PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os03g62230.1
Common NameLOC9267218, Os03g0838800, OSJNBa0042I09.12
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family C2H2
Protein Properties Length: 386aa    MW: 41923.8 Da    PI: 6.6026
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g62230.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H221.46.8e-07165186223
                       EETTTTEEESSHHHHHHHHHHT CS
           zf-C2H2   2 kCpdCgksFsrksnLkrHirtH 23 
                        C+ Cgk F+r  nL+ H+r H
  LOC_Os03g62230.1 165 FCGVCGKGFKRDANLRMHMRGH 186
                       6*******************98 PP
2zf-C2H211.50.00092289303620
                       TTEEESSHHHHHHHH CS
           zf-C2H2   6 CgksFsrksnLkrHi 20 
                       Cg+sFsrk+ L  H 
  LOC_Os03g62230.1 289 CGTSFSRKDKLFAHV 303
                       **************7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.32E-5162189No hitNo description
PROSITE profilePS5015711.697164191IPR007087Zinc finger, C2H2
SMARTSM003550.011164186IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.2E-5166190IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280166186IPR007087Zinc finger, C2H2
SMARTSM0035539219252IPR015880Zinc finger, C2H2-like
SMARTSM0035531257279IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009089anatomyendosperm
PO:0007042developmental stagewhole plant fruit formation stage
PO:0007633developmental stageendosperm development stage
Sequence ? help Back to Top
Protein Sequence    Length: 386 aa     Download sequence    Send to blast
MMMSSSADHF SNNNNNQAMY LEQDEDFSQM IMELCDFDAS STTQARHGGE AAAAAAGNAR  60
AVLTYLTFLE QKIGHLRGII SSTPNPPPQI VAAELSCIVV QLVSISKNLA AARRGGDDAD  120
ADAKHDGSSD ADEGADGDGE RAPPRGSYEV VQIEKEEILA PHVHFCGVCG KGFKRDANLR  180
MHMRGHGEEY KSAAALAKPG GSPSRSPAAA DAAARRRFYS CPYVGCKRNR EHKSFQPLKT  240
PTCVKNHYRR SHCDKSFTCR RCNVKRFSVV ADLRTHEKHC GRDRWVCSCG TSFSRKDKLF  300
AHVAIFDGHS PALPPEDYDD DAASGQLPHA AGEAVGRTVD TNRFFSDGLM IKGSMEDERG  360
SLSPMGLDYC EFDGIDLFAA AAFDF*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.758210.0callus| flower| panicle| stem
Os.990990.0callus
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1567642200.0
Expression AtlasQ851N2-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots (e.g. root tips and lateral roots), leaves, flowers (e.g. stigma, sepal, anther, and filament), stems, siliques and cotyledons. {ECO:0000269|PubMed:23935008}.
Functional Description ? help Back to Top
Source Description
UniProtProbable 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g62230.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By shock H(+) and Al(3+) treatments. {ECO:0000269|PubMed:17535918}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g62230
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1044870.0AC104487.3 Oryza sativa chromosome 3 BAC OSJNBa0042I09 genomic sequence, complete sequence.
GenBankAK2876050.0AK287605.1 Oryza sativa Japonica Group cDNA, clone: J065055P16, full insert sequence.
GenBankAP0149590.0AP014959.1 Oryza sativa Japonica Group DNA, chromosome 3, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015630047.10.0zinc finger protein STOP1 homolog
SwissprotQ9C8N51e-100STOP1_ARATH; Protein SENSITIVE TO PROTON RHIZOTOXICITY 1
TrEMBLQ851N20.0Q851N2_ORYSJ; Os03g0838800 protein
STRINGOGLUM03G40140.10.0(Oryza glumipatula)
STRINGORGLA03G0371300.10.0(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP151238111
Representative plantOGRP8301663
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G34370.33e-94C2H2 family protein
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. Balzergue C, et al.
    Low phosphate activates STOP1-ALMT1 to rapidly inhibit root cell elongation.
    Nat Commun, 2017. 8: p. 15300
    [PMID:28504266]
  5. 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]
  6. Jiang F, et al.
    Identification and characterization of suppressor mutants of stop1.
    BMC Plant Biol., 2017. 17(1): p. 128
    [PMID:28738784]
  7. 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]
  8. 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]
  9. 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]