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 XP_009130198.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family MIKC_MADS
Protein Properties Length: 209aa    MW: 24744.5 Da    PI: 9.7059
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009130198.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF93.87.7e-30959151
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                    k+ien + rqvtfskRrng+lKKA+ELSvLCda+v++i+fs++g+lye+s+
  XP_009130198.1  9 KKIENATSRQVTFSKRRNGLLKKAYELSVLCDAQVSLIVFSQRGRLYEFSN 59
                    68***********************************************95 PP
2K-box66.87.2e-2377170497
           K-box   4 ssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkk 97 
                      ++++ +e   ++l++e++ +  +ie L+  +R+llG++L s+sl+eLq++ +qL++sl k+R+kK +l++eq+e+l+ kek+l een +L++k
  XP_009130198.1  77 ETNNHDSEIYVQRLKEEASHMITKIELLEFHKRKLLGQELASCSLEELQEIDSQLQRSLAKVRAKKAQLFREQLEKLKAKEKQLLEENVRLHQK 170
                     44455788889******************999************************************************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006632.099161IPR002100Transcription factor, MADS-box
SMARTSM004323.1E-40160IPR002100Transcription factor, MADS-box
PRINTSPR004047.8E-31323IPR002100Transcription factor, MADS-box
CDDcd002654.28E-42378No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.79E-33383IPR002100Transcription factor, MADS-box
PfamPF003195.9E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004047.8E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004047.8E-313859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129713.28787177IPR002487Transcription factor, K-box
PfamPF014862.3E-2287170IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009838Biological Processabscission
GO:0009909Biological Processregulation of flower development
GO:0010150Biological Processleaf senescence
GO:0080187Biological Processfloral organ senescence
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: 209 aa     Download sequence    Send to blast
MVRGKIEMKK IENATSRQVT FSKRRNGLLK KAYELSVLCD AQVSLIVFSQ RGRLYEFSNS  60
DMWKTIERYR KYTKDHETNN HDSEIYVQRL KEEASHMITK IELLEFHKRK LLGQELASCS  120
LEELQEIDSQ LQRSLAKVRA KKAQLFREQL EKLKAKEKQL LEENVRLHQK TVLEPWRGST  180
DQQEKFRVID LNLEVETDLV IGLPEKHCK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P8e-21181181Myocyte-specific enhancer factor 2B
1tqe_Q8e-21181181Myocyte-specific enhancer factor 2B
1tqe_R8e-21181181Myocyte-specific enhancer factor 2B
1tqe_S8e-21181181Myocyte-specific enhancer factor 2B
6c9l_A8e-21181181Myocyte-specific enhancer factor 2B
6c9l_B8e-21181181Myocyte-specific enhancer factor 2B
6c9l_C8e-21181181Myocyte-specific enhancer factor 2B
6c9l_D8e-21181181Myocyte-specific enhancer factor 2B
6c9l_E8e-21181181Myocyte-specific enhancer factor 2B
6c9l_F8e-21181181Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the shoot apical meristem (SAM) during the vegetative phase and the floral transition. After floral transition, expressed in apical meristem (AM), inflorescence meristem (IM) and floral primordia. {ECO:0000269|PubMed:21609362}.
UniprotTISSUE SPECIFICITY: Expressed in quiescent center (QC) cells of root tips (PubMed:18162590, PubMed:21689171). Expressed at the base of the petiole of cotyledons and leaves, in flower buds, petals, sepals and abscission zone of flowers and siliques. {ECO:0000269|PubMed:18162590, ECO:0000269|PubMed:21689171}.
Functional Description ? help Back to Top
Source Description
UniProtMADS-box transcription factor that acts with AGL71 and AGL72 in the control of flowering time. Promotes flowering at the shoot apical and axillary meristems. Seems to act through a gibberellin-dependent pathway. Interacts genetically with SOC1 and its expression is directly regulated by SOC1 (PubMed:21609362). Plays a role in controlling flower organ senescence and abscission by repressing ethylene responses and regulating the expression of BOP2 and IDA (PubMed:21689171). {ECO:0000269|PubMed:21609362, ECO:0000269|PubMed:21689171}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00576DAPTransfer from AT5G62165Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009130198.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0542200.0AY054220.1 Arabidopsis thaliana At2g45660/F17K2.19 mRNA, complete cds.
GenBankAY0652060.0AY065206.1 Arabidopsis thaliana unknown protein (At5g62165) mRNA, complete cds.
GenBankAY0660350.0AY066035.1 Arabidopsis thaliana At2g45660/F17K2.19 mRNA, complete cds.
GenBankAY0965090.0AY096509.1 Arabidopsis thaliana unknown protein (At5g62165) mRNA, complete cds.
GenBankAY1412130.0AY141213.1 Arabidopsis thaliana MADS-box protein AGL42 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009130198.11e-151PREDICTED: MADS-box protein AGL42
RefseqXP_022554905.11e-151MADS-box protein AGL42
RefseqXP_022576288.11e-151MADS-box protein AGL42
SwissprotQ9FIS11e-130AGL42_ARATH; MADS-box protein AGL42
TrEMBLA0A078GYX11e-150A0A078GYX1_BRANA; BnaA02g33230D protein
TrEMBLA0A398AJG81e-150A0A398AJG8_BRACM; Uncharacterized protein
TrEMBLM4EKG41e-150M4EKG4_BRARP; Uncharacterized protein
STRINGBra029281.1-P1e-151(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM7828413
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62165.31e-120AGAMOUS-like 42