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_00737.1_g00005.1

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: 172aa MW: 18938.6 Da PI: 10.1059

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00737.1_g00005.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	129.1	2.4e-40	86	170	1	85
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgs 85 s+yk+kaal++++++p+f++l+sg++kl+++G+lll++a+a+++r+ydW++kq+f+ls+te+++lv+l+++esceffhdp ++++ Rsa1.0_00737.1_g00005.1 86 SIYKGKAALTIEPRAPEFVSLQSGAFKLSKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRESCEFFHDPNKGKG 170 7*******************************************************************************99876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	4.4E-43	75	169	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	5.49E-38	78	169	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	2.0E-36	87	170	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: 172 aa Download sequence Send to blast
MSQLLSSPPM AVNSRTFLTH RFPEARFLTA GGFVGKGHCF AVKVKPMEER VKLTLKSRYS 60 DSSSPPYSPP QNGEGGSSPR FYVGHSIYKG KAALTIEPRA PEFVSLQSGA FKLSKEGFLL 120 LQFAPAAGVR QYDWSRKQVF SLSVTEIGNL VSLGPRESCE FFHDPNKGKG YD

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koq_A	9e-61	77	170	5	98	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_00737.1_g00005.1

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_018483253.1	1e-121	PREDICTED: single-stranded DNA-binding protein WHY3, chloroplastic isoform X1
Swissprot	Q66GR6	8e-81	WHY3_ARATH; Single-stranded DNA-binding protein WHY3, chloroplastic
TrEMBL	A0A3P6EY56	6e-99	A0A3P6EY56_BRAOL; Uncharacterized protein
STRING	Bo7g080560.1	1e-98	(Brassica oleracea)

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	4e-80	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]