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

Lj0g3v0163799.2

Organism

Lotus japonicus

Taxonomic ID

34305

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus

Family

Whirly

Protein Properties

Length: 259aa MW: 28371.6 Da PI: 9.7446

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj0g3v0163799.2	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	174.8	1.8e-54	76	216	1	139
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanata..erkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrk 92 s+yk+ka l++ ++ p+f+ ldsg++k++r+G +l+++a+a++ +r ydW++kq+f+ls+ e++ l++l++++scef dp++++s+eGk+rk Lj0g3v0163799.2 76 SLYKGKAVLTLSPKPPEFSMLDSGAVKVSREGYILFQFAPAVGggTRLYDWNRKQVFSLSVNEMGALISLGARGSCEFVRDPFKGKSDEGKIRK 169 68*************************************95338******************************************** PP Whirly 93 alkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139 +lkvePl dGsG+++nlsv+n+l +++es+ vPv+kae av++sl++ Lj0g3v0163799.2 170 VLKVEPLLDGSGHLFNLSVQNKLKNVDESIFVPVTKAELAVFNSLFN 216 ****************************************99986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.30.31.10	3.2E-67	68	234	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	1.26E-61	69	247	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	2.2E-51	77	213	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: 259 aa Download sequence Send to blast
MVHSIAIKPC PIPTHSFITT KSITFRGFSP SSSATPTTSL TLPSLSVKCR QTELFDSPQR 60 PPPPPDLPPR VYVDHSLYKG KAVLTLSPKP PEFSMLDSGA VKVSREGYIL FQFAPAVGGG 120 TRLYDWNRKQ VFSLSVNEMG ALISLGARGS CEFVRDPFKG KSDEGKIRKV LKVEPLLDGS 180 GHLFNLSVQN KLKNVDESIF VPVTKAELAV FNSLFNFILP YLLGWNAFGN SIKPGVYSRV 240 HNASQDTEQN MNGTVGDNL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4koo_A	3e-83	67	233	5	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_B	3e-83	67	233	5	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_C	3e-83	67	233	5	169	Single-stranded DNA-binding protein WHY1, chloroplastic
4koo_D	3e-83	67	233	5	169	Single-stranded DNA-binding protein WHY1, chloroplastic
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Lja.4254	0.0	pod\| root

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	Lj0g3v0163799.2

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_028792530.1	1e-102	single-stranded DNA-binding protein WHY1, chloroplastic-like
Swissprot	Q9M9S3	1e-92	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	A0A1S2XIW0	4e-96	A0A1S2XIW0_CICAR; single-stranded DNA-binding protein WHY1, chloroplastic-like isoform X1
STRING	XP_004490009.1	5e-96	(Cicer arietinum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF6416	32	51

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14410.1	2e-89	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]