PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID GRMZM2G139073_P01
Common NameMADS11, si1, silky1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea
Family MIKC_MADS
Protein Properties Length: 227aa    MW: 25841.3 Da    PI: 9.213
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GRMZM2G139073_P01genomeMaizeSequenceView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF90.58.4e-29959151
                       S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
             SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                       krien +nrqvt+skRr+gi+KKA EL vLCda+va+i+fsstgk +e++s
  GRMZM2G139073_P01  9 KRIENATNRQVTYSKRRTGIMKKARELTVLCDAQVAIIMFSSTGKYHEFCS 59
                       79***********************************************96 PP

2K-box86.94.1e-2971168198
              K-box   1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenk 92 
                        yq++ g+sl+ +++e++q+ l+ Lk+ ++ L++e+R+++GedL+sL++ eL+ Leq+++ +lk++R +K++++ +q+++ +kk k  +e+ k
  GRMZM2G139073_P01  71 YQQAIGTSLWIEQYENMQRTLSHLKDINRGLRTEIRQRMGEDLDSLDFDELRGLEQNVDAALKEVRHRKYHVISTQTDTYKKKVKHSHEAYK 162
                        67888999************************************************************************************ PP

              K-box  93 aLrkkl 98 
                        +L+++l
  GRMZM2G139073_P01 163 NLQQEL 168
                        ***987 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004322.6E-42160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006632.59161IPR002100Transcription factor, MADS-box
SuperFamilySSF554552.22E-36295IPR002100Transcription factor, MADS-box
CDDcd002652.26E-43280No hitNo description
PRINTSPR004042.4E-28323IPR002100Transcription factor, MADS-box
PfamPF003193.0E-241057IPR002100Transcription factor, MADS-box
PRINTSPR004042.4E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004042.4E-283859IPR002100Transcription factor, MADS-box
PfamPF014864.1E-2282168IPR002487Transcription factor, K-box
PROSITE profilePS5129715.39284174IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010093Biological Processspecification of floral organ identity
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:0000037anatomyshoot apex
PO:0006340anatomyadult vascular leaf
PO:0006505anatomycentral spike of ear inflorescence
PO:0009025anatomyvascular leaf
PO:0020040anatomyleaf base
PO:0020104anatomyleaf sheath
PO:0020126anatomytassel inflorescence
PO:0020142anatomystem internode
PO:0001007developmental stagepollen development stage
PO:0001052developmental stagevascular leaf expansion stage
PO:0001083developmental stageinflorescence development stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
PO:0007063developmental stageLP.07 seven leaves visible stage
PO:0007072developmental stageLP.18 eighteen leaves visible stage
PO:0007101developmental stageLP.09 nine leaves visible stage
PO:0007104developmental stageLP.15 fifteen leaves visible stage
PO:0007116developmental stageLP.11 eleven leaves visible stage
PO:0021004developmental stageinflorescence initiation stage
Sequence ? help Back to Top
Protein Sequence    Length: 227 aa     Download sequence    Send to blast
MGRGKIEIKR IENATNRQVT YSKRRTGIMK KARELTVLCD AQVAIIMFSS TGKYHEFCSP  60
GTDIKTIFDR YQQAIGTSLW IEQYENMQRT LSHLKDINRG LRTEIRQRMG EDLDSLDFDE  120
LRGLEQNVDA ALKEVRHRKY HVISTQTDTY KKKVKHSHEA YKNLQQELGM REDPAFGYVD  180
NTGAGVAWDG AAAALGGAPP DMYAFRVVPS QPNLHGMAYG FHDLRLG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-17173171MEF2C
5f28_B2e-17173171MEF2C
5f28_C2e-17173171MEF2C
5f28_D2e-17173171MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Zm.4870.0cell culture| endosperm| pollen| tassel
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasGRMZM2G139073
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in lodicules, stamens and carpels. {ECO:0000269|PubMed:10394955, ECO:0000269|PubMed:12506001, ECO:0000269|PubMed:12905025, ECO:0000269|PubMed:14558657}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the development of floral organs. Required for normal development of lodicules and stamens (whorls 2 and 3). May function as a heterodimer with MADS4. {ECO:0000269|PubMed:12506001, ECO:0000269|PubMed:12905025, ECO:0000269|PubMed:14558657}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00077ChIP-seqTransfer from AT3G54340Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapGRMZM2G139073_P01
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0399880.0BT039988.1 Zea mays full-length cDNA clone ZM_BFc0056L03 mRNA, complete cds.
