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 orange1.1g028923m
Organism
Citrus sinensis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family MIKC_MADS
Protein Properties Length: 203aa    MW: 23517.1 Da    PI: 9.4662
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g028923mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF977.8e-31959151
                       S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
             SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                       krien + rqvtfskRrng+lKKA+ELSvLCdaeva+iifs++gklye+ss
  orange1.1g028923m  9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSS 59
                       79***********************************************96 PP
2K-box80.73.5e-2782171998
              K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                          e ++++ ++e +++  ++e L+  +R+llG++Le++++ eLqqLe+qLe+sl++iR++Kn+l++eqie+l++kek l een++Lr++ 
  orange1.1g028923m  82 IVEDHSQHAKEETSNMMTKLEFLEVAKRKLLGDGLEPCTIDELQQLENQLERSLSRIRARKNQLFREQIEKLKEKEKILIEENTKLREQC 171
                        667889*********************************************************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.539161IPR002100Transcription factor, MADS-box
SMARTSM004322.7E-40160IPR002100Transcription factor, MADS-box
CDDcd002656.44E-42371No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004044.2E-31323IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.7E-32373IPR002100Transcription factor, MADS-box
PfamPF003194.5E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004044.2E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004044.2E-313859IPR002100Transcription factor, MADS-box
PfamPF014869.0E-2784171IPR002487Transcription factor, K-box
PROSITE profilePS5129715.84487177IPR002487Transcription 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: 203 aa     Download sequence    Send to blast
MVRGKTQMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFSP RGKLYEFSSC  60
SINKTIERYQ KKTKDIGINS KIVEDHSQHA KEETSNMMTK LEFLEVAKRK LLGDGLEPCT  120
IDELQQLENQ LERSLSRIRA RKNQLFREQI EKLKEKEKIL IEENTKLREQ CGMQPRQASE  180
EQEVYMDVET QLSIGPPERR VA*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-18184186MEF2C
5f28_B1e-18184186MEF2C
5f28_C1e-18184186MEF2C
5f28_D1e-18184186MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Csi.98521e-177stem
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Mostly expressed in the outer layers of the root meristem (lateral root cap and epidermis) and in the central cylinder cells of mature roots. Also present in rosette leaves and seedlings and, to a lesser extent, in cauline leaves and flowers. Enriched in apices including the shoot apical meristem and developing leaf primordia. {ECO:0000269|PubMed:11115127, ECO:0000269|PubMed:12837945, ECO:0000269|PubMed:12949148, ECO:0000269|PubMed:16778081}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that promotes flowering, especially in response to vernalization by short periods of cold, in an FLC-inpedendent manner. {ECO:0000269|PubMed:16778081}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Maintained at very low levels by the polycomb-group (PcG) proteins MSI1, CLF, and EMF2 via histone methylation (H3K27me3). Derepressed upon cold treatment (vernalization). {ECO:0000269|PubMed:16778081}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006440496.21e-146agamous-like MADS-box protein AGL19
RefseqXP_024044550.11e-146agamous-like MADS-box protein AGL19
RefseqXP_024044551.11e-146agamous-like MADS-box protein AGL19
RefseqXP_024044552.11e-146agamous-like MADS-box protein AGL19
SwissprotO827432e-84AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A2H5NTB81e-121A0A2H5NTB8_CITUN; Uncharacterized protein
STRINGXP_006477351.11e-142(Citrus sinensis)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.11e-77AGAMOUS-like 19
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Suter L,Rüegg M,Zemp N,Hennig L,Widmer A
    Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis.
    Plant Physiol., 2014. 166(4): p. 1928-42
    [PMID:25339407]