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 orange1.1g028363m
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: 211aa    MW: 24509.2 Da    PI: 9.6784
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g028363mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF96.98.3e-31959151
                       S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
             SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                       krien + rqvtfskRrng+lKKA+ELSvLCdaeva+iifs++gklye+ss
  orange1.1g028363m  9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSS 59
                       79***********************************************96 PP
2K-box65.22.3e-2282179998
              K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskK........nellleqieelqkkekelqeenk 92 
                          e ++++ ++e +++  ++e L+  +R+llG++Le++++ eLqqLe+qLe+sl++iR++K        n+l++eqie+l++kek l een+
  orange1.1g028363m  82 IVEDHSQHAKEETSNMMTKLEFLEVAKRKLLGDGLEPCTIDELQQLENQLERSLSRIRARKfrnlvfsqNQLFREQIEKLKEKEKILIEENT 173
                        667889******************************************************86666666689********************* PP

              K-box  93 aLrkkl 98 
                        +Lr++ 
  orange1.1g028363m 174 KLREQC 179
                        ***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
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
CDDcd002657.39E-42371No hitNo description
SuperFamilySSF554551.96E-32373IPR002100Transcription factor, MADS-box
PRINTSPR004044.5E-31323IPR002100Transcription factor, MADS-box
PfamPF003194.9E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004044.5E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004044.5E-313859IPR002100Transcription factor, MADS-box
PfamPF014861.2E-2484179IPR002487Transcription factor, K-box
PROSITE profilePS5129714.44987185IPR002487Transcription 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: 211 aa     Download sequence    Send to blast
MVRGKTQMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFSP RGKLYEFSSC  60
SINKTIERYQ KKTKDIGINS KIVEDHSQHA KEETSNMMTK LEFLEVAKRK LLGDGLEPCT  120
IDELQQLENQ LERSLSRIRA RKFRNLVFSQ NQLFREQIEK LKEKEKILIE ENTKLREQCG  180
MQPRQASEEQ EVYMDVETQL SIGPPERRVA *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-18184186MEF2C
5f28_B2e-18184186MEF2C
5f28_C2e-18184186MEF2C
5f28_D2e-18184186MEF2C
6byy_A2e-18169169MEF2 CHIMERA
6byy_B2e-18169169MEF2 CHIMERA
6byy_C2e-18169169MEF2 CHIMERA
6byy_D2e-18169169MEF2 CHIMERA
6bz1_A2e-18169169MEF2 CHIMERA
6bz1_B2e-18169169MEF2 CHIMERA
6bz1_C2e-18169169MEF2 CHIMERA
6bz1_D2e-18169169MEF2 CHIMERA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Csi.98521e-101stem
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_006477351.11e-152agamous-like MADS-box protein AGL19 isoform X1
RefseqXP_006477352.11e-152agamous-like MADS-box protein AGL19 isoform X1
RefseqXP_006477353.11e-152agamous-like MADS-box protein AGL19 isoform X1
RefseqXP_006477354.11e-152agamous-like MADS-box protein AGL19 isoform X1
SwissprotO827432e-82AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A2H5NTB81e-130A0A2H5NTB8_CITUN; Uncharacterized protein
STRINGXP_006477351.11e-151(Citrus sinensis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM7828413
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.11e-75AGAMOUS-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]