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_Os02g01355.1
Common NameLOC107276190, OsJ_05013
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: 272aa    MW: 30235.2 Da    PI: 7.8913
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g01355.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF87.38.3e-285099251
                      ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      rie+ + rqvtfskRr g+lKKA+ELSvLCdaeva+i+fs++g+ly ++s
  LOC_Os02g01355.1 50 RIEDATSRQVTFSKRRSGLLKKAFELSVLCDAEVALIVFSPRGRLYQFAS 99
                      8***********************************************86 PP
2K-box74.14e-25123214899
             K-box   8 sleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
                       + ee+  ++++ e++ L k+ie ++  + +llGe+L+s+s++eLq+Le qLeksl +iR+kK+++l++qi el++ke +l +en+ Lr + +
  LOC_Os02g01355.1 123 EGEESCVQKWRSEATTLGKKIEAIEGYKSKLLGEGLGSCSVQELQELEVQLEKSLCSIRQKKQKMLMDQILELREKEMNLLKENMVLRDQCK 214
                       3678889*********************************************************************************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd002653.93E-3432118No hitNo description
PROSITE profilePS5006629.71641101IPR002100Transcription factor, MADS-box
SMARTSM004321.8E-3541100IPR002100Transcription factor, MADS-box
PROSITE patternPS0035004397IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.96E-2943120IPR002100Transcription factor, MADS-box
PRINTSPR004043.5E-284363IPR002100Transcription factor, MADS-box
PfamPF003194.3E-265097IPR002100Transcription factor, MADS-box
PRINTSPR004043.5E-286378IPR002100Transcription factor, MADS-box
PRINTSPR004043.5E-287899IPR002100Transcription factor, MADS-box
PfamPF014865.9E-25126213IPR002487Transcription factor, K-box
PROSITE profilePS5129713.808129219IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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: 272 aa     Download sequence    Send to blast
MAAAAAGMGG GGGVQHQETT TTVVQVAAEA SRKKVEVRSA GRRGRREMRR IEDATSRQVT  60
FSKRRSGLLK KAFELSVLCD AEVALIVFSP RGRLYQFASA SSDLQRTIDR YLNHTKNSSA  120
HEEGEESCVQ KWRSEATTLG KKIEAIEGYK SKLLGEGLGS CSVQELQELE VQLEKSLCSI  180
RQKKQKMLMD QILELREKEM NLLKENMVLR DQCKALSSPW STSVGELKNK QADDDVHRHE  240
DYSGGGVRDD DDRRMMEDVE TDLVIGRPGS I*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1n6j_A2e-1843122276Myocyte-specific enhancer factor 2B
1n6j_B2e-1843122276Myocyte-specific enhancer factor 2B
1tqe_P2e-1843122377Myocyte-specific enhancer factor 2B
1tqe_Q2e-1843122377Myocyte-specific enhancer factor 2B
1tqe_R2e-1843122377Myocyte-specific enhancer factor 2B
1tqe_S2e-1843122377Myocyte-specific enhancer factor 2B
6c9l_A2e-1843122377Myocyte-specific enhancer factor 2B
6c9l_B2e-1843122377Myocyte-specific enhancer factor 2B
6c9l_C2e-1843122377Myocyte-specific enhancer factor 2B
6c9l_D2e-1843122377Myocyte-specific enhancer factor 2B
6c9l_E2e-1843122377Myocyte-specific enhancer factor 2B
6c9l_F2e-1843122377Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.751391e-129root
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasB9F1P7
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Low expression in the young panicle continues to decline as the organ mature. {ECO:0000269|PubMed:15144377, ECO:0000269|PubMed:17166135}.
UniprotTISSUE SPECIFICITY: Expressed in mature leaves and at low levels in roots and young panicles. {ECO:0000269|PubMed:15144377, ECO:0000269|PubMed:17166135}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor active in flowering time control. May control internode elongation and promote floral transition phase. May act upstream of the floral regulators MADS1, MADS14, MADS15 and MADS18 in the floral induction pathway. {ECO:0000269|PubMed:15144377, ECO:0000269|PubMed:17166135}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os02g01355.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs02g01355
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0040491e-171AP004049.2 Oryza sativa Japonica Group genomic DNA, chromosome 2, BAC clone:OJ1212_C06.
GenBankAP0067201e-171AP006720.1 Oryza sativa Japonica Group genomic DNA, chromosome 2, clone:OJA1212_C06.
GenBankAP0149581e-171AP014958.1 Oryza sativa Japonica Group DNA, chromosome 2, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015625202.10.0MADS-box protein SOC1 isoform X1
SwissprotQ9XJ601e-68MAD50_ORYSJ; MADS-box transcription factor 50
TrEMBLB9F1P70.0B9F1P7_ORYSJ; Uncharacterized protein
STRINGORGLA02G0003200.10.0(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP14133379
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G45660.12e-50AGAMOUS-like 20
Publications ? help Back to Top
  1. Thomson MJ,Edwards JD,Septiningsih EM,Harrington SE,McCouch SR
    Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL.
    Genetics, 2006. 172(4): p. 2501-14
    [PMID:16452146]
  2. Park SJ, et al.
    Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod.
    Plant J., 2008. 56(6): p. 1018-29
    [PMID:18774969]
  3. Lee S,Jeong DH,An G
    A possible working mechanism for rice SVP-group MADS-box proteins as negative regulators of brassinosteroid responses.
    Plant Signal Behav, 2008. 3(7): p. 471-4
    [PMID:19704489]
  4. Maas LF,McClung A,McCouch S
    Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice.
    Theor. Appl. Genet., 2010. 120(5): p. 895-908
    [PMID:19949767]
  5. Sun C, et al.
    The histone methyltransferase SDG724 mediates H3K36me2/3 deposition at MADS50 and RFT1 and promotes flowering in rice.
    Plant Cell, 2012. 24(8): p. 3235-47
    [PMID:22892321]
  6. Choi SC, et al.
    Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3.
    Plant Physiol., 2014. 164(3): p. 1326-37
    [PMID:24420930]
  7. Núñez-López L,Aguirre-Cruz A,Barrera-Figueroa BE,Peña-Castro JM
    Improvement of enzymatic saccharification yield in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor.
    PeerJ, 2015. 3: p. e817
    [PMID:25780769]
  8. Jin J, et al.
    MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice.
    Plant Physiol., 2015. 168(4): p. 1275-85
    [PMID:25855537]
  9. Liu X, et al.
    Brassinosteroid (BR) biosynthetic gene lhdd10 controls late heading and plant height in rice (Oryza sativa L.).
    Plant Cell Rep., 2016. 35(2): p. 357-68
    [PMID:26518431]
  10. Hwang YH, et al.
    Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time.
    Plant Cell Rep., 2016. 35(4): p. 857-65
    [PMID:26754793]
  11. 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]
  12. Alter P, et al.
    Flowering Time-Regulated Genes in Maize Include the Transcription Factor ZmMADS1.
    Plant Physiol., 2016. 172(1): p. 389-404
    [PMID:27457125]