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 GSBRNA2T00156103001
Common NameGSBRNA2T00156103001
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: 437aa    MW: 50922.6 Da    PI: 8.0189
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00156103001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH246.6e-08153172625
                          -SGGGGTS--TTTTT-SS-S CS
              zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                          C+f+++tG C++G+rC++ H
  GSBRNA2T00156103001 153 CPFHLKTGACRFGPRCSRVH 172
                          ******************99 PP
2zf-CCCH19.12.4e-062322461327
                          S--TTTTT-SS-SSS CS
              zf-CCCH  13 GtCkyGdrCkFaHgp 27 
                           tC++G+ C+F+Hg+
  GSBRNA2T00156103001 232 KTCSRGSACNFIHGF 246
                          49***********95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.512147175IPR000571Zinc finger, CCCH-type
PfamPF006428.1E-6152172IPR000571Zinc finger, CCCH-type
PRINTSPR018481.4E-15153172IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.4E-15172192IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3302.3E-5178236IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018481.4E-15209224IPR009145U2 auxiliary factor small subunit
PROSITE profilePS501036.85233247IPR000571Zinc finger, CCCH-type
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: 437 aa     Download sequence    Send to blast
MSRKEKRKAM KKMKRKEVAE KEREDAEAKL NDPAEQEKLK EIEEEEAKKR DKESKEFEDS  60
ERAWREAMER RCKDLEASRR GPPDIIFKGN EIILRKNKVK VPKKPVAAQV DVNEIVDRPT  120
SNPLPPGIEA FSKYQNFSSA QQILDTEQDK AHCPFHLKTG ACRFGPRCSR VHFHPDKSCT  180
ILMKNMYNGP GIAWEQEDEG LEYTDEEAEH FYEEFYEDVT EFQKYGELIN FKTCSRGSAC  240
NFIHGFLNPG GDYEWADHDK PPPRFWIRKM TALFGYSDEY VKHMEFEYSG SLTDFRSDQP  300
TDSHRQLSRR SRSRDHDHVN VGSKPCHRNS KNHCDSTRGH KLSRHEEKRH GGDESPTSTR  360
DGSLEKEIYK ERRYAKETTR HESKWSEHSH GQRVMKKRIN GRYPVDDSPD GDDDGRGETG  420
HRRKSSKRHA GKETMP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A1e-15138234396Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00156103001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2266842e-75AK226684.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL07-54-F13.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009144452.10.0PREDICTED: zinc finger CCCH domain-containing protein 5-like
SwissprotQ9SY741e-171C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLM4DTV10.0M4DTV1_BRARP; Uncharacterized protein
STRINGBra019944.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM59752025
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.16e-60C3H family protein
Publications ? help Back to Top
  1. Lorković ZJ,Wieczorek Kirk DA,Lambermon MH,Filipowicz W
    Pre-mRNA splicing in higher plants.
    Trends Plant Sci., 2000. 5(4): p. 160-7
    [PMID:10740297]
  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]