PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Sobic.001G086400.2.p
Common NameSb01g007780, SORBIDRAFT_01g007780
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: 176aa    MW: 20131.1 Da    PI: 9.8744
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.001G086400.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF88.73.1e-281059251
                          ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
                SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                          rienk+ rqvtf+kRrng+lKKA+ELS+LCdaeva+++fs+ g+ly +ss
  Sobic.001G086400.2.p 10 RIENKISRQVTFAKRRNGLLKKAYELSILCDAEVALVLFSHAGRLYQFSS 59
                          9***********************************************96 PP
2K-box100.13.1e-3383173999
                 K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkk 97 
                            ++ ++++ +qe+ +Lk+++e Lq++qR+llGedL +Ls  eL qLe+q++k lk+iRs+K+++ll+++ +l++ke++lq++n+ L++k
  Sobic.001G086400.2.p  83 PSSDEMQNNYQEYVNLKARVEVLQHSQRNLLGEDLAPLSPSELDQLESQVDKTLKQIRSRKTQVLLDELCDLKRKEQMLQDANRVLKRK 171
                           567889**********************************************************************************9 PP

                 K-box  98 le 99 
                           + 
  Sobic.001G086400.2.p 172 VS 173
                           85 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.02161IPR002100Transcription factor, MADS-box
SMARTSM004322.9E-36160IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.57E-30284IPR002100Transcription factor, MADS-box
CDDcd002651.81E-38279No hitNo description
PRINTSPR004042.3E-29323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003196.3E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004042.3E-292338IPR002100Transcription factor, MADS-box
PRINTSPR004042.3E-293859IPR002100Transcription factor, MADS-box
PfamPF014865.3E-2985172IPR002487Transcription factor, K-box
PROSITE profilePS5129714.56688175IPR002487Transcription 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: 176 aa     Download sequence    Send to blast
MGRGKVVLQR IENKISRQVT FAKRRNGLLK KAYELSILCD AEVALVLFSH AGRLYQFSSS  60
SNLLKTLERY QRYIYASADA AVPSSDEMQN NYQEYVNLKA RVEVLQHSQR NLLGEDLAPL  120
SPSELDQLES QVDKTLKQIR SRKTQVLLDE LCDLKRKEQM LQDANRVLKR KVSDS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_A2e-25751751104Developmental protein SEPALLATA 3
4ox0_B2e-25751751104Developmental protein SEPALLATA 3
4ox0_C2e-25751751104Developmental protein SEPALLATA 3
4ox0_D2e-25751751104Developmental protein SEPALLATA 3
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.209632e-46ovary| panicle
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in leaves and at low levels in roots and spikelets (rice flower). {ECO:0000269|Ref.7}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.001G086400.2.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
GenBankBT0424060.0BT042406.1 Zea mays full-length cDNA clone ZM_BFb0221D10 mRNA, complete cds.
GenBankEU9617990.0EU961799.1 Zea mays clone 238290 MADS-box transcription factor 34 mRNA, complete cds.
GenBankKJ7269320.0KJ726932.1 Zea mays clone pUT3478 MADS transcription factor (MADS24) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021311786.11e-120MADS-box transcription factor 34
SwissprotQ6Q9H61e-112MAD34_ORYSJ; MADS-box transcription factor 34
TrEMBLC5X0931e-123C5X093_SORBI; Uncharacterized protein
STRINGSb01g007780.11e-123(Sorghum bicolor)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G15800.11e-76MIKC_MADS family protein
Publications ? help Back to Top
  1. Kobayashi K,Maekawa M,Miyao A,Hirochika H,Kyozuka J
    PANICLE PHYTOMER2 (PAP2), encoding a SEPALLATA subfamily MADS-box protein, positively controls spikelet meristem identity in rice.
    Plant Cell Physiol., 2010. 51(1): p. 47-57
    [PMID:19933267]
  2. Gao X, et al.
    The SEPALLATA-like gene OsMADS34 is required for rice inflorescence and spikelet development.
    Plant Physiol., 2010. 153(2): p. 728-40
    [PMID:20395452]
  3. Khanday I,Yadav SR,Vijayraghavan U
    Rice LHS1/OsMADS1 controls floret meristem specification by coordinated regulation of transcription factors and hormone signaling pathways.
    Plant Physiol., 2013. 161(4): p. 1970-83
    [PMID:23449645]
  4. Lin X, et al.
    The pleiotropic SEPALLATA-like gene OsMADS34 reveals that the 'empty glumes' of rice (Oryza sativa) spikelets are in fact rudimentary lemmas.
    New Phytol., 2014. 202(2): p. 689-702
    [PMID:24372518]
  5. Conrad LJ, et al.
    The polycomb group gene EMF2B is essential for maintenance of floral meristem determinacy in rice.
    Plant J., 2014. 80(5): p. 883-94
    [PMID:25279942]
  6. Liu M,Li H,Su Y,Li W,Shi C
    G1/ELE Functions in the Development of Rice Lemmas in Addition to Determining Identities of Empty Glumes.
    Front Plant Sci, 2016. 7: p. 1006
    [PMID:27462334]