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_Os02g07430.1
Common NameLOC4328443, MADS29, OJ1116_A06.26, Os02g0170300, OsJ_05554, P0030G02.16
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: 261aa    MW: 28993.9 Da    PI: 6.8509
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g07430.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF86.71.3e-27959151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      krien +nrqvtfskRr g+lKKA+EL vLCda+v v+ifsstgk++ey+s
  LOC_Os02g07430.1  9 KRIENATNRQVTFSKRRGGLLKKANELAVLCDARVGVVIFSSTGKMFEYCS 59
                      79***********************************************96 PP
2K-box71.91.9e-24721712100
             K-box   2 qkssgks.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenka 93 
                       q+ ++++  e ++ ++   e++++++e+e+L   +R++ G+dL++L+l +++ LeqqLe s++k+R++K++ll +q+++l++ke+ l+++n  
  LOC_Os02g07430.1  72 QTVTNTHfEEINHDQQIFVEMTRMRNEMEKLDGGIRRFTGDDLSNLTLADINDLEQQLEFSVTKVRARKHQLLNQQLDNLRRKEHILEDQNSF 164
                       5556666666778899999************************************************************************** PP

             K-box  94 Lrkklee 100
                       L ++++e
  LOC_Os02g07430.1 165 LCRMINE 171
                       *998875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004321.3E-41160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006632.198161IPR002100Transcription factor, MADS-box
CDDcd002659.01E-43278No hitNo description
SuperFamilySSF554552.22E-32288IPR002100Transcription factor, MADS-box
PRINTSPR004043.8E-29323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.6E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004043.8E-292338IPR002100Transcription factor, MADS-box
PRINTSPR004043.8E-293859IPR002100Transcription factor, MADS-box
PfamPF014868.8E-2481169IPR002487Transcription factor, K-box
PROSITE profilePS5129713.42285175IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008360Biological Processregulation of cell shape
GO:0019252Biological Processstarch biosynthetic process
GO:0043068Biological Processpositive regulation of programmed cell death
GO:0048316Biological Processseed development
GO:0048481Biological Processplant ovule development
GO:0080155Biological Processregulation of double fertilization forming a zygote and endosperm
GO:2000029Biological Processregulation of proanthocyanidin biosynthetic process
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
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: 261 aa     Download sequence    Send to blast
MGRGKIEIKR IENATNRQVT FSKRRGGLLK KANELAVLCD ARVGVVIFSS TGKMFEYCSP  60
TCSLRELIEH YQTVTNTHFE EINHDQQIFV EMTRMRNEME KLDGGIRRFT GDDLSNLTLA  120
DINDLEQQLE FSVTKVRARK HQLLNQQLDN LRRKEHILED QNSFLCRMIN ENHHQAAVGG  180
GDVKAMVEMA PVLSMLTAAP AYYGEESSST ALQLTPPLHA VDAAAAAGFR LQPTQPNLQD  240
PGCSSSSFHA AAAGHGLQLW *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A3e-18185183MEF2C
5f28_B3e-18185183MEF2C
5f28_C3e-18185183MEF2C
5f28_D3e-18185183MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.561650.0flower| panicle
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2620937460.0
Expression AtlasQ6H711-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in developing seeds. {ECO:0000269|PubMed:14701936}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os02g07430.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs02g07430
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1095220.0AK109522.1 Oryza sativa Japonica Group cDNA clone:002-115-F04, full insert sequence.
GenBankFJ7509330.0FJ750933.1 Oryza sativa clone KCS006F06 MADS-box transcription factor 29 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015624837.10.0MADS-box transcription factor 29 isoform X1
RefseqXP_025879036.10.0MADS-box transcription factor 29 isoform X1
SwissprotQ6H7110.0MAD29_ORYSJ; MADS-box transcription factor 29
TrEMBLA2X1E20.0A2X1E2_ORYSI; Uncharacterized protein
TrEMBLD3U2G50.0D3U2G5_ORYSA; MADS-box transcription factor 29
TrEMBLI1NXP10.0I1NXP1_ORYGL; Uncharacterized protein
STRINGOS02T0170300-010.0(Oryza sativa)
STRINGORGLA02G0049700.10.0(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP185037100
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G23260.28e-45MIKC_MADS family protein
Publications ? help Back to Top
  1. 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]
  2. Lee S, et al.
    Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case.
    Plant Cell Physiol., 2003. 44(12): p. 1403-11
    [PMID:14701936]
  3. Li M,Sun P,Zhou H,Chen S,Yu S
    Identification of quantitative trait loci associated with germination using chromosome segment substitution lines of rice (Oryza sativa L.).
    Theor. Appl. Genet., 2011. 123(3): p. 411-20
    [PMID:21512773]
  4. Yin LL,Xue HW
    The MADS29 transcription factor regulates the degradation of the nucellus and the nucellar projection during rice seed development.
    Plant Cell, 2012. 24(3): p. 1049-65
    [PMID:22408076]
  5. Yang X, et al.
    Live and let die - the B(sister) MADS-box gene OsMADS29 controls the degeneration of cells in maternal tissues during seed development of rice (Oryza sativa).
    PLoS ONE, 2012. 7(12): p. e51435
    [PMID:23251532]
  6. Nayar S,Sharma R,Tyagi AK,Kapoor S
    Functional delineation of rice MADS29 reveals its role in embryo and endosperm development by affecting hormone homeostasis.
    J. Exp. Bot., 2013. 64(14): p. 4239-53
    [PMID:23929654]
  7. Nayar S,Kapoor M,Kapoor S
    Post-translational regulation of rice MADS29 function: homodimerization or binary interactions with other seed-expressed MADS proteins modulate its translocation into the nucleus.
    J. Exp. Bot., 2014. 65(18): p. 5339-50
    [PMID:25096923]
  8. Schilling S, et al.
    Non-canonical structure, function and phylogeny of the Bsister MADS-box gene OsMADS30 of rice (Oryza sativa).
    Plant J., 2015. 84(6): p. 1059-72
    [PMID:26473514]