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 472923
Common NameARALYDRAFT_472923
Organism
Arabidopsis lyrata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family MIKC_MADS
Protein Properties Length: 248aa    MW: 28544.5 Da    PI: 8.2906
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
472923genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF99.81.1e-31959151
            S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
  SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
            krienk+nrqvtf+kRrng+lKKA+ELSvLCdaeva+iifs++gklye++s
  472923  9 KRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCS 59
            79***********************************************96 PP
2K-box93.63.2e-31931751698
   K-box  16 slqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
             s+qqe+ kLk++++ Lqr+qR+llGedL++Ls keL++Le+qL++slk+iR+ +++++l+q+++lq ke++l e+nk+Lr +l
  472923  93 SSQQEYLKLKDRYDALQRTQRNLLGEDLGPLSTKELESLERQLDSSLKQIRALRTQFMLDQLNDLQSKERMLTETNKTLRLRL 175
             68*****************************************************************************9876 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 profilePS5006633.515161IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.44E-33276IPR002100Transcription factor, MADS-box
CDDcd002652.98E-45276No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004049.0E-33323IPR002100Transcription factor, MADS-box
PfamPF003192.3E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004049.0E-332338IPR002100Transcription factor, MADS-box
PRINTSPR004049.0E-333859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129714.99391181IPR002487Transcription factor, K-box
PfamPF014866.5E-2694175IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0001708Biological Processcell fate specification
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010093Biological Processspecification of floral organ identity
GO:0048481Biological Processplant ovule development
GO:0048833Biological Processspecification of floral organ number
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: 248 aa     Download sequence    Send to blast
MGRGRVELKR IENKINRQVT FAKRRNGLLK KAYELSVLCD AEVALIIFSN RGKLYEFCSS  60
SSMLRTLERY QKCNYGAPEP NVPSREALAV ELSSQQEYLK LKDRYDALQR TQRNLLGEDL  120
GPLSTKELES LERQLDSSLK QIRALRTQFM LDQLNDLQSK ERMLTETNKT LRLRLADGYQ  180
MPLQLNPNQE EVDHYGRHHQ HSQAFFQPLE CEPILQIGYQ GQQDGMGAGP SLNNYMLGWL  240
PYDTNSI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_A4e-66751781104Developmental protein SEPALLATA 3
4ox0_B4e-66751781104Developmental protein SEPALLATA 3
4ox0_C4e-66751781104Developmental protein SEPALLATA 3
4ox0_D4e-66751781104Developmental protein SEPALLATA 3
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor active in inflorescence development and floral organogenesis. Functions with SEPALLATA1/AGL2 and SEPALLATA2/AGL4 to ensure proper development of petals, stamens and carpels and to prevent the indeterminate growth of the flower meristem. Interacts with APETALA1, AGAMOUS or APETALA3/PISTILLATA to form complexes, that could be involved in genes regulation during floral meristem development (PubMed:10821278, PubMed:11206550). Binds specifically to the CArG box DNA sequence 5'-CC (A/T)6 GG-3' (PubMed:16080001). {ECO:0000269|PubMed:10821278, ECO:0000269|PubMed:11206550, ECO:0000269|PubMed:16080001}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00605ChIP-seqTransfer from AT1G24260Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMap472923
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF0155520.0AF015552.1 Arabidopsis thaliana MADS-box (AGL9) mRNA, complete cds.
GenBankBT0331570.0BT033157.1 Arabidopsis thaliana unknown protein (At1g24260) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002890717.10.0developmental protein SEPALLATA 3 isoform X1
SwissprotO224561e-176SEP3_ARATH; Developmental protein SEPALLATA 3
TrEMBLD7KBN40.0D7KBN4_ARALL; Uncharacterized protein
STRINGfgenesh2_kg.1__2877__AT1G24260.10.0(Arabidopsis lyrata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM62202644
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G24260.21e-179MIKC_MADS family protein
Publications ? help Back to Top
  1. Maejima K, et al.
    Recognition of floral homeotic MADS domain transcription factors by a phytoplasmal effector, phyllogen, induces phyllody.
    Plant J., 2014. 78(4): p. 541-54
    [PMID:24597566]
  2. MacLean AM, et al.
    Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner.
    PLoS Biol., 2014. 12(4): p. e1001835
    [PMID:24714165]
  3. Iglesias FM, et al.
    The arabidopsis DNA polymerase δ has a role in the deposition of transcriptionally active epigenetic marks, development and flowering.
    PLoS Genet., 2015. 11(2): p. e1004975
    [PMID:25693187]
  4. He Q,Fu AY,Zhang GC,Li TJ,Zhang JH
    Arabidopsis thaliana SEPALLATA3 protein prokaryotic expression and purification.
    Cell. Mol. Biol. (Noisy-le-grand), 2015. 61(2): p. 60-3
    [PMID:26025404]
  5. Maejima K, et al.
    Degradation of class E MADS-domain transcription factors in Arabidopsis by a phytoplasmal effector, phyllogen.
    Plant Signal Behav, 2015. 10(8): p. e1042635
    [PMID:26179462]
  6. Muiño JM, et al.
    Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor.
    Mol. Biol. Evol., 2016. 33(1): p. 185-200
    [PMID:26429922]
  7. Shi Q,Zhou J,Wang P,Lin X,Xu Y
    Protein expression and characterization of SEP3 from Arabidopsis thaliana.
    Genet. Mol. Res., 2015. 14(4): p. 12529-36
    [PMID:26505403]
  8. He Q,Fu AY,Zhang GC,Li TJ,Zhang JH
    Cloning, Prokaryotic Expression and Purification of CpfS1 Gene from Arabidopsis Thaliana.
    Cell. Mol. Biol. (Noisy-le-grand), 2015. 61(8): p. 123-7
    [PMID:26718440]
  9. Soza VL,Snelson CD,Hewett Hazelton KD,Di Stilio VS
    Partial redundancy and functional specialization of E-class SEPALLATA genes in an early-diverging eudicot.
    Dev. Biol., 2016. 419(1): p. 143-155
    [PMID:27502434]
  10. Conn VM, et al.
    A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation.
    Nat Plants, 2017. 3: p. 17053
    [PMID:28418376]
  11. Käppel S,Melzer R,Rümpler F,Gafert C,Theißen G
    The floral homeotic protein SEPALLATA3 recognizes target DNA sequences by shape readout involving a conserved arginine residue in the MADS-domain.
    Plant J., 2018. 95(2): p. 341-357
    [PMID:29744943]