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 Pahal.C02957.1
Organism
Panicum hallii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family MIKC_MADS
Protein Properties Length: 216aa    MW: 25064.4 Da    PI: 8.2556
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pahal.C02957.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF85.14.1e-27959151
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                    krien++nrqvtfskRr+g+ KKA E+ vLCdaev v+ifss gkly+y+s
  Pahal.C02957.1  9 KRIENSTNRQVTFSKRRAGLVKKAREIGVLCDAEVGVVIFSSGGKLYDYCS 59
                    79***********************************************96 PP
2K-box61.24.3e-2171160190
           K-box   1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqee 90 
                     yq++sgk l+++k++sl+ e++++kke++n+q e+Rhl+GedL+sL+  eL  +e++L+++ ++ R+k +++++++ ++ ++ e+e++  
  Pahal.C02957.1  71 YQTNSGKILWDEKHKSLSAEIDRVKKENDNMQIELRHLKGEDLNSLQPTELIAIEEALQNGQTNQRDKLMDHWRMHKRNGKMLEDEHKLL 160
                     89999999*****************************************************************99999999999988765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004323.8E-40160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006632.043161IPR002100Transcription factor, MADS-box
SuperFamilySSF554552.75E-33295IPR002100Transcription factor, MADS-box
CDDcd002653.73E-43280No hitNo description
PRINTSPR004047.1E-29323IPR002100Transcription factor, MADS-box
PfamPF003191.5E-241057IPR002100Transcription factor, MADS-box
PRINTSPR004047.1E-292338IPR002100Transcription factor, MADS-box
PRINTSPR004047.1E-293859IPR002100Transcription factor, MADS-box
PfamPF014861.7E-1382164IPR002487Transcription factor, K-box
PROSITE profilePS5129711.7784170IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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: 216 aa     Download sequence    Send to blast
MGRGKIEIKR IENSTNRQVT FSKRRAGLVK KAREIGVLCD AEVGVVIFSS GGKLYDYCSP  60
RTSLSRILEK YQTNSGKILW DEKHKSLSAE IDRVKKENDN MQIELRHLKG EDLNSLQPTE  120
LIAIEEALQN GQTNQRDKLM DHWRMHKRNG KMLEDEHKLL SFRMAYQHQQ DVELSGGMRE  180
LEIGYHQVQH DRDFTSQMPF TFRVQPSHPN LQEDE*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P3e-19171169Myocyte-specific enhancer factor 2B
1tqe_Q3e-19171169Myocyte-specific enhancer factor 2B
1tqe_R3e-19171169Myocyte-specific enhancer factor 2B
1tqe_S3e-19171169Myocyte-specific enhancer factor 2B
5f28_A3e-19186178MEF2C
5f28_B3e-19186178MEF2C
5f28_C3e-19186178MEF2C
5f28_D3e-19186178MEF2C
6byy_A3e-19171169MEF2 CHIMERA
6byy_B3e-19171169MEF2 CHIMERA
6byy_C3e-19171169MEF2 CHIMERA
6byy_D3e-19171169MEF2 CHIMERA
6c9l_A3e-19171169Myocyte-specific enhancer factor 2B
6c9l_B3e-19171169Myocyte-specific enhancer factor 2B
6c9l_C3e-19171169Myocyte-specific enhancer factor 2B
6c9l_D3e-19171169Myocyte-specific enhancer factor 2B
6c9l_E3e-19171169Myocyte-specific enhancer factor 2B
6c9l_F3e-19171169Myocyte-specific enhancer factor 2B
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the development of floral organs. B-class protein required for normal development of lodicules and stamens (whorls 2 and 3). May function as a heterodimer with MADS16. {ECO:0000269|PubMed:9869408}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKJ7269300.0KJ726930.1 Zea mays clone pUT3475 MADS transcription factor (MADS29) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025808084.11e-161MADS-box transcription factor 4-like
SwissprotQ407031e-132MADS4_ORYSJ; MADS-box transcription factor 4
TrEMBLA0A2S3HBW31e-159A0A2S3HBW3_9POAL; Uncharacterized protein
TrEMBLA0A2T7EDL91e-159A0A2T7EDL9_9POAL; Uncharacterized protein
STRINGPavir.J33965.1.p1e-158(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP34343877
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G20240.16e-72MIKC_MADS family protein
Publications ? help Back to Top
  1. Ronai Z, et al.
    Transcription factor binding study by capillary zone electrophoretic mobility shift assay.
    Electrophoresis, 2003. 24(1-2): p. 96-100
    [PMID:12652578]
  2. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  3. Kang HG,An G
    Morphological alterations by ectopic expression of the rice OsMADS4 gene in tobacco plants.
    Plant Cell Rep., 2005. 24(2): p. 120-6
    [PMID:15703945]
  4. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]
  5. Chen C, et al.
    Adapting rice anther culture to gene transformation and RNA interference.
    Sci. China, C, Life Sci., 2006. 49(5): p. 414-28
    [PMID:17172048]
  6. Yoshida H, et al.
    superwoman1-cleistogamy, a hopeful allele for gene containment in GM rice.
    Plant Biotechnol. J., 2007. 5(6): p. 835-46
    [PMID:17764519]
  7. Yao SG,Ohmori S,Kimizu M,Yoshida H
    Unequal genetic redundancy of rice PISTILLATA orthologs, OsMADS2 and OsMADS4, in lodicule and stamen development.
    Plant Cell Physiol., 2008. 49(5): p. 853-7
    [PMID:18378529]
  8. Seok HY, et al.
    Rice ternary MADS protein complexes containing class B MADS heterodimer.
    Biochem. Biophys. Res. Commun., 2010. 401(4): p. 598-604
    [PMID:20888318]
  9. Wang H, et al.
    OsMADS32 interacts with PI-like proteins and regulates rice flower development.
    J Integr Plant Biol, 2015. 57(5): p. 504-13
    [PMID:25081486]