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_Os04g27960.1
Common NameOs04g0346900, OSJNBa0020I02.5
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 B3
Protein Properties Length: 418aa    MW: 45375.6 Da    PI: 9.8565
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g27960.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B343.17.7e-1424116498
                       E-..-HHHHTT-EE--HHH.HTT.....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
                B3   4 vltpsdvlksgrlvlpkkfaeeh.....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                       vl+ps+  k   +++  + a++      gg  ++  t ++ ++ g+ W+v + +r ++gr +l++GW eF+ a+gL +g fvv+++    ++ 
  LOC_Os04g27960.1  24 VLVPSSFRK---MRICDELAAQLgvgvgGGGAPRAATARVASPLGKAWDVGV-VRDGDGRAFLGRGWAEFAAAHGLGVGWFVVLRH---GGGV 109
                       555555444...568888887779999955566888****************.688888899***********************6...4566 PP

                       .EEEEE- CS
                B3  92 lvvkvfr 98 
                       l v +f+
  LOC_Os04g27960.1 110 LAVEAFD 116
                       6777776 PP
2B346.47.3e-151532241486
                       T-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                B3  14 grlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                       + +++p kf++++  g++ +s + ++ ++ g+sW+v+l  +k +++++l++GW +F + +g+  gD+v+F++ g
  LOC_Os04g27960.1 153 DKMRIPDKFVRDYiTGENLNSNMAIILSPLGKSWRVEL--DKDQSGVFLGGGWLQFLSFHGISRGDVVIFSVFG 224
                       5699**********555567889999************..******************************9655 PP
3B379.73.1e-25310404184
                       EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS............-EEEEEE..EEETTE.EEE-TTHHHHHHHHT--TT-EE CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesg............rsWevkliyrkksgr.yvltkGWkeFvkangLkegDfv 80 
                       ++k++++++vl++++l+l ++f+e++g+++e+s+tl++ d+++            rsWev+   r+++++ y+l++GW++F+++ng+++gD++
  LOC_Os04g27960.1 310 WIKKEINEYVLERCILSLARTFCESIGLVEESSITLMMIDTTStqgdqggsssssRSWEVTG--RRYKDAcYLLGAGWRRFCEDNGVRSGDVC 400
                       789*************************************99999*****************..9999999********************** PP

                       EEEE CS
                B3  81 vFkl 84 
                       vF++
  LOC_Os04g27960.1 401 VFTV 404
                       **95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM010190.0321118IPR003340B3 DNA binding domain
SuperFamilySSF1019362.16E-1122110IPR015300DNA-binding pseudobarrel domain
PfamPF023625.0E-1123116IPR003340B3 DNA binding domain
CDDcd100171.46E-1023116No hitNo description
Gene3DG3DSA:2.40.330.107.3E-1223120IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS508639.61565118IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.109.6E-15136223IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.3E-16137225IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086311.73140243IPR003340B3 DNA binding domain
CDDcd100177.08E-15141228No hitNo description
SMARTSM010191.2E-8143238IPR003340B3 DNA binding domain
PfamPF023624.4E-13153224IPR003340B3 DNA binding domain
SuperFamilySSF1019361.84E-14306415IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.9E-16307415IPR015300DNA-binding pseudobarrel domain
PfamPF023622.8E-14310405IPR003340B3 DNA binding domain
PROSITE profilePS5086311.801310417IPR003340B3 DNA binding domain
SMARTSM010191.0E-4311415IPR003340B3 DNA binding domain
CDDcd100172.40E-7315403No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 418 aa     Download sequence    Send to blast
MGSRGDHGGG GGGRGAARAT QLKVLVPSSF RKMRICDELA AQLGVGVGGG GAPRAATARV  60
ASPLGKAWDV GVVRDGDGRA FLGRGWAEFA AAHGLGVGWF VVLRHGGGVL AVEAFDTTCC  120
LRVFGAPPAE AGRATDTSRK PQFLTVLLPG IMDKMRIPDK FVRDYITGEN LNSNMAIILS  180
PLGKSWRVEL DKDQSGVFLG GGWLQFLSFH GISRGDVVIF SVFGPNGRQK DFKAKGISIY  240
QGTGEQQEAP SFSRRKCNNK KKSRFGEDDG NQQEMPCSRK GSGNKGRTSD RETKRMRKTR  300
SVYEIGPRSW IKKEINEYVL ERCILSLART FCESIGLVEE SSITLMMIDT TSTQGDQGGS  360
SSSSRSWEVT GRRYKDACYL LGAGWRRFCE DNGVRSGDVC VFTVLDTTLW RVDIERC*
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ7XS75
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g27960.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g27960
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAL6629631e-160AL662963.3 Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBa0020I02, complete sequence.
GenBankAP0149601e-160AP014960.1 Oryza sativa Japonica Group DNA, chromosome 4, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025881011.10.0putative B3 domain-containing protein Os04g0346900
SwissprotQ7XS750.0Y4469_ORYSJ; Putative B3 domain-containing protein Os04g0346900
TrEMBLA0A0E0GZC20.0A0A0E0GZC2_ORYNI; Uncharacterized protein
TrEMBLB8ASH00.0B8ASH0_ORYSI; Uncharacterized protein
STRINGONIVA04G06690.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP42535187
Representative plantOGRP10106410
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G00260.15e-14B3 family protein