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

Csa09g004980.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

Whirly

Protein Properties

Length: 304aa MW: 33377 Da PI: 10.1304

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa09g004980.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	214.2	1.3e-66	125	264	1	139
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpa.akgsneGkvrkal 94 s+yk+kaal+v++++p+f+al+sg++kl+++G+lll++a+a+++r+ydW++kq+f+ls+te+++lv+l+++esceffhdp kgs+eGkvrk+l Csa09g004980.1 125 SIYKGKAALTVEPRAPEFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRESCEFFHDPYkGKGSDEGKVRKVL 219 7*****************************************************************************945679***** PP Whirly 95 kvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139 kvePlpdGsG f+nlsv+n l++++e++++P+++aefavl+s+++ Csa09g004980.1 220 KVEPLPDGSGRFFNLSVQNRLLNVDENVYIPITRAEFAVLISAFN 264 ****************************************996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	1.2E-76	113	286	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	7.38E-79	117	303	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	7.4E-58	126	261	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: 304 aa Download sequence Send to blast
SLLKPFCCSS IVIQTNPSGE DEALRGKNKK TMSQLLSSPP MAAVLSKTNH KFTDARFLSS 60 HSILTSGGFA GKIGPLKKPA ARLKLTVKSR QDDYFEKKRF GDVSSSSSSP QNTEGSSPRF 120 FVGHSIYKGK AALTVEPRAP EFVALESGAF KLTKEGFLLL QFAPAAGVRQ YDWSRKQVFS 180 LSVTEIGNLV SLGPRESCEF FHDPYKGKGS DEGKVRKVLK VEPLPDGSGR FFNLSVQNRL 240 LNVDENVYIP ITRAEFAVLI SAFNFILPHL IGWNAFASSI KPEDSNRLNN ASPKYGGDYE 300 WSR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koq_A	1e-112	113	281	2	169	Single-stranded DNA-binding protein WHY3, 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 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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa09g004980.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By salicylic acid (SA). {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	BT015336	0.0	BT015336.1 Arabidopsis thaliana At2g02740 gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010425045.1	0.0	PREDICTED: single-stranded DNA-binding protein WHY3, chloroplastic-like
Swissprot	Q66GR6	1e-178	WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBL	R0H5N7	1e-177	R0H5N7_9BRAS; Uncharacterized protein
STRING	XP_010425045.1	0.0	(Camelina sativa)

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
AT2G02740.1	1e-180	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]