQT 60 DYFEKQRFGD SSERVLSKCE GGPARFYVGH SIYKGKAAVT VEPRAPEFVS LDSGAFKLSK 120 DGSLLLQFAP AAGVRQYDWS KKQVWFHPFN FR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koo_A	3e-36	79	145	2	68	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B	3e-36	79	145	2	68	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C	3e-36	79	145	2	68	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D	3e-36	79	145	2	68	Single-stranded DNA-binding protein WHY1, chloroplastic
Search in ModeBase

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00057787001

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_009110543.1	4e-75	PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic
Swissprot	Q9M9S3	1e-65	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	A0A078JNN5	1e-106	A0A078JNN5_BRANA; BnaAnng23380D protein
STRING	Bra016702.1-P	1e-74	(Brassica rapa)

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	4e-62	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] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] 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]