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

Pta003932

Organism

Pinus taeda

Taxonomic ID

3352

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pinus; Pinus

Family

Whirly

Protein Properties

Length: 259aa MW: 28678.8 Da PI: 9.0372

Description

Whirly family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
gnl\|UG\|Pta#S24904783	PU_unref	Unigene	View CDS
PUT-157a-Pinus_taeda-20875	PU_ref	plantGDB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Whirly	167.2	4.3e-52	79	216	2	139
Whirly 2 vyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrkalkvePlpd 101 +yk+kaal +++++p++++ldsg ++l+++G ++le+a+a+++r+ydW+kkq fals+ e+++l+++ +ke+ceffhdp+ ++s++Gk++k+lkv l d Pta003932 79 LYKGKAALGIQPKAPEYTTLDSGGIRLSKEGCVFLEFAPAVGTRQYDWSKKQIFALSVLELGTLLSFDPKEPCEFFHDPFLGKSEAGKIQKVLKVGMLQD 178 7************************************************************************************************* PP Whirly 102 GsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139 G+f+nl v+ ++ +es+ +P++k+ef+v++s+++ Pta003932 179 AGGYFFNLRVSDRTLNIDESLFMPITKGEFSVMQSAFN 216 *********************************996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51257	5	1	16	No hit	No description
Gene3D	G3DSA:2.30.31.10	3.1E-69	68	238	IPR009044	ssDNA-binding transcriptional regulator
SuperFamily	SSF54447	3.84E-62	72	256	IPR009044	ssDNA-binding transcriptional regulator
Pfam	PF08536	2.5E-51	79	214	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
MLRFHGLGTH FLGAACARPI QPLRTASISS RSFLKVVKAS FNDDSSQSHS FSSSPDHSAV 60 TQPGFLRGQP SKIYVKYTLY KGKAALGIQP KAPEYTTLDS GGIRLSKEGC VFLEFAPAVG 120 TRQYDWSKKQ IFALSVLELG TLLSFDPKEP CEFFHDPFLG KSEAGKIQKV LKVGMLQDAG 180 GYFFNLRVSD RTLNIDESLF MPITKGEFSV MQSAFNFILP YLMGWHAYMN SEKPNESGHL 240 TSASPSIGKK AELEWDVPF

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1l3a_A	8e-76	72	257	37	220	p24: plant transcriptional regulator PBF-2
1l3a_B	8e-76	72	257	37	220	p24: plant transcriptional regulator PBF-2
1l3a_C	8e-76	72	257	37	220	p24: plant transcriptional regulator PBF-2
1l3a_D	8e-76	72	257	37	220	p24: plant transcriptional regulator PBF-2
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pta.10579	0.0	root\| xylem

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}.

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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_172893.1	8e-81	ssDNA-binding transcriptional regulator
Refseq	XP_018447906.1	9e-81	PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic
Swissprot	Q9M9S3	7e-82	WHY1_ARATH; Single-stranded DNA-binding protein WHY1, chloroplastic
TrEMBL	A9NQE8	1e-119	A9NQE8_PICSI; Uncharacterized protein
STRING	AT1G14410.1	3e-80	(Arabidopsis thaliana)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14410.1	8e-84	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]