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_Os10g39130.2
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 MIKC_MADS
Protein Properties Length: 152aa    MW: 17567.3 Da    PI: 10.3177
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os10g39130.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF94.93.6e-30959151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      krien + rqvtfskRrng+lKKA+ELSvLCdaeva+i+fs++g+lye++s
  LOC_Os10g39130.2  9 KRIENPTSRQVTFSKRRNGLLKKAFELSVLCDAEVALIVFSPRGRLYEFAS 59
                      79***********************************************86 PP
2K-box44.56.5e-1679143670
             K-box   6 gksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKn 70 
                       ++++ +++ ++ + +   L k++e L ++ R++lGe+Le  s++eL+ Le +Leksl kiR kK 
  LOC_Os10g39130.2  79 NNKTIQQDIQQVKDDTLGLAKKLEALDESRRKILGENLEGFSIEELRGLEMKLEKSLHKIRLKKV 143
                       445778889999***************************************************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004324.1E-39160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.314161IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-31323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
CDDcd002655.72E-40379No hitNo description
SuperFamilySSF554557.33E-32385IPR002100Transcription factor, MADS-box
PfamPF003192.1E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-313859IPR002100Transcription factor, MADS-box
PfamPF014866.5E-1484142IPR002487Transcription factor, K-box
PROSITE profilePS512979.36987151IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010048Biological Processvernalization response
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 152 aa     Download sequence    Send to blast
MVRGRTELKR IENPTSRQVT FSKRRNGLLK KAFELSVLCD AEVALIVFSP RGRLYEFASA  60
PSLQKTIDRY KAYTKDHVNN KTIQQDIQQV KDDTLGLAKK LEALDESRRK ILGENLEGFS  120
IEELRGLEMK LEKSLHKIRL KKVYISYFQY S*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A3e-18177176MEF2C
5f28_B3e-18177176MEF2C
5f28_C3e-18177176MEF2C
5f28_D3e-18177176MEF2C
6byy_A4e-18177176MEF2 CHIMERA
6byy_B4e-18177176MEF2 CHIMERA
6byy_C4e-18177176MEF2 CHIMERA
6byy_D4e-18177176MEF2 CHIMERA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.378130.0callus| flower| leaf| panicle| root| seed| stem
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os10g39130.2
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs10g39130
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankCT8418610.0CT841861.1 Oryza rufipogon (W1943) cDNA clone: ORW1943C105F20, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015614799.13e-99MADS-box transcription factor 56
SwissprotP0C5B21e-100MAD56_ORYSJ; MADS-box transcription factor 56
TrEMBLA0A0E0R1U61e-105A0A0E0R1U6_ORYRU; Uncharacterized protein
STRINGOS10T0536100-011e-98(Oryza sativa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G11880.12e-60AGAMOUS-like 14
Publications ? help Back to Top
  1. Rice Chromosome 10 Sequencing Consortium
    In-depth view of structure, activity, and evolution of rice chromosome 10.
    Science, 2003. 300(5625): p. 1566-9
    [PMID:12791992]
  2. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  3. Bai Z, et al.
    The impact and origin of copy number variations in the Oryza species.
    BMC Genomics, 2016. 17: p. 261
    [PMID:27025496]
  4. Shibaya T, et al.
    Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice.
    Plant Cell Physiol., 2016. 57(9): p. 1828-38
    [PMID:27318280]
  5. Han Z,Zhang B,Zhao H,Ayaad M,Xing Y
    Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice.
    Front Plant Sci, 2016. 7: p. 1270
    [PMID:27621738]