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

RrC25265_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 430aa MW: 47712.7 Da PI: 6.7209

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC25265_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	21.4	6.7e-07	180	200	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++Cgk F+r nL+ H+r H RrC25265_p1 180 CTICGKGFKRDANLRMHMRGH 200 *******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50157	11.468	178	205	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.024	178	200	IPR015880	Zinc finger, C2H2-like
SuperFamily	SSF57667	5.45E-5	179	202	No hit	No description
Gene3D	G3DSA:3.30.160.60	9.3E-6	180	231	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	180	200	IPR007087	Zinc finger, C2H2
SMART	SM00355	50	229	262	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	45	267	289	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010044	Biological Process	response to aluminum ion
GO:0010447	Biological Process	response to acidic pH
GO:0005634	Cellular Component	nucleus
GO:0003676	Molecular Function	nucleic acid binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 430 aa Download sequence Send to blast
EEEEEEEAPN FQDFKASSGQ AFLQGVKAQA WEPRTILSNL SFMEHKIHEL QHLVHLIILG 60 RNGQQLQEEQ QQLITADLTS IIIQLISTAG SLLPSVNHNN NMSSTTALGS ALFPYPREAN 120 NLASQTKELD LPKPIVEESH IHEMKNEDDA EEGGEDLPPG SYEIKQLEKE EILAAHTNFC 180 TICGKGFKRD ANLRMHMRGH GDEYKTPAAL AKPNKEALPG SEPLLIKRYS CPFPGCKRNK 240 DHKKFQPLKT ILCVKNHYKR THCDKSFTCS RCHTKKFSVI ADLKTHEKHC GKNKWLCSCG 300 TTFSRKDKLF GHIALFQGHT PAIPLEETKP SAQRGSSDCG NSNTGMIGFN LGSATNVNQE 360 TSQPGFMDGK IRFEDSFSPL SFDTCNFGGF HEFPRPIFDD SESSFQMLIS SACGLSPRNG 420 DGGSASNTSL

Sequence ? help Back to Top

Protein Sequence Length: 430 aa Download sequence Send to blast

EEEEEEEAPN FQDFKASSGQ AFLQGVKAQA WEPRTILSNL SFMEHKIHEL QHLVHLIILG  60
RNGQQLQEEQ QQLITADLTS IIIQLISTAG SLLPSVNHNN NMSSTTALGS ALFPYPREAN  120
NLASQTKELD LPKPIVEESH IHEMKNEDDA EEGGEDLPPG SYEIKQLEKE EILAAHTNFC  180
TICGKGFKRD ANLRMHMRGH GDEYKTPAAL AKPNKEALPG SEPLLIKRYS CPFPGCKRNK  240
DHKKFQPLKT ILCVKNHYKR THCDKSFTCS RCHTKKFSVI ADLKTHEKHC GKNKWLCSCG  300
TTFSRKDKLF GHIALFQGHT PAIPLEETKP SAQRGSSDCG NSNTGMIGFN LGSATNVNQE  360
TSQPGFMDGK IRFEDSFSPL SFDTCNFGGF HEFPRPIFDD SESSFQMLIS SACGLSPRNG  420
DGGSASNTSL

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor. Together with STOP2, plays a critical role in tolerance to major stress factors in acid soils such as proton H(+) and aluminum ion Al(3+). Required for the expression of genes in response to acidic stress (e.g. ALMT1 and MATE), and Al-activated citrate exudation. {ECO:0000269\|PubMed:17535918, ECO:0000269\|PubMed:18826429, ECO:0000269\|PubMed:19321711, ECO:0000269\|PubMed:23935008}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00196	ampDAP	Transfer from AT1G34370	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By shock H(+) and Al(3+) treatments. {ECO:0000269\|PubMed:17535918}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC232513	0.0	AC232513.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB065E07, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018451688.1	0.0	PREDICTED: protein SENSITIVE TO PROTON RHIZOTOXICITY 1-like
Swissprot	Q9C8N5	0.0	STOP1_ARATH; Protein SENSITIVE TO PROTON RHIZOTOXICITY 1
TrEMBL	V4K6X3	0.0	V4K6X3_EUTSA; Uncharacterized protein
STRING	XP_006396064.1	0.0	(Eutrema salsugineum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6977	26	44

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G34370.2	0.0	C2H2 family protein

Publications ? help Back to Top
Kobayashi Y, et al. Molecular and physiological analysis of Al³⁺ and H⁺ rhizotoxicities at moderately acidic conditions. Plant Physiol., 2013. 163(1): p. 180-92 [PMID:23839867] Yokosho K,Yamaji N,Ma JF Global transcriptome analysis of Al-induced genes in an Al-accumulating species, common buckwheat (Fagopyrum esculentum Moench). Plant Cell Physiol., 2014. 55(12): p. 2077-91 [PMID:25273892] Geng X, et al. LEUNIG_HOMOLOG transcriptional co-repressor mediates aluminium sensitivity through PECTIN METHYLESTERASE46-modulated root cell wall pectin methylesterification in Arabidopsis. Plant J., 2017. 90(3): p. 491-504 [PMID:28181322] Balzergue C, et al. Low phosphate activates STOP1-ALMT1 to rapidly inhibit root cell elongation. Nat Commun, 2017. 8: p. 15300 [PMID:28504266] Pelagio-Flores R,Esparza-Reynoso S,Garnica-Vergara A,López-Bucio J,Herrera-Estrella A Trichoderma-Induced Acidification Is an Early Trigger for Changes in Arabidopsis Root Growth and Determines Fungal Phytostimulation. Front Plant Sci, 2017. 8: p. 822 [PMID:28567051] Jiang F, et al. Identification and characterization of suppressor mutants of stop1. BMC Plant Biol., 2017. 17(1): p. 128 [PMID:28738784] Daspute AA, et al. Transcriptional Regulation of Aluminum-Tolerance Genes in Higher Plants: Clarifying the Underlying Molecular Mechanisms. Front Plant Sci, 2017. 8: p. 1358 [PMID:28848571] Sharma A,Wai CM,Ming R,Yu Q Diurnal Cycling Transcription Factors of Pineapple Revealed by Genome-Wide Annotation and Global Transcriptomic Analysis. Genome Biol Evol, 2017. 9(9): p. 2170-2190 [PMID:28922793] Zhang Y, et al. The Cell Cycle Checkpoint Regulator ATR Is Required for Internal Aluminum Toxicity-Mediated Root Growth Inhibition in Arabidopsis. Front Plant Sci, 2018. 9: p. 118 [PMID:29491872]