PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID ONIVA12G04960.1
Organism
Oryza nivara
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
Family C3H
Protein Properties Length: 550aa    MW: 62890.2 Da    PI: 6.8352
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA12G04960.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH24.54.9e-082850527
                     --SGGGGTS--TTTTT-SS-SSS CS
          zf-CCCH  5 lCrffartGtCkyGdrCkFaHgp 27
                      C +++r+G CkyG +C+F+H+p
  ONIVA12G04960.1 28 DCLHYLRFGRCKYGMNCRFNHPP 50
                     699******************96 PP
2zf-CCCH35.32e-1190115126
                      --S---SGGGGTS--TTTTT-SS-SS CS
          zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHg 26 
                      ++t lC++++  G+Ck+G++CkF+H+
  ONIVA12G04960.1  90 PGTGLCSYYMNRGICKFGSNCKFHHP 115
                      5799*********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.8822351IPR000571Zinc finger, CCCH-type
SMARTSM003560.00792350IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.44E-52553IPR000571Zinc finger, CCCH-type
PfamPF006423.4E-52850IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.109.5E-42950IPR000571Zinc finger, CCCH-type
SMARTSM003562.8E-589116IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.50789117IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.31E-690116IPR000571Zinc finger, CCCH-type
PfamPF006426.5E-991115IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.103.1E-592114IPR000571Zinc finger, CCCH-type
SuperFamilySSF483713.17E-33305488IPR016024Armadillo-type fold
Gene3DG3DSA:1.25.40.1801.2E-32308467IPR016021MIF4G-like domain
PfamPF028546.2E-25313469IPR003890MIF4G-like, type 3
SMARTSM005431.1E-11313541IPR003890MIF4G-like, type 3
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003723Molecular FunctionRNA binding
GO:0005515Molecular Functionprotein binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 550 aa     Download sequence    Send to blast
MGCLYNHPAK HAGGCDKLEH PQRPGEHDCL HYLRFGRCKY GMNCRFNHPP DRLPQQQVYF  60
PWKACHCHHS EGKSEAEHVK LNFLGLPLRP GTGLCSYYMN RGICKFGSNC KFHHPNSGSG  120
HEKWDGSLQT NQISSGVNIY SVLDHGELNE QPVPSIDDFQ RGNSCFQPAE QTRYTRDQLL  180
KLRETVDVPK DIMKLIQDIN VELRAEDESR APNETNYVPT LSYKRFQETD SHDWHSRSLQ  240
TPVVAEEEKS QDDTREAKEP YAFGWKQKEF NKQDQKSFQS DSKAQAGPTL ALHKAEDPWS  300
IQRSTVPEKY KVLKTVKGIL NLLTPEKFDI LKDQLIEAGI TRTDILKDVI DLILEKAVAE  360
PTLCPMYAQF CSYLNENLTA FPPKDTHCEQ ITFKQALSDK CQQAFEIARN VRADIYKLTG  420
REQEMERRDK ERLVKHQILG KIRLIRDLLK QKMVPDKIVH HIAQAVTDCE NFHFEPLENV  480
DLLNIIFDGV LDSVLPGTEA NKVVNAIIGI EKCSIASNDA GIIHKDVNRR NEEAKLQKSS  540
NDIPNNLIDP
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4iul_A4e-1531246822182Eukaryotic translation initiation factor 4 gamma 2
4iul_B4e-1531246822182Eukaryotic translation initiation factor 4 gamma 2
Search in ModeBase
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1194530.0AK119453.1 Oryza sativa Japonica Group cDNA clone:001-133-D12, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015641846.10.0zinc finger CCCH domain-containing protein 42 isoform X1
SwissprotQ5Z5Q30.0C3H43_ORYSJ; Zinc finger CCCH domain-containing protein 43
TrEMBLA2YDI50.0A2YDI5_ORYSI; Uncharacterized protein
STRINGONIVA12G04960.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP143301322
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G32930.13e-24zinc finger nuclease 2
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]