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_Os02g42950.2
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: 149aa    MW: 15828.9 Da    PI: 9.9479
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g42950.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY135.47.1e-422310495170
             YABBY  95 svssekl....senedeevprvpp..virPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170
                       + +++++    + +++ e+p+  p  ++rPPekrqrvPsaynrfik+eiqrika+nPdishreafsaaaknWahfP+ihfgl
  LOC_Os02g42950.2  23 NAPAMQMppakPVQQEPELPKNAPasANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 104
                       222333345557788888998877678*****************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046901.5E-3916104IPR006780YABBY protein
SuperFamilySSF470951.57E-84297IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.109.5E-55396IPR009071High 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: 149 aa     Download sequence    Send to blast
MEQAASASLS SITGRSSSSC ASNAPAMQMP PAKPVQQEPE LPKNAPASAN RPPEKRQRVP  60
SAYNRFIKDE IQRIKAGNPD ISHREAFSAA AKNWAHFPHI HFGLMPDQGF KKTFKPQDGS  120
EDILLKDSLY AAAAAAAAAA ANMGVTPF*
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_Os02g42950.2
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_015622736.11e-103protein YABBY 4
SwissprotA2X7Q31e-104YAB4_ORYSI; Protein YABBY 4
SwissprotQ6H6681e-104YAB4_ORYSJ; Protein YABBY 4
TrEMBLA0A0D3F8511e-102A0A0D3F851_9ORYZ; Uncharacterized protein
TrEMBLA0A0D9YVL21e-102A0A0D9YVL2_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0CP171e-102A0A0E0CP17_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0GAC61e-102A0A0E0GAC6_ORYNI; Uncharacterized protein
TrEMBLA0A0E0NID71e-102A0A0E0NID7_ORYRU; Uncharacterized protein
TrEMBLI1P2J51e-102I1P2J5_ORYGL; Uncharacterized protein
STRINGOGLUM02G26190.11e-103(Oryza glumipatula)
STRINGOMERI02G24350.11e-103(Oryza meridionalis)
STRINGORUFI02G27080.11e-103(Oryza rufipogon)
STRINGOS02T0643200-011e-103(Oryza sativa)
STRINGONIVA02G28110.11e-103(Oryza nivara)
STRINGORGLA02G0220100.11e-103(Oryza glaberrima)
STRINGOBART02G25670.11e-103(Oryza barthii)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G45190.15e-45YABBY 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]