GenBankEU9662370.0EU966237.1 Zea mays clone 292756 MADS-box transcription factor 16 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001104951.11e-172silky 1
SwissprotQ944S91e-139MAD16_ORYSJ; MADS-box transcription factor 16
TrEMBLQ9M6N91e-171Q9M6N9_MAIZE; MADS transcription factor
STRINGGRMZM2G139073_P011e-172(Zea mays)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP57283552
Representative plantOGRP51991121
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G54340.19e-65MIKC_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. Chen ZX, et al.
    Morphogenesis and molecular basis on naked seed rice, a novel homeotic mutation of OsMADS1 regulating transcript level of AP3 homologue in rice.
    Planta, 2006. 223(5): p. 882-90
    [PMID:16254725]
  3. Zhang Q, et al.
    Morphological, anatomical and genetic analysis for a rice mutant with abnormal hull.
    J Genet Genomics, 2007. 34(6): p. 519-26
    [PMID:17601611]
  4. Yoshida H, et al.
    superwoman1-cleistogamy, a hopeful allele for gene containment in GM rice.
    Plant Biotechnol. J., 2007. 5(6): p. 835-46
    [PMID:17764519]
  5. Yao SG,Ohmori S,Kimizu M,Yoshida H
    Unequal genetic redundancy of rice PISTILLATA orthologs, OsMADS2 and OsMADS4, in lodicule and stamen development.
    Plant Cell Physiol., 2008. 49(5): p. 853-7
    [PMID:18378529]
  6. Alexandrov NN, et al.
    Insights into corn genes derived from large-scale cDNA sequencing.
    Plant Mol. Biol., 2009. 69(1-2): p. 179-94
    [PMID:18937034]
  7. Xiao H, et al.
    STAMENLESS 1, encoding a single C2H2 zinc finger protein, regulates floral organ identity in rice.
    Plant J., 2009. 59(5): p. 789-801
    [PMID:19453444]
  8. Seok HY, et al.
    Rice ternary MADS protein complexes containing class B MADS heterodimer.
    Biochem. Biophys. Res. Commun., 2010. 401(4): p. 598-604
    [PMID:20888318]
  9. Li H, et al.
    Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate.
    Plant Cell, 2011. 23(7): p. 2536-52
    [PMID:21784949]
  10. Sato H,Yoshida K,Mitsuda N,Ohme-Takagi M,Takamizo T
    Male-sterile and cleistogamous phenotypes in tall fescue induced by chimeric repressors of SUPERWOMAN1 and OsMADS58.
    Plant Sci., 2012. 183: p. 183-9
    [PMID:22195592]
  11. Ohmori S,Tabuchi H,Yatou O,Yoshida H
    Agronomic traits and gene containment capability of cleistogamous rice lines with the superwoman1-cleistogamy mutation.
    Breed. Sci., 2012. 62(2): p. 124-32
    [PMID:23136523]
  12. Yun D, et al.
    OsMADS16 genetically interacts with OsMADS3 and OsMADS58 in specifying floral patterning in rice.
    Mol Plant, 2013. 6(3): p. 743-56
    [PMID:23300256]
  13. Lombardo F, et al.
    The superwoman1-cleistogamy2 mutant is a novel resource for gene containment in rice.
    Plant Biotechnol. J., 2017. 15(1): p. 97-106
    [PMID:27336225]