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 ONIVA05G27760.1
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: 148aa    MW: 16693.9 Da    PI: 4.8167
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA05G27760.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH31.14e-101438226
                     -S---SGGGGTS--TTTTT-SS-SS CS
          zf-CCCH  2 ktelCrffartGtCkyGdrCkFaHg 26
                     ++++C+f+++ G C++GdrC++ H 
  ONIVA05G27760.1 14 DRVNCPFYFKIGACRHGDRCSRLHN 38
                     6899********************7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.0651240IPR000571Zinc finger, CCCH-type
SMARTSM003560.00681339IPR000571Zinc finger, CCCH-type
PfamPF006421.0E-71438IPR000571Zinc finger, CCCH-type
PRINTSPR018483.5E-431837IPR009145U2 auxiliary factor small subunit
PRINTSPR018483.5E-433757IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3301.6E-2044132IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018483.5E-437590IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549285.57E-1277132IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018483.5E-43103125IPR009145U2 auxiliary factor small subunit
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000398Biological ProcessmRNA splicing, via spliceosome
GO:0089701Cellular ComponentU2AF
GO:0000166Molecular Functionnucleotide binding
GO:0003723Molecular FunctionRNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 148 aa     Download sequence    Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHNRP TVSPTIVLAN MYQRPDMITP  60
GVDAQGQPID PEKMQEHFED FYEDIYEELS KFGEVETLNV CDNLADHMIG NVYVQFREEE  120
QAVAAHNALQ GSLRRTAATV GATVILCM
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A3e-4411251120Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtNecessary for the splicing of pre-mRNA. {ECO:0000250}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1241430.0AC124143.2 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone OSJNBb0053D02, complete sequence.
GenBankAK0701980.0AK070198.1 Oryza sativa Japonica Group cDNA clone:J023041B11, full insert sequence.
GenBankAK1047670.0AK104767.1 Oryza sativa Japonica Group cDNA clone:001-039-A01, full insert sequence.
GenBankAP0149610.0AP014961.1 Oryza sativa Japonica Group DNA, chromosome 5, cultivar: Nipponbare, complete sequence.
GenBankY183480.0Y18348.1 Oryza sativa mRNA for U2 snRNP auxiliary factor, small subunit 35b.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015639721.13e-95splicing factor U2af small subunit B
RefseqXP_015639722.13e-95splicing factor U2af small subunit B
SwissprotQ6AUG02e-96U2AFB_ORYSJ; Splicing factor U2af small subunit B
TrEMBLA0A0E0HIG91e-108A0A0E0HIG9_ORYNI; Uncharacterized protein
STRINGONIVA05G27760.11e-109(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP126133
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G44785.14e-30C3H 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. Domon C,Lorković ZJ,Valcárcel J,Filipowicz W
    Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants.
    J. Biol. Chem., 1998. 273(51): p. 34603-10
    [PMID:9852132]