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 Sobic.009G142500.1.p
Common NameSb09g020770, SORBIDRAFT_09g020770
Organism
Sorghum bicolor
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
Family MIKC_MADS
Protein Properties Length: 213aa    MW: 24765.2 Da    PI: 9.7297
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.009G142500.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF79.91.8e-25959151
                          S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
                SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                          krien++nrqvt skRr+g+ KKA E+ vLCdaev v+ifss gkl++y+s
  Sobic.009G142500.1.p  9 KRIENSTNRQVTVSKRRAGLVKKAREIGVLCDAEVGVVIFSSGGKLHDYCS 59
                          79***********************************************96 PP
2K-box64.53.8e-2271167197
                 K-box   1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqe 89 
                           yq++sgk l+++k++ l+ e++++kke++n+q ++Rhl+GedL+sL+ +eL  +e+ L+++ ++ R+k+++++++  ++ ++ e+e++ 
  Sobic.009G142500.1.p  71 YQTNSGKILWDEKHKILSAEIDRIKKENDNMQIQLRHLKGEDLNSLQPRELIAIEEGLQNGQTNMREKQMDHWRMRKRNGKMLEDENRM 159
                           89999999**********************************************************************99999999988 PP

                 K-box  90 enkaLrkk 97 
                              +++++
  Sobic.009G142500.1.p 160 LSFRMHQQ 167
                           87777766 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006630.852161IPR002100Transcription factor, MADS-box
SMARTSM004321.7E-37160IPR002100Transcription factor, MADS-box
SuperFamilySSF554556.93E-32296IPR002100Transcription factor, MADS-box
CDDcd002657.57E-41280No hitNo description
PRINTSPR004044.3E-27323IPR002100Transcription factor, MADS-box
PfamPF003191.4E-221057IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-272338IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-273859IPR002100Transcription factor, MADS-box
PfamPF014866.3E-1582164IPR002487Transcription factor, K-box
PROSITE profilePS5129712.47384170IPR002487Transcription 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: 213 aa     Download sequence    Send to blast
MGRGKIEIKR IENSTNRQVT VSKRRAGLVK KAREIGVLCD AEVGVVIFSS GGKLHDYCSP  60
RTSLSRILEK YQTNSGKILW DEKHKILSAE IDRIKKENDN MQIQLRHLKG EDLNSLQPRE  120
LIAIEEGLQN GQTNMREKQM DHWRMRKRNG KMLEDENRML SFRMHQQAVD LSGGMRELEI  180
GYHQVQHDRE FTSQMPFTFR VQPNHPNLQE DE*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P7e-18175173Myocyte-specific enhancer factor 2B
1tqe_Q7e-18175173Myocyte-specific enhancer factor 2B
1tqe_R7e-18175173Myocyte-specific enhancer factor 2B
1tqe_S7e-18175173Myocyte-specific enhancer factor 2B
6byy_A9e-18175173MEF2 CHIMERA
6byy_B9e-18175173MEF2 CHIMERA
6byy_C9e-18175173MEF2 CHIMERA
6byy_D9e-18175173MEF2 CHIMERA
6c9l_A7e-18175173Myocyte-specific enhancer factor 2B
6c9l_B7e-18175173Myocyte-specific enhancer factor 2B
6c9l_C7e-18175173Myocyte-specific enhancer factor 2B
6c9l_D7e-18175173Myocyte-specific enhancer factor 2B
6c9l_E7e-18175173Myocyte-specific enhancer factor 2B
6c9l_F7e-18175173Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in lodicules, at intermediate levels in stamens, and weakly in carpels. Expressed in pollen. {ECO:0000269|PubMed:10394955, ECO:0000269|PubMed:12905025, ECO:0000269|Ref.1}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.009G142500.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
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_002439824.11e-157MADS-box transcription factor 4
SwissprotQ407031e-126MADS4_ORYSJ; MADS-box transcription factor 4
TrEMBLC5YY691e-156C5YY69_SORBI; Uncharacterized protein
STRINGSb09g020770.11e-157(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP34343877
Representative plantOGRP53021222
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G20240.12e-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]