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.003G027000.1.p
Common NameSb03g002525, SORBIDRAFT_03g002525
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: 270aa    MW: 30421.5 Da    PI: 9.4331
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.003G027000.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF99.11.8e-315099150
                          S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
                SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                          krien++nrqvtf+kRrng+lKKA+ELSvLCdaeva+i+fss+g+lyey+
  Sobic.003G027000.1.p 50 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 99
                          79***********************************************8 PP
2K-box101.41.2e-331192145100
                 K-box   5 sgks.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenk 92 
                           ++   ++e  a+++qqe++kL++ i++Lq+ +R ++G++++++sl++L+qLe +Lek+++kiR++Knell+++++++qk+e +lq +n+
  Sobic.003G027000.1.p 119 NS-GtVAEVSAQHYQQESSKLRQTISSLQNANRTIVGDSIHTMSLRDLKQLEGRLEKGISKIRARKNELLYAEVDYMQKREMDLQTDNM 206
                           33.2489999******************************************************************************* PP

                 K-box  93 aLrkklee 100
                           +Lr+k++e
  Sobic.003G027000.1.p 207 YLRSKIAE 214
                           *****986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006633.51542102IPR002100Transcription factor, MADS-box
SMARTSM004321.1E-4042101IPR002100Transcription factor, MADS-box
CDDcd002659.02E-4743116No hitNo description
SuperFamilySSF554553.66E-3343114IPR002100Transcription factor, MADS-box
PROSITE patternPS0035004498IPR002100Transcription factor, MADS-box
PRINTSPR004045.6E-334464IPR002100Transcription factor, MADS-box
PfamPF003191.1E-265198IPR002100Transcription factor, MADS-box
PRINTSPR004045.6E-336479IPR002100Transcription factor, MADS-box
PRINTSPR004045.6E-3379100IPR002100Transcription factor, MADS-box
PfamPF014866.4E-25127212IPR002487Transcription factor, K-box
PROSITE profilePS5129713.805128218IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048366Biological Processleaf development
GO:0048440Biological Processcarpel development
GO:0048443Biological Processstamen development
GO:0048497Biological Processmaintenance of floral organ identity
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: 270 aa     Download sequence    Send to blast
MQRGTAAPPP PPPMLNMMTD LSCRPSEVTE QLAAPTGSGD KQGRGKIEIK RIENTTNRQV  60
TFCKRRNGLL KKAYELSVLC DAEVALIVFS SRGRLYEYAN NSVKSTIERY KKANSDTSNS  120
GTVAEVSAQH YQQESSKLRQ TISSLQNANR TIVGDSIHTM SLRDLKQLEG RLEKGISKIR  180
ARKNELLYAE VDYMQKREMD LQTDNMYLRS KIAENNETGQ PAMNMMGVPS TSEYEHMVPF  240
DSRNFLQVNI MQQPQHYSHQ LQPTTLQLG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1egw_A6e-2143114172MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_B6e-2143114172MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_C6e-2143114172MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_D6e-2143114172MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
3kov_A1e-2043114172Myocyte-specific enhancer factor 2A
3kov_B1e-2043114172Myocyte-specific enhancer factor 2A
3kov_I1e-2043114172Myocyte-specific enhancer factor 2A
3kov_J1e-2043114172Myocyte-specific enhancer factor 2A
3p57_A1e-2043114172Myocyte-specific enhancer factor 2A
3p57_B1e-2043114172Myocyte-specific enhancer factor 2A
3p57_C1e-2043114172Myocyte-specific enhancer factor 2A
3p57_D1e-2043114172Myocyte-specific enhancer factor 2A
3p57_I1e-2043114172Myocyte-specific enhancer factor 2A
3p57_J1e-2043114172Myocyte-specific enhancer factor 2A
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.124650.0ovary
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed at early stage of flower development in stamen anlagen before stamen initiation, and at later stage in lodicule and ovule primordia initiation region. {ECO:0000269|PubMed:10945340, ECO:0000269|PubMed:16326928}.
UniprotTISSUE SPECIFICITY: Expressed in lemmas, paleas and lodicules. {ECO:0000269|PubMed:10945340}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the development of floral organs. Acts as C-class protein in association with MADS58. Involved in the control of lodicule number (whorl 2), stamen specification (whorl 3) and floral meristem determinacy (whorl 4), but not in the regulation of carpel morphogenesis. Plays a more predominant role in controlling lodicule development and in specifying stamen identity than MADS58. {ECO:0000269|PubMed:11828031, ECO:0000269|PubMed:16326928, ECO:0000269|PubMed:9869408}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00609ChIP-seqTransfer from AT4G18960Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.003G027000.1.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
GenBankEU9608100.0EU960810.1 Zea mays clone 228787 MADS-box transcription factor 3 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002454985.10.0MADS-box transcription factor 3 isoform X2
SwissprotQ407041e-147MADS3_ORYSJ; MADS-box transcription factor 3
TrEMBLC5XL840.0C5XL84_SORBI; Uncharacterized protein
STRINGSb03g002525.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP64937144
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G18960.11e-107MIKC_MADS family protein
Publications ? help Back to Top
  1. Kyozuka J,Shimamoto K
    Ectopic expression of OsMADS3, a rice ortholog of AGAMOUS, caused a homeotic transformation of lodicules to stamens in transgenic rice plants.
    Plant Cell Physiol., 2002. 43(1): p. 130-5
    [PMID:11828031]
  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]