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 RrC1891_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family C3H
Protein Properties Length: 131aa    MW: 14835.8 Da    PI: 4.633
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1891_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH31.43.3e-101438226
                -S---SGGGGTS--TTTTT-SS-SS CS
     zf-CCCH  2 ktelCrffartGtCkyGdrCkFaHg 26
                ++++C+f+++ G C++GdrC++ H 
  RrC1891_p1 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
PfamPF006428.5E-81438IPR000571Zinc finger, CCCH-type
SuperFamilySSF902298.11E-51641IPR000571Zinc finger, CCCH-type
PRINTSPR018488.7E-431837IPR009145U2 auxiliary factor small subunit
PRINTSPR018488.7E-433757IPR009145U2 auxiliary factor small subunit
PROSITE profilePS501028.7444131IPR000504RNA recognition motif domain
Gene3DG3DSA:3.30.70.3308.3E-2044131IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018488.7E-437590IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549284.34E-1077131IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018488.7E-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: 131 aa     Download sequence    Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHNRP TISPTLLLSN MYQRPDMITP  60
GVDPQGQPLD PSKIQAHFED FYEDIFEELD KFGEMESLNV CDNLADHMIG NVYVLFKEED  120
QAAAALKALQ G
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A7e-4511311126Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtNecessary for the splicing of pre-mRNA (By similarity). Probably active at the 3' splice sites. {ECO:0000250}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013606215.12e-95PREDICTED: splicing factor U2af small subunit B
SwissprotQ9FMY54e-85U2AFB_ARATH; Splicing factor U2af small subunit B
TrEMBLA0A0D3E6435e-94A0A0D3E643_BRAOL; Uncharacterized protein
STRINGBo9g058670.18e-95(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM2112344
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G44785.11e-31C3H family protein
Publications ? help Back to Top
  1. Day IS, et al.
    Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: insights into regulated splicing.
    Plant J., 2012. 71(6): p. 936-47
    [PMID:22563826]
  2. Kim DW,Jeon SJ,Hwang SM,Hong JC,Bahk JD
    The C3H-type zinc finger protein GDS1/C3H42 is a nuclear-speckle-localized protein that is essential for normal growth and development in Arabidopsis.
    Plant Sci., 2016. 250: p. 141-153
    [PMID:27457991]
  3. Park HY, et al.
    The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms.
    Plant Cell Rep., 2017. 36(7): p. 1113-1123
    [PMID:28432478]