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.008G072900.1.p
Common NameSb08g006460, SORBIDRAFT_08g006460
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: 30378.6 Da    PI: 9.5079
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.008G072900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF95.81.9e-30958150
                          S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
                SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                          krien++ rqvtf+kRrng+lKKA+ELSvLCdaeva+i+fss+g+lyey+
  Sobic.008G072900.1.p  9 KRIENNTSRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 58
                          79***********************************************8 PP
2K-box104.51.3e-34801756100
                 K-box   6 gks.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenka 93 
                           g   le++ ++ +qqe+akL+++i++Lq+++Rhl+G+++++L+lkeL+qLe++Lek+++k+R++Knell ++i+++ k+e elq+++++
  Sobic.008G072900.1.p  80 GPPlLEHNAQQFYQQESAKLRNQIQMLQNTNRHLVGDSVGNLTLKELKQLESRLEKGISKVRARKNELLAAEINYMAKRETELQNDHMN 168
                           4556788899******************************************************************************* PP

                 K-box  94 Lrkklee 100
                           Lr+k+ee
  Sobic.008G072900.1.p 169 LRTKIEE 175
                           *****97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004326.3E-41160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006633.585161IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.57E-32275IPR002100Transcription factor, MADS-box
CDDcd002654.68E-45271No hitNo description
PRINTSPR004044.9E-32323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.6E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004044.9E-322338IPR002100Transcription factor, MADS-box
PRINTSPR004044.9E-323859IPR002100Transcription factor, MADS-box
PfamPF014863.9E-2585173IPR002487Transcription factor, K-box
PROSITE profilePS5129714.93389179IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048283Biological Processindeterminate inflorescence morphogenesis
GO:0048316Biological Processseed development
GO:0048481Biological Processplant ovule development
GO:0080155Biological Processregulation of double fertilization forming a zygote and endosperm
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
MGRGRIEIKR IENNTSRQVT FCKRRNGLLK KAYELSVLCD AEVALIVFSS RGRLYEYANN  60
SVKATIERYK KVHTVGSSSG PPLLEHNAQQ FYQQESAKLR NQIQMLQNTN RHLVGDSVGN  120
LTLKELKQLE SRLEKGISKV RARKNELLAA EINYMAKRET ELQNDHMNLR TKIEEGEQQL  180
QQVTVARSVA AAAAATNVEL NPFLEMDTKC FFPGGPFATL DMKCFFPGGY QMLEATAAQH  240
RQMLTTELNL GYQLALPNSD AANNNPHQF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P6e-20169169Myocyte-specific enhancer factor 2B
1tqe_Q6e-20169169Myocyte-specific enhancer factor 2B
1tqe_R6e-20169169Myocyte-specific enhancer factor 2B
1tqe_S6e-20169169Myocyte-specific enhancer factor 2B
6c9l_A6e-20169169Myocyte-specific enhancer factor 2B
6c9l_B6e-20169169Myocyte-specific enhancer factor 2B
6c9l_C6e-20169169Myocyte-specific enhancer factor 2B
6c9l_D6e-20169169Myocyte-specific enhancer factor 2B
6c9l_E6e-20169169Myocyte-specific enhancer factor 2B
6c9l_F6e-20169169Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.124810.0ovary
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed during ovule development. First detected in the ovule primordia and later in the inner and outer integuments, nucellus tissue and the inner layer of the carpel wall. {ECO:0000269|PubMed:10528264}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.008G072900.1.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
GenBankBT0365260.0BT036526.1 Zea mays full-length cDNA clone ZM_BFb0120G12 mRNA, complete cds.
GenBankBT0390740.0BT039074.1 Zea mays full-length cDNA clone ZM_BFb0368I18 mRNA, complete cds.
GenBankZMU315220.0U31522.1 Zea Mays MADS box protein (ZmOV23) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002441989.10.0MADS-box transcription factor 13
RefseqXP_021301477.10.0MADS-box transcription factor 13
SwissprotQ2QW531e-121MAD13_ORYSJ; MADS-box transcription factor 13
TrEMBLC5YTL70.0C5YTL7_SORBI; Uncharacterized protein
STRINGSb08g006460.10.0(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
AT2G42830.18e-85MIKC_MADS family protein
Publications ? help Back to Top
  1. Gindullis F,Rose A,Patel S,Meier I
    Four signature motifs define the first class of structurally related large coiled-coil proteins in plants.
    BMC Genomics, 2002. 3: p. 9
    [PMID:11972898]
  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. Yamaki S,Satoh H,Nagato Y
    Gypsy embryo specifies ovule curvature by regulating ovule/integument development in rice.
    Planta, 2005. 222(3): p. 408-17
    [PMID:16001259]
  4. Dreni L, et al.
    The D-lineage MADS-box gene OsMADS13 controls ovule identity in rice.
    Plant J., 2007. 52(4): p. 690-9
    [PMID:17877710]
  5. Yamaki S,Nagato Y,Kurata N,Nonomura K
    Ovule is a lateral organ finally differentiated from the terminating floral meristem in rice.
    Dev. Biol., 2011. 351(1): p. 208-16
    [PMID:21146515]
  6. Li H,Liang W,Yin C,Zhu L,Zhang D
    Genetic interaction of OsMADS3, DROOPING LEAF, and OsMADS13 in specifying rice floral organ identities and meristem determinacy.
    Plant Physiol., 2011. 156(1): p. 263-74
    [PMID:21444646]
  7. Li H, et al.
    Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate.
    Plant Cell, 2011. 23(7): p. 2536-52
    [PMID:21784949]