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 Potri.003G119700.5
Common NamePOPTR_0003s11960g
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family MIKC_MADS
Protein Properties Length: 163aa    MW: 18643.6 Da    PI: 10.5974
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.003G119700.5genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF97.17.2e-31959151
                        S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
              SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                        krien + rqvtfskRrng+lKKA+ELSvLCdaeva+i+fss+gklye+ss
  Potri.003G119700.5  9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIVFSSRGKLYEFSS 59
                        79***********************************************96 PP
2K-box62.41.7e-21831541081
               K-box  10 eeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelq 81 
                          + + +  +++   L k+ie L+ ++R+llGe+Le++s  +LqqLe+qL +sl++iR++Kn+l++e ie+l+
  Potri.003G119700.5  83 VQDNIQPVKEDTFTLAKKIELLEVSKRKLLGEGLETCSTDDLQQLENQLGRSLTRIRARKNQLFRERIEKLK 154
                         45678889999999*******************************************************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006632.142161IPR002100Transcription factor, MADS-box
SMARTSM004323.6E-41160IPR002100Transcription factor, MADS-box
PRINTSPR004049.5E-32323IPR002100Transcription factor, MADS-box
CDDcd002653.79E-42371No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.02E-32372IPR002100Transcription factor, MADS-box
PfamPF003198.6E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004049.5E-322338IPR002100Transcription factor, MADS-box
PRINTSPR004049.5E-323859IPR002100Transcription factor, MADS-box
PfamPF014868.5E-2184155IPR002487Transcription factor, K-box
PROSITE profilePS5129711.75787162IPR002487Transcription 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: 163 aa     Download sequence    Send to blast
MVRGKTQMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIVFSS RGKLYEFSSS  60
SINRTIERYQ KRAKDVGISS KMVQDNIQPV KEDTFTLAKK IELLEVSKRK LLGEGLETCS  120
TDDLQQLENQ LGRSLTRIRA RKNQLFRERI EKLKGEVIPY DS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-19169169MEF2C
5f28_B2e-19169169MEF2C
5f28_C2e-19169169MEF2C
5f28_D2e-19169169MEF2C
6byy_A3e-19169169MEF2 CHIMERA
6byy_B3e-19169169MEF2 CHIMERA
6byy_C3e-19169169MEF2 CHIMERA
6byy_D3e-19169169MEF2 CHIMERA
6bz1_A3e-19169169MEF2 CHIMERA
6bz1_B3e-19169169MEF2 CHIMERA
6bz1_C3e-19169169MEF2 CHIMERA
6bz1_D3e-19169169MEF2 CHIMERA
Search in ModeBase
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.003G119700.5
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ5008801e-175DQ500880.1 Populus tomentosa MADS box transcription factor (MADS3) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024452474.11e-107agamous-like MADS-box protein AGL19 isoform X1
RefseqXP_024452475.11e-107agamous-like MADS-box protein AGL19 isoform X1
RefseqXP_024452478.11e-107agamous-like MADS-box protein AGL19 isoform X3
SwissprotO827433e-74AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLB9GW461e-106B9GW46_POPTR; Uncharacterized protein
STRINGcassava4.1_026051m3e-86(Manihot esculenta)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.11e-76AGAMOUS-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]