PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os01g14010.1
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: 496aa    MW: 51394.2 Da    PI: 8.894
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os01g14010.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.74.7e-066183123
                      EEETTTTEEESSHHHHHHHHHHT CS
           zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                      ++C++Cgk F r  nL+ H r H
  LOC_Os01g14010.1 61 FVCEICGKGFQRDQNLQLHRRGH 83
                      89*******************88 PP
2zf-C2H212.80.00037137159123
                       EEETTTTEEESSHHHHHHHHHHT CS
           zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                       +kC +C+k++  +s+ k H +t+
  LOC_Os01g14010.1 137 WKCDKCSKRYAVQSDWKAHSKTC 159
                       58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.11E-76083No hitNo description
PROSITE profilePS5015711.6146183IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.4E-56183IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0126183IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806383IPR007087Zinc finger, C2H2
SMARTSM00355260102132IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.4E-4125158IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.11E-7132157No hitNo description
SMARTSM00355140137157IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 496 aa     Download sequence    Send to blast
MATSEAAAIS NPFAPLTNHQ QEHPPPPPPP AKKKRNLPGT PDPEAEVIAL SPRTLMATNR  60
FVCEICGKGF QRDQNLQLHR RGHNLPWKLR QRSGKEPRKR VYVCPEKSCV HHNPSRALGD  120
LTGIKKHFCR KHGEKKWKCD KCSKRYAVQS DWKAHSKTCG TREYRCDCGT LFSRRDSFIT  180
HRAFCDALAE ETARLNAASG AAAAAAAATA TSLCGQSYLF AGSGGPGMAG MRPNMMMPPA  240
AAAAGGQLRA GQMLGPAAGG VGGDLCDGGV ARHGGLSLWG GEALPSMGHI GVLASGGAAT  300
VPPQLYVDLF APSSGAPPPQ FDAAQLSWLY GNGKLSSSNA SELTSATAAA KEAESVPSVF  360
SNQQHAKPAA PTDMSATALL QKAAQIGAVT STAAMPLVSP FEPTKPGGAT ASPADECGKF  420
DGAALFAAAS HHNANLGGAM SELTGAAGNV PYDVLSAVRH HAGLKDAGGV GREETRDFLG  480
VGVQALCSSS IHGWI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-35133200370Zinc finger protein JACKDAW
5b3h_F1e-35133200370Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.550910.0flower| panicle
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329926770.0
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00125DAPTransfer from AT1G03840Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os01g14010.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs01g14010
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0032010.0AP003201.3 Oryza sativa Japonica Group genomic DNA, chromosome 1, BAC clone:B1066G12.
GenBankAP0149570.0AP014957.1 Oryza sativa Japonica Group DNA, chromosome 1, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015634949.10.0zinc finger protein NUTCRACKER
SwissprotQ9ZWA61e-134IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLB8ABF40.0B8ABF4_ORYSI; Uncharacterized protein
STRINGORGLA01G0080600.10.0(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP20238320
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.11e-115C2H2 family protein
Publications ? help Back to Top
  1. Muñoz-Strale D,León G
    Identification of two highly specific pollen promoters using transcriptomic data.
    Plant Physiol. Biochem., 2014. 83: p. 292-9
    [PMID:25208507]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]