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 GSBRNA2T00083668001
Common NameGSBRNA2T00083668001
Organism
Brassica napus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C3H
Protein Properties Length: 141aa    MW: 16107.3 Da    PI: 11.8064
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00083668001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH33.47.9e-111438226
                         -S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH  2 ktelCrffartGtCkyGdrCkFaHg 26
                         ++++C+f+ ++G C++GdrC+++H 
  GSBRNA2T00083668001 14 DRVNCPFYNKMGACRHGDRCSRIHN 38
                         6899********************7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.4791240IPR000571Zinc finger, CCCH-type
SMARTSM003564.1E-41339IPR000571Zinc finger, CCCH-type
PfamPF006421.3E-81438IPR000571Zinc finger, CCCH-type
PRINTSPR018483.1E-151837IPR009145U2 auxiliary factor small subunit
PRINTSPR018483.1E-153757IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3307.6E-47099IPR012677Nucleotide-binding alpha-beta plait domain
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: 141 aa     Download sequence    Send to blast
MAEHLASIYG TEKDRVNCPF YNKMGACRHG DRCSRIHNRP AISPTLLLSN MRRPAQDPRA  60
FRGSIRGAQE FKEEDQAAAA LQALQGRSYL GRPIIGEFSP IVSREKRRKL FGRRSYRRGS  120
RSRSISPRGR REYGRRDRDS *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A1e-2211021142Splicing 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00083668001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1895557e-70AC189555.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH006E24, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018447245.18e-42PREDICTED: splicing factor U2af small subunit A
RefseqXP_018447246.18e-42PREDICTED: splicing factor U2af small subunit A
SwissprotQ9ZQW83e-37U2AFA_ORYSJ; Splicing factor U2af small subunit A
TrEMBLA0A078I8T36e-96A0A078I8T3_BRANA; BnaC05g21650D protein
STRINGBo5g054590.12e-64(Brassica oleracea)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G44785.12e-27C3H 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. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]
  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]