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 PSME_00056295-RA
Organism
Pseudotsuga menziesii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pseudotsuga
Family MIKC_MADS
Protein Properties Length: 195aa    MW: 22259.3 Da    PI: 6.768
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PSME_00056295-RAgenomePRSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF85.33.6e-27959151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      krien + rq tfskRr g+lKKA ELS+LCdae+av+ifss+gklye++s
  PSME_00056295-RA  9 KRIENPTSRQATFSKRRGGLLKKARELSILCDAEIAVLIFSSSGKLYEFAS 59
                      79***********************************************86 PP
2K-box61.14.4e-2186178899
             K-box   8 s.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
                       +  e++++++ + ++akL+ + e Lq  ++h  GedLe L+  +Lq Le++Le ++ ++R++Kn+ +l+ i+e  + e++l een++Lr+k++
  PSME_00056295-RA  86 DcSENNQNNNQNIQAAKLRIQAEHLQLMLKHTSGEDLEGLDTDQLQTLEENLELGIGRVRARKNQCMLSRIKEISNIEQDLIEENRTLRRKMN 178
                       3233344444445789**************************************************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006632.436161IPR002100Transcription factor, MADS-box
SMARTSM004321.9E-40160IPR002100Transcription factor, MADS-box
CDDcd002655.27E-43278No hitNo description
SuperFamilySSF554559.55E-33276IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-29323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.1E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-292338IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-293859IPR002100Transcription factor, MADS-box
PfamPF014862.6E-1789177IPR002487Transcription factor, K-box
PROSITE profilePS5129712.44593183IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010440Biological Processstomatal lineage progression
GO:0048574Biological Processlong-day photoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008134Molecular Functiontranscription factor binding
GO:0042803Molecular Functionprotein homodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 195 aa     Download sequence    Send to blast
MGRGKIEIKR IENPTSRQAT FSKRRGGLLK KARELSILCD AEIAVLIFSS SGKLYEFAST  60
EMKTILDRYS KCFEQSSQSE SQALVDCSEN NQNNNQNIQA AKLRIQAEHL QLMLKHTSGE  120
DLEGLDTDQL QTLEENLELG IGRVRARKNQ CMLSRIKEIS NIEQDLIEEN RTLRRKMNDF  180
LNNECLTAVP HTLET
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6byy_A8e-23189186MEF2 CHIMERA
6byy_B8e-23189186MEF2 CHIMERA
6byy_C8e-23189186MEF2 CHIMERA
6byy_D8e-23189186MEF2 CHIMERA
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1141149GRVRARKNQ
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00410DAPTransfer from AT3G57230Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMap-Retrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001266821.12e-49uncharacterized protein LOC100832541
RefseqXP_010230319.12e-49uncharacterized protein LOC100832541 isoform X1
RefseqXP_024313924.12e-49uncharacterized protein LOC100832541 isoform X1
RefseqXP_024538443.12e-49MADS-box transcription factor 27 isoform X3
RefseqXP_024540272.12e-49MADS-box transcription factor 27 isoform X7
SwissprotQ6VAM46e-46MAD23_ORYSJ; MADS-box transcription factor 23
TrEMBLQ8LLC85e-50Q8LLC8_SPIAN; MADS-box gene 2 protein
STRINGBRADI2G25090.17e-49(Brachypodium distachyon)
STRINGPP1S209_130V6.22e-48(Physcomitrella patens)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G57230.11e-45AGAMOUS-like 16
Publications ? help Back to Top
  1. Puig J, et al.
    Analysis of the expression of the AGL17-like clade of MADS-box transcription factors in rice.
    Gene Expr. Patterns, 2013 Jun-Jul. 13(5-6): p. 160-70
    [PMID:23466806]
  2. Yu C, et al.
    The effects of fluctuations in the nutrient supply on the expression of five members of the AGL17 clade of MADS-box genes in rice.
    PLoS ONE, 2014. 9(8): p. e105597
    [PMID:25140876]
  3. Wang H, et al.
    A Signaling Cascade from miR444 to RDR1 in Rice Antiviral RNA Silencing Pathway.
    Plant Physiol., 2016. 170(4): p. 2365-77
    [PMID:26858364]