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.003G379000.1.p
Common NameSb03g041860, SORBIDRAFT_03g041860
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: 210aa    MW: 24118.6 Da    PI: 8.2331
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.003G379000.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF94.16.3e-30959151
                          S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
                SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                          krien++nrqvtfskRrngilKKA E+SvLCdaev v+ifss gkly+y+s
  Sobic.003G379000.1.p  9 KRIENSTNRQVTFSKRRNGILKKAREISVLCDAEVGVVIFSSAGKLYDYCS 59
                          79***********************************************96 PP
2K-box707.4e-2471167197
                 K-box   1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqe 89 
                           yq++sgk l+++k++sl+ e++++kke++++q e+Rhl+GedL+sL+ k+L  +e++L+++l++  +k +e++ + + + +++e+e++ 
  Sobic.003G379000.1.p  71 YQTNSGKILWDEKHKSLSAEIDRIKKENDTMQIELRHLKGEDLNSLQPKDLIMIEEALDNGLTNQNEKLMEHWERRVANNKMMEDENKL 159
                           89999999********************************************************************************* PP

                 K-box  90 enkaLrkk 97 
                              +L+++
  Sobic.003G379000.1.p 160 LAFKLHQQ 167
                           ****9997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004329.0E-43160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006633.249161IPR002100Transcription factor, MADS-box
SuperFamilySSF554557.72E-35296IPR002100Transcription factor, MADS-box
CDDcd002656.58E-45280No hitNo description
PRINTSPR004041.2E-30323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.9E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-303859IPR002100Transcription factor, MADS-box
PfamPF014861.1E-1282164IPR002487Transcription factor, K-box
PROSITE profilePS5129711.6584170IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010093Biological Processspecification of floral organ identity
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
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: 210 aa     Download sequence    Send to blast
MGRGKIEIKR IENSTNRQVT FSKRRNGILK KAREISVLCD AEVGVVIFSS AGKLYDYCSP  60
KTSLSKILEK YQTNSGKILW DEKHKSLSAE IDRIKKENDT MQIELRHLKG EDLNSLQPKD  120
LIMIEEALDN GLTNQNEKLM EHWERRVANN KMMEDENKLL AFKLHQQDIA LSGSMRELEL  180
GYHPDRDLAA QMPITFRVQP SHPNLQDNN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A5e-20186178MEF2C
5f28_B5e-20186178MEF2C
5f28_C5e-20186178MEF2C
5f28_D5e-20186178MEF2C
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in lodicules and stamens from early to late stage of flower development. {ECO:0000269|PubMed:10945340, ECO:0000269|Ref.1}.
UniprotTISSUE SPECIFICITY: Highly expressed in anthers and carpels. Expressed in pollen, tapetum and stigma. {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 (whorl 2). {ECO:0000269|PubMed:14704206}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00080ChIP-seqTransfer from AT5G20240Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.003G379000.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ2929590.0AJ292959.1 Zea mays mRNA for putative MADS-domain transcription factor (m16 gene).
GenBankBT0648490.0BT064849.1 Zea mays full-length cDNA clone ZM_BFb0210M20 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021310970.11e-155MADS-box transcription factor 2
SwissprotQ407021e-144MADS2_ORYSJ; MADS-box transcription factor 2
TrEMBLC5XEK81e-153C5XEK8_SORBI; Uncharacterized protein
STRINGSb03g041860.11e-152(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
AT5G20240.11e-74MIKC_MADS family protein
Publications ? help Back to Top
  1. 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]