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 LOC_Os03g53960.1
Common NameLOC4334126, OsJ_12585
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family MYB_related
Protein Properties Length: 571aa    MW: 63797 Da    PI: 7.5522
Description MYB_related family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g53960.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding39.61.2e-12111151445
                       S-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHH CS
   Myb_DNA-binding   4 WTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwq 45 
                       W ++E+ ll+++++++G g+W+ +a+++g ++t  qc++++ 
  LOC_Os03g53960.1 111 WNADEEILLLEGIEMYGLGNWAEVAEHVG-TKTKAQCIDHYT 151
                       *****************************.**********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0250242.1E-18537566IPR016827Transcriptional adaptor 2
SMARTSM002911.6E-104792IPR000433Zinc finger, ZZ-type
PfamPF005693.3E-94990IPR000433Zinc finger, ZZ-type
CDDcd023352.79E-265199No hitNo description
PROSITE profilePS5013510.8245194IPR000433Zinc finger, ZZ-type
SuperFamilySSF578502.71E-1451114No hitNo description
PROSITE patternPS0135705380IPR000433Zinc finger, ZZ-type
SuperFamilySSF466898.97E-13104157IPR009057Homeodomain-like
PROSITE profilePS5129322.533106158IPR017884SANT domain
SMARTSM007172.4E-11107156IPR001005SANT/Myb domain
PfamPF002492.7E-12110151IPR001005SANT/Myb domain
CDDcd001678.88E-12111152No hitNo description
Gene3DG3DSA:1.10.10.606.8E-9111153IPR009057Homeodomain-like
SuperFamilySSF466891.36E-22467559IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006357Biological Processregulation of transcription from RNA polymerase II promoter
GO:0009631Biological Processcold acclimation
GO:0009733Biological Processresponse to auxin
GO:0009735Biological Processresponse to cytokinin
GO:0016573Biological Processhistone acetylation
GO:0042127Biological Processregulation of cell proliferation
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003713Molecular Functiontranscription coactivator activity
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 571 aa     Download sequence    Send to blast
MGRSRGVPNS GDDETNHRSK RRRVASSGDA PDSLSAACGG AGEGGGKKAL YHCNYCNKDI  60
SGKIRIKCSK CPDFDLCVEC FSVGAEVTPH RSNHPYRVMD NLSFPLICPD WNADEEILLL  120
EGIEMYGLGN WAEVAEHVGT KTKAQCIDHY TTAYMNSPCY PLPDMSHVNG KNRKELLAMA  180
KVQGESKKGT SVLPGDLTPK DESPFSPPRV KVEDALGEGL AGRSPSHIAG GANKKASNVG  240
QFKDGANVAK VEDGHVDRSI GVKKPRYSAD EGPSLTELSG YNSKRHEFDP EYDNDAEQAL  300
AEMEFKETDS ETDRELKLRV LRIYLSRLDE RKRRKEFILE RNLLFPNPLE KDLTNEDKEV  360
YHRYKVFMRF LSKEEHEALV RSVLEERKIR RRIQELQECR SAGCRTLAEA KIHIEQKRKK  420
EHEVNAQKAK ESGQLLSNTK VVHKTNRPMK IESDGNLDQK KGGASLDSTG RDSPKTTGHA  480
GTKHWDDWDI VGFPGAELLS TSEKNLCCQN RLLPNHYLKM QEVLMQEIFK GSVAKKEDAH  540
VLFKVDPAKV DNVYDMVTKK LGTNEEAPTV *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6cw2_C3e-38511665120Transcriptional adapter 2
6cw3_E4e-38511665120Transcriptional adapter 2
6cw3_G4e-38511665120Transcriptional adapter 2
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
11923KRRRV
2330335RKRRKE
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.592660.0callus| flower| leaf| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329826200.0
Expression AtlasB9FBU4-
Functional Description ? help Back to Top
Source Description
UniProtRequired for the function of some acidic activation domains, which activate transcription from a distant site. The exact mechanism of action is not yet known. ADA2 and GCN5 function to acetylate nucleosomes, opening up the promoter region (By similarity). {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g53960.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g53960
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0725970.0AK072597.1 Oryza sativa Japonica Group cDNA clone:J023128E10, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015631988.10.0transcriptional adapter ADA2
SwissprotQ75LL60.0TADA2_ORYSJ; Transcriptional adapter ADA2
TrEMBLA0A0E0P1D30.0A0A0E0P1D3_ORYRU; Transcriptional adapter
TrEMBLB8AJW80.0B8AJW8_ORYSI; Transcriptional adapter
TrEMBLB9FBU40.0B9FBU4_ORYSJ; Transcriptional adapter
STRINGORUFI03G35760.10.0(Oryza rufipogon)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP77083847
Representative plantOGRP2480912
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]