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_Os05g50080.1
Common NameLOC4339693, OJ1126_B10.1, OJ1268_B08.22, Os05g0576300, OsJ_19647
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: 344aa    MW: 37169.1 Da    PI: 8.4178
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os05g50080.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH48.41.5e-15269294126
                       --S---SGGGGTS--TTTTT-SS-SS CS
           zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHg 26 
                       +ktelC+ + +tG C+yGd+C+FaHg
  LOC_Os05g50080.1 269 FKTELCNKWEETGACPYGDQCQFAHG 294
                       79***********************9 PP
2zf-CCCH23.78.6e-08307332126
                       --S---SGGGGTS--TTTTT-SS-SS CS
           zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHg 26 
                       ykt  Cr  +++G C+yG rC+F H+
  LOC_Os05g50080.1 307 YKTQVCRMVLAGGVCPYGHRCHFRHS 332
                       9**********************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1000.109.3E-19263301IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.31E-10265300IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.601268296IPR000571Zinc finger, CCCH-type
SMARTSM003567.2E-10268295IPR000571Zinc finger, CCCH-type
PfamPF006421.1E-12269294IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.101.5E-12302332IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.15E-8302334IPR000571Zinc finger, CCCH-type
SMARTSM003568.9E-5306333IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.685306334IPR000571Zinc finger, CCCH-type
PfamPF006424.3E-5307332IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0051511Biological Processnegative regulation of unidimensional cell growth
GO:0061158Biological Process3'-UTR-mediated mRNA destabilization
GO:1901347Biological Processnegative regulation of secondary cell wall biogenesis
GO:0005829Cellular Componentcytosol
GO:0003677Molecular FunctionDNA binding
GO:0003730Molecular FunctionmRNA 3'-UTR binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0020048anatomymicrospore
PO:0001009developmental stageD pollen mother cell meiosis stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 344 aa     Download sequence    Send to blast
MQEALLPPAH PGRFYSDFGP KPFGSGDQRL SSPNLLTNGG DLFYGCYSPF SPTRVLSPPP  60
PRRAASFSHC SSSSDSVVDD GDGAGAAAAT EHRLHLAHLA LQYQEMANRF ELCLSHLADA  120
ADEAAALRQE NAELRVANND LACRIAKFGG RQSSAIALAG DLRRLRLPKE QTVPALPPPP  180
QSPPAALMNP VAVPEKQAVL PKSISIRSTG YQKLNQGGKH RVSKPVNVGS QRVFVGIDGA  240
EGGEHKVGVK KEEPPMGGLE FEVYNQGMFK TELCNKWEET GACPYGDQCQ FAHGVAELRP  300
VIRHPRYKTQ VCRMVLAGGV CPYGHRCHFR HSITPADRFS FGH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1rgo_A2e-22269332467Butyrate response factor 2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.546440.0callus| panicle
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329915630.0
Expression AtlasQ6L5G1-
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os05g50080.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs05g50080
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1063540.0AK106354.1 Oryza sativa Japonica Group cDNA clone:002-102-A03, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015640820.10.0zinc finger CCCH domain-containing protein 39
SwissprotQ6L5G10.0C3H39_ORYSJ; Zinc finger CCCH domain-containing protein 39
TrEMBLA0A0E0HIW00.0A0A0E0HIW0_ORYNI; Uncharacterized protein
TrEMBLA0A0E0PRL80.0A0A0E0PRL8_ORYRU; Uncharacterized protein
TrEMBLB8AX890.0B8AX89_ORYSI; Uncharacterized protein
STRINGORUFI05G28740.10.0(Oryza rufipogon)
STRINGOS05T0576300-010.0(Oryza sativa)
STRINGONIVA05G28820.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP27753784
Representative plantOGRP20581636
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G66810.11e-58C3H 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. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]
  3. Wang D, et al.
    Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.
    BMC Genomics, 2008. 9: p. 44
    [PMID:18221561]