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_Os06g49080.1
Common NameLOC4341994, OJ1215_E11.23, Os06g0704300
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 C3H
Protein Properties Length: 391aa    MW: 42663.1 Da    PI: 8.8792
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os06g49080.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH31.62.8e-10526325
                      S---SGGGGTS--TTTTT-SS-S CS
           zf-CCCH  3 telCrffartGtCkyGdrCkFaH 25
                      +e+Cr+f+r G CkyG++C++ H
  LOC_Os06g49080.1  5 QEICRNFQR-GSCKYGAQCRYLH 26
                      79*******.************* PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003561.0E-7228IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010316.906229IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.44E-5327IPR000571Zinc finger, CCCH-type
PfamPF006421.2E-7526IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.103.4E-7626IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005635Cellular Componentnuclear envelope
GO:0003677Molecular FunctionDNA binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009089anatomyendosperm
PO:0007042developmental stagewhole plant fruit formation stage
PO:0007633developmental stageendosperm development stage
Sequence ? help Back to Top
Protein Sequence    Length: 391 aa     Download sequence    Send to blast
MSRRQEICRN FQRGSCKYGA QCRYLHASPH QQQQQQQAKP NPFGFGTGSR QQQQPSFGSQ  60
FQQQQQQQQK PNPFGFGVQG ANAQSRNAPG PAKPFQNKWV RDPSAPTKQT EAVQPPQAQA  120
AHTSCEDPQS CRQQISEDFK NEAPIWKLTC YAHLRNGPCN IKGDISFEEL RAKAYEEGKQ  180
GHSLQSIVEG ERNLQNAKLM EFTNLLNSAR PSQTPSFPTM SSFPEVKNNS SFGASQTNGP  240
PVFSSFSQIG AATNIGPGPG TTAPGMPASS PFGHPSSAPL AAPTFGSSQM KFGVSSVFGN  300
QGSGQPFGSF QAPRFPSSKS PASSVQHRDI DRQSQELLNG MVTPPSVMFE ESVGNNKNEN  360
QDDSIWLKEK WAIGEIPLDE PPQRHVSHVF *
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.548860.0callus| flower| leaf| panicle| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1154698150.0
Expression AtlasQ5Z807-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the adaxial face of the collar, nodes and the basal region of elongating internodes. {ECO:0000269|PubMed:18953406}.
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional activator that binds double-stranded DNA and the single-stranded RNA polymers poly(rA), poly(rU) and poly(rG), but not poly(rC). Mediates optimal plant architecture through brassinosteroid (BR) signaling. May act as a negative regulator in sterol homeostasis (PubMed:18953406). Acts as negative regulator of BR signaling. Binds to the specific DNA sequence 5'-CTCGC-3' of BZR1 promoter and negatively regulates BZR1. Acts as an antagonistic transcription factor of BZR1 to attenuate the BR signaling pathway and regulate leaf bending. Represses the expression of ILI1, and activates that of IBH1 to balance the regulation activity of BZR1 (PubMed:22570626). {ECO:0000269|PubMed:18953406, ECO:0000269|PubMed:22570626}.
Function -- GeneRIF ? help Back to Top
  1. OsLIC may be a transcription activator to control rice plant architecture.
    [PMID: 18953406]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os06g49080.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by 24-epibrassinolide. {ECO:0000269|PubMed:18953406, ECO:0000269|PubMed:22570626}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs06g49080
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1070080.0AK107008.1 Oryza sativa Japonica Group cDNA clone:002-120-E10, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015641399.10.0zinc finger CCCH domain-containing protein 46
SwissprotQ5Z8070.0C3H46_ORYSJ; Zinc finger CCCH domain-containing protein 46
TrEMBLA0A0E0Q2B80.0A0A0E0Q2B8_ORYRU; Uncharacterized protein
TrEMBLB9FQS90.0B9FQS9_ORYSJ; Uncharacterized protein
STRINGOS06T0704300-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP94472829
Representative plantOGRP78131415
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G75340.14e-50C3H 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. Wang D, et al.
    Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.
    BMC Genomics, 2008. 9: p. 44
    [PMID:18221561]
  3. Wang L, et al.
    OsLIC, a Novel CCCH-Type Zinc Finger Protein with Transcription Activation, Mediates Rice Architecture via Brassinosteroids Signaling.
    PLoS ONE, 2008. 3(10): p. e3521
    [PMID:18953406]