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_Os02g42950.1
Common NameLOC4330130, OJ1282_H11.2, Os02g0643200, OsJ_007454, YAB4
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 YABBY
Protein Properties Length: 257aa    MW: 27021.8 Da    PI: 8.0253
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g42950.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY216.58.5e-67202125170
             YABBY   5 ssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshl.deslkee.....................lleel 75 
                       s +eq+Cyv+Cn C+tilav vP +slfk+vtvrCGhC++llsvnl+      +a     + ++ ++                     l+e+ 
  LOC_Os02g42950.1  20 SPTEQLCYVHCNCCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAPAPAPAnQLHFGPSllsptsphglldevafqtpslLMEQA 112
                       579********************************************9996666544320445555577778999977777776665323322 PP

             YABBY  76 kveeenlksnvekeesastsvssekl....senedeevprvpp..virPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWah 162
                        +++ +  +  +++++as+  +++++    + +++ e+p+  p  ++rPPekrqrvPsaynrfik+eiqrika+nPdishreafsaaaknWah
  LOC_Os02g42950.1 113 ASASLSSITGRSSSSCASNA-PAMQMppakPVQQEPELPKNAPasANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAH 204
                       22222222222233333333.3333478777888899999877678*********************************************** PP

             YABBY 163 fPkihfgl 170
                       fP+ihfgl
  LOC_Os02g42950.1 205 FPHIHFGL 212
                       ******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046901.1E-7021212IPR006780YABBY protein
SuperFamilySSF470954.71E-8150205IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.102.5E-4161204IPR009071High mobility group box domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009909Biological Processregulation of flower development
GO:0009933Biological Processmeristem structural organization
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010093Biological Processspecification of floral organ identity
GO:0010154Biological Processfruit development
GO:0010158Biological Processabaxial cell fate specification
GO:0010159Biological Processspecification of organ position
GO:0010450Biological Processinflorescence meristem growth
GO:1902183Biological Processregulation of shoot apical meristem development
GO:2000024Biological Processregulation of leaf development
GO:0005634Cellular Componentnucleus
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009037anatomylemma
PO:0001047developmental stagelemma development stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 257 aa     Download sequence    Send to blast
MSSSSSSSAV FPLDHLAAPS PTEQLCYVHC NCCDTILAVG VPCSSLFKTV TVRCGHCANL  60
LSVNLRGLLL PAPAPAPANQ LHFGPSLLSP TSPHGLLDEV AFQTPSLLME QAASASLSSI  120
TGRSSSSCAS NAPAMQMPPA KPVQQEPELP KNAPASANRP PEKRQRVPSA YNRFIKDEIQ  180
RIKAGNPDIS HREAFSAAAK NWAHFPHIHF GLMPDQGFKK TFKPQDGSED ILLKDSLYAA  240
AAAAAAAAAN MGVTPF*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.547930.0panicle| seed
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ6H668
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Preferentially expressed in immature organs containing meristems and organ primordia. Expressed in phloem of developing vascular tissues of young seedling shoots. Expressed in the phloem of midvein vasculature of young leaves. Does not show polar expression pattern in leaf primordia. {ECO:0000269|PubMed:17216490, ECO:0000269|PubMed:17676337}.
Functional Description ? help Back to Top
Source Description
UniProtSeems to be associated with phloem cell differentiation. {ECO:0000269|PubMed:17676337}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00620PBMTransfer from AT2G45190Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os02g42950.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs02g42950
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB2740160.0AB274016.1 Oryza sativa Japonica Group OsYABBY4 mRNA for OsYABBY4 protein, complete cds.
GenBankAK1067840.0AK106784.1 Oryza sativa Japonica Group cDNA clone:002-115-H10, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015622736.10.0protein YABBY 4
SwissprotA2X7Q30.0YAB4_ORYSI; Protein YABBY 4
SwissprotQ6H6680.0YAB4_ORYSJ; Protein YABBY 4
TrEMBLA0A0D3F8510.0A0A0D3F851_9ORYZ; Uncharacterized protein
TrEMBLA0A0D9YVL20.0A0A0D9YVL2_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0CP170.0A0A0E0CP17_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0GAC60.0A0A0E0GAC6_ORYNI; Uncharacterized protein
TrEMBLI1P2J50.0I1P2J5_ORYGL; Uncharacterized protein
STRINGOGLUM02G26190.10.0(Oryza glumipatula)
STRINGOMERI02G24350.10.0(Oryza meridionalis)
STRINGOS02T0643200-010.0(Oryza sativa)
STRINGONIVA02G28110.10.0(Oryza nivara)
STRINGORGLA02G0220100.10.0(Oryza glaberrima)
STRINGOBART02G25670.10.0(Oryza barthii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP144538121
Representative plantOGRP46851123
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G45190.14e-61YABBY family protein
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]
  2. Toriba T, et al.
    Molecular characterization the YABBY gene family in Oryza sativa and expression analysis of OsYABBY1.
    Mol. Genet. Genomics, 2007. 277(5): p. 457-68
    [PMID:17216490]
  3. Liu HL,Xu YY,Xu ZH,Chong K
    A rice YABBY gene, OsYABBY4, preferentially expresses in developing vascular tissue.
    Dev. Genes Evol., 2007. 217(9): p. 629-37
    [PMID:17676337]
  4. Yang C,Ma Y,Li J
    The rice YABBY4 gene regulates plant growth and development through modulating the gibberellin pathway.
    J. Exp. Bot., 2016. 67(18): p. 5545-5556
    [PMID:27578842]