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

Rsa1.0_20288.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

Whirly

Protein Properties

Length: 75aa MW: 8341.62 Da PI: 8.2154

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_20288.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	69.3	7e-22	22	74	59	110
Whirly 59 atevaelvdlaskesceffhdpa.akgsneGkvrkalkvePlpdGsGlfvnls 110 +te+ +lv+l+++esce fhdp kgs+eGkvrk+lkvePl++GsG f+nls Rsa1.0_20288.1_g00001.1 22 VTEICNLVSLGPRESCEVFHDPDkGKGSDEGKVRKVLKVEPLSNGSGRFFNLS 74 7*******************945679*********************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF08536	7.3E-16	22	74	IPR013742	Plant transcription factor
SuperFamily	SSF54447	1.33E-12	22	74	IPR009044	ssDNA-binding transcriptional regulator
Gene3D	G3DSA:2.30.31.10	2.2E-15	22	74	IPR009044	ssDNA-binding transcriptional regulator

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: 75 aa Download sequence Send to blast
MLKRPVCSCS WCSSVRLEQE IVTEICNLVS LGPRESCEVF HDPDKGKGSD EGKVRKVLKV 60 EPLSNGSGRF FNLSK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koq_A	3e-25	22	74	72	123	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	Rsa1.0_20288.1_g00001.1

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010425045.1	4e-26	PREDICTED: single-stranded DNA-binding protein WHY3, chloroplastic-like
Refseq	XP_010502280.1	3e-26	PREDICTED: single-stranded DNA-binding protein WHY3, chloroplastic
Refseq	XP_020879965.1	4e-26	single-stranded DNA-binding protein WHY3, chloroplastic isoform X3
Swissprot	Q66GR6	1e-26	WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBL	V4L025	1e-24	V4L025_EUTSA; Uncharacterized protein
STRING	Bostr.0556s0088.1.p	1e-25	(Boechera stricta)
STRING	XP_010425045.1	1e-25	(Camelina sativa)
STRING	XP_010502280.1	1e-25	(Camelina sativa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02740.1	5e-29	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]