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_Os04g33950.1
Common NameOs04g0416100, OSNPB_040416100
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 E2F/DP
Protein Properties Length: 320aa    MW: 35238 Da    PI: 9.064
Description E2F/DP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g33950.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1E2F_TDP83.32e-26139204171
           E2F_TDP   1 rkeksLrlltqkflkllekseegivtlnevakeLvsedvknkrRRiYDilNVLealnliekkekneirwkg 71 
                       r+++sL+llt+kf++ll+++++gi++ln++ak L   dv  ++RRiYDi+NVLe+ +liekk kn+irw+g
  LOC_Os04g33950.1 139 RYDNSLGLLTRKFINLLKQTQDGILDLNDAAKIL---DV--RKRRIYDITNVLEGTGLIEKKLKNRIRWRG 204
                       689*******************************...**..9***************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.104.7E-27136205IPR011991Winged helix-turn-helix DNA-binding domain
SMARTSM013721.3E-32139204IPR003316E2F/DP family, winged-helix DNA-binding domain
SuperFamilySSF467852.72E-17139202IPR011991Winged helix-turn-helix DNA-binding domain
PfamPF023194.3E-23141204IPR003316E2F/DP family, winged-helix DNA-binding domain
CDDcd146601.32E-41214318No hitNo description
SuperFamilySSF1440741.05E-30215318No hitNo description
PfamPF164212.4E-28219318IPR032198E2F transcription factor, CC-MB domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005667Cellular Componenttranscription factor complex
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009072anatomyplant ovary
PO:0007042developmental stagewhole plant fruit formation stage
Sequence ? help Back to Top
Protein Sequence    Length: 320 aa     Download sequence    Send to blast
MSSGGGRPPA AQHIVRSVRQ RFVPLPPPLA RAPFAAAPGD YHRFAAASRG GEIEEGIVIR  60
RTPLKRKTPC GESEAAESSE RMMTSPGFTE GVGSPLMTPV SGKTSRTTKS MAKFNKAGPQ  120
TPISNAGSPG NPSTPASSRY DNSLGLLTRK FINLLKQTQD GILDLNDAAK ILDVRKRRIY  180
DITNVLEGTG LIEKKLKNRI RWRGSDDSGT NLDSDISCLK TEVENLYIQE QALDRSISEI  240
REKMEELTED ESNHRWLFVT EDDIKGLPCF QNEALIAIKG PRGTTVEVPD PDEAGDYLQR  300
RYRILLRSTM GPIDIYLVR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1cf7_A3e-23132204273PROTEIN (TRANSCRIPTION FACTOR E2F-4)
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1174196RKRRIYDITNVLEGTGLIEKKLK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.525090.0callus| flower| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329775990.0
Expression AtlasQ0JDB0-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in a cell cycle-dependent manner. Most abundant at the G1/S transition. Lower but constant level in the following phases. {ECO:0000269|PubMed:11669580, ECO:0000269|PubMed:11786543, ECO:0000269|PubMed:16514015}.
UniprotTISSUE SPECIFICITY: Expressed in proliferating cells and several differentiated tissues. Detected in inflorescence and shoot apical meristems, cotyledonary vascular tissues, leaf primordia, young leaves, base of trichomes, central cylinder and elongation zone of roots, lateral root primordia, flowers, pistils of immature flowers and pollen grains. {ECO:0000269|PubMed:16514015}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The binding of retinoblastoma-related proteins represses transactivation. Involved in the control of cell-cycle progression from G1 to S phase and from G2 to M phase. Stimulates cell proliferation and delays differentiation. Represses cell enlargement and endoreduplication in auxin-free conditions. {ECO:0000269|PubMed:11669580, ECO:0000269|PubMed:11786543, ECO:0000269|PubMed:11862494, ECO:0000269|PubMed:11891240, ECO:0000269|PubMed:12913157, ECO:0000269|PubMed:16055635, ECO:0000269|PubMed:16514015}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g33950.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by light and by auxin. May be up-regulated by E2FA. {ECO:0000269|PubMed:16055635, ECO:0000269|PubMed:16514015, ECO:0000269|PubMed:18424613}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g33950
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0675810.0AK067581.1 Oryza sativa Japonica Group cDNA clone:J013113N12, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015637107.10.0transcription factor E2FA isoform X2
SwissprotQ9FV718e-96E2FB_ARATH; Transcription factor E2FB
TrEMBLQ0JDB00.0Q0JDB0_ORYSJ; Os04g0416100 protein
STRINGOS04T0416100-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP62537148
Representative plantOGRP12251749
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G36010.12e-98E2F transcription factor 3
Publications ? help Back to Top
  1. Heyndrickx KS,Vandepoele K
    Systematic identification of functional plant modules through the integration of complementary data sources.
    Plant Physiol., 2012. 159(3): p. 884-901
    [PMID:22589469]
  2. Wu M,Liu L,Hijazi H,Chan C
    A multi-layer inference approach to reconstruct condition-specific genes and their regulation.
    Bioinformatics, 2013. 29(12): p. 1541-52
    [PMID:23610368]
  3. Kobayashi K, et al.
    Transcriptional repression by MYB3R proteins regulates plant organ growth.
    EMBO J., 2015. 34(15): p. 1992-2007
    [PMID:26069325]