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_Os04g35800.1
Common NameLOC4335921, OJ000114_01.2, Os04g0438700
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: 347aa    MW: 38697.9 Da    PI: 9.6572
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g35800.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH20.11.1e-06283306126
                       --S---SGGGGTS--TTTTT-SS-SS CS
           zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHg 26 
                       y+ e Cr++++   C++ ++C+FaH+
  LOC_Os04g35800.1 283 YGVEVCRDYLK-NMCNR-ESCRFAHP 306
                       899********.*****.*******9 PP
2zf-CCCH19.12.4e-06317339327
                       S---SGGGGTS--TTTTT-SS-SSS CS
           zf-CCCH   3 telCrffartGtCkyGdrCkFaHgp 27 
                        e Cr+f r G+C++ + C+F H+p
  LOC_Os04g35800.1 317 VEVCRDFKR-GECNR-PACRFYHPP 339
                       589******.*****.*******96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.183103131IPR000571Zinc finger, CCCH-type
SMARTSM003560.037103130IPR000571Zinc finger, CCCH-type
PfamPF146080.1109129No hitNo description
PROSITE profilePS5010311.836138165IPR000571Zinc finger, CCCH-type
SMARTSM003560.21138164IPR000571Zinc finger, CCCH-type
PfamPF146083.5150163No hitNo description
Gene3DG3DSA:4.10.1000.104.1E-6179207IPR000571Zinc finger, CCCH-type
SMARTSM003565.3E-4181208IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.807181209IPR000571Zinc finger, CCCH-type
SMARTSM003560.73212236IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.291216237IPR000571Zinc finger, CCCH-type
PfamPF146082.1217234No hitNo description
Gene3DG3DSA:4.10.1000.105.8E-4281305IPR000571Zinc finger, CCCH-type
SMARTSM003564.7E-4282307IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.338282308IPR000571Zinc finger, CCCH-type
PfamPF146080.012288306No hitNo description
PROSITE profilePS5010312.596314340IPR000571Zinc finger, CCCH-type
SMARTSM003565.4E-4314339IPR000571Zinc finger, CCCH-type
PfamPF146080.13320338No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009009anatomyplant embryo
PO:0001081developmental stagemature plant embryo stage
PO:0007042developmental stagewhole plant fruit formation stage
Sequence ? help Back to Top
Protein Sequence    Length: 347 aa     Download sequence    Send to blast
MASAETPNPD AEIPNTDAAA AADPAAAAPA AAATDPAAAG SPSPPLPPRK RRLSPTPSPT  60
RRSSRSRSRS PRRGRSRSRS RSRSRGRSAS PRYPDGKRRR HNDLNVEVCR DFLRDRCARA  120
DIECKYAHPH PTVAVDRDSK VTACADSLRN NCFRGRTCRY YHPPPHIQES LLRSIGVEDP  180
KVKMQVCRDF TRGRCSRSAN ECRFLHHSPL EDCAIVCQDF LRGRCDRKSC RYSHVMAHPM  240
PPPMRDIPMQ YPDMVYMPPP APLGVPMMMP PPSAPAAFSG NNYGVEVCRD YLKNMCNRES  300
CRFAHPDLNN EVMNTQVEVC RDFKRGECNR PACRFYHPPA SSNSIG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5u6h_A2e-141041711479Muscleblind-like protein 1
5u9b_A2e-141041711479Muscleblind-like protein 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
17686RSRSRSRSRGR
27886RSRSRSRGR
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.510940.0callus| leaf| panicle| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329706520.0
Expression AtlasQ0JD07-
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g35800.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g35800
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0606340.0AK060634.1 Oryza sativa Japonica Group cDNA clone:001-027-B10, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015636416.10.0zinc finger CCCH domain-containing protein 28 isoform X1
RefseqXP_015636417.10.0zinc finger CCCH domain-containing protein 28 isoform X1
RefseqXP_025880587.10.0zinc finger CCCH domain-containing protein 28 isoform X1
SwissprotQ0JD070.0C3H28_ORYSJ; Zinc finger CCCH domain-containing protein 28
TrEMBLI1PLI00.0I1PLI0_ORYGL; Uncharacterized protein
STRINGOS04T0438700-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP109041922
Representative plantOGRP1013666
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]