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 Rsa1.0_04944.1_g00002.1
Organism
Raphanus sativus
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: 59aa    MW: 6698.6 Da    PI: 8.5111
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_04944.1_g00002.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH19.41.9e-061438226
                             -S---SGGGGTS--TTTTT-SS-SS CS
                  zf-CCCH  2 ktelCrffartGtCkyGdrCkFaHg 26
                             ++++C+ +++ G C++  rC+ +H 
  Rsa1.0_04944.1_g00002.1 14 DRVNCPVYFKIGACRHDTRCSSSHN 38
                             689*********************7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS501039.2441240IPR000571Zinc finger, CCCH-type
PRINTSPR018485.0E-161837IPR009145U2 auxiliary factor small subunit
PRINTSPR018485.0E-163757IPR009145U2 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:0003723Molecular FunctionRNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 59 aa     Download sequence    Send to blast
MAEHLASTFG TEKDRVNCPV YFKIGACRHD TRCSSSHNRP TISSTLLLSN LYQRPDQML
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A1e-18155155Splicing 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}.
UniProtNecessary for the splicing of pre-mRNA (By similarity). Probably active at the 3' splice sites. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_04944.1_g00002.1
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_018463526.16e-30PREDICTED: splicing factor U2af small subunit B, partial
RefseqXP_024170378.11e-28splicing factor U2af small subunit B
RefseqXP_024170379.11e-28splicing factor U2af small subunit B
RefseqXP_024170380.11e-28splicing factor U2af small subunit B
SwissprotQ9FMY57e-29U2AFB_ARATH; Splicing factor U2af small subunit B
SwissprotQ9S7098e-29U2AFA_ARATH; Splicing factor U2af small subunit A
TrEMBLA0A2P6PC103e-27A0A2P6PC10_ROSCH; Putative transcription factor C3H family
TrEMBLA0A3L6PQ211e-27A0A3L6PQ21_PANMI; Splicing factor U2af 38 kDa subunit
STRINGAES599413e-29(Medicago truncatula)
STRINGXP_010270687.12e-29(Nelumbo nucifera)
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
AT3G44785.18e-25C3H 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]