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

Carubv10008876m

Common Name

CARUB_v10008876mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 515aa MW: 56887.3 Da PI: 4.9091

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10008876m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	21	8.6e-07	259	280	2	23
EETTTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCpdCgksFsrksnLkrHirtH 23 C++Cgk F+r nL+ H+r H Carubv10008876m 259 FCTICGKGFKRDANLRMHMRGH 280 6*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	2.14E-5	256	284	No hit	No description
PROSITE profile	PS50157	12.03	258	285	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0026	258	280	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	7.9E-6	259	311	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	260	280	IPR007087	Zinc finger, C2H2
SMART	SM00355	68	309	342	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	45	347	369	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: 515 aa Download sequence Send to blast
METEDDLCQQ TNWGSSSSKL QEQGSSDGGG NQAFSGFTSE QKWEEASILD YEMDGVEPDL 60 QVFDEMKASG EENVQANVDF LQGVRAQAWD PSTMLSNLSF MEQKIHELQE LVHLLVGRGE 120 QVQGCQDELA AQQQQQLITT DLTSIIIQLI STAGSLLPSV KHNMSTAPGP YTGQPGSAMF 180 PCAREANNVA SQSQNNNNCG AQEFDLPKAV VVDERESHVV EEHEMKDEDD AEEGENLPPG 240 SYEILQLEKE EILAPHTHFC TICGKGFKRD ANLRMHMRGH GDEYKTAAAL AKPNKESIPG 300 SEPMLIKRYS CPFLGCKRNK EHRKFQPLKT ILCVKNHYKR THCDKSFTCS RCHTKKFSVI 360 ADLKTHEKHC GKNKWLCSCG TTFSRKDKLF GHIALFQGHT PAIPIEETKP SASSSTQREN 420 SEGGNNNQGM VGFNLGSPSN ANQETAQFGM MDGNISFEDS FSPMNFETCS FGGFHDFPRL 480 MFDDSDSSFQ TLIANTCGFS SPRNVGESVL DTSI*

Sequence ? help Back to Top

Protein Sequence Length: 515 aa Download sequence Send to blast

METEDDLCQQ TNWGSSSSKL QEQGSSDGGG NQAFSGFTSE QKWEEASILD YEMDGVEPDL  60
QVFDEMKASG EENVQANVDF LQGVRAQAWD PSTMLSNLSF MEQKIHELQE LVHLLVGRGE  120
QVQGCQDELA AQQQQQLITT DLTSIIIQLI STAGSLLPSV KHNMSTAPGP YTGQPGSAMF  180
PCAREANNVA SQSQNNNNCG AQEFDLPKAV VVDERESHVV EEHEMKDEDD AEEGENLPPG  240
SYEILQLEKE EILAPHTHFC TICGKGFKRD ANLRMHMRGH GDEYKTAAAL AKPNKESIPG  300
SEPMLIKRYS CPFLGCKRNK EHRKFQPLKT ILCVKNHYKR THCDKSFTCS RCHTKKFSVI  360
ADLKTHEKHC GKNKWLCSCG TTFSRKDKLF GHIALFQGHT PAIPIEETKP SASSSTQREN  420
SEGGNNNQGM VGFNLGSPSN ANQETAQFGM MDGNISFEDS FSPMNFETCS FGGFHDFPRL  480
MFDDSDSSFQ TLIANTCGFS SPRNVGESVL DTSI*

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10008876m

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	AB300237	0.0	AB300237.1 Arabidopsis thaliana STOP1 gene for C2-H2 zinc finger protein, complete cds, ecotype: Est-1.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006307261.1	0.0	protein SENSITIVE TO PROTON RHIZOTOXICITY 1
Refseq	XP_023644963.1	0.0	protein SENSITIVE TO PROTON RHIZOTOXICITY 1
Swissprot	Q9C8N5	0.0	STOP1_ARATH; Protein SENSITIVE TO PROTON RHIZOTOXICITY 1
TrEMBL	R0ICF5	0.0	R0ICF5_9BRAS; Uncharacterized protein
STRING	Cagra.12398s0002.1.p	0.0	(Capsella grandiflora)
STRING	XP_006307261.1	0.0	(Capsella rubella)

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

Link Out ? help Back to Top
Phytozome	Carubv10008876m
Entrez Gene	17898824

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]