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 GSBRNA2T00117437001
Common NameGSBRNA2T00117437001
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: 245aa    MW: 28291.3 Da    PI: 10.6996
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00117437001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH30.18.3e-101438226
                         -S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH  2 ktelCrffartGtCkyGdrCkFaHg 26
                         ++++C+f+++ G C++GdrC++ H 
  GSBRNA2T00117437001 14 DRVNCPFYFKIGACRHGDRCSRLHN 38
                         6899********************7 PP
2zf-CCCH20.58.5e-0796119226
                          -S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH   2 ktelCrffartGtCkyGdrCkFaHg 26 
                          +++ Cr + +   C++G+ C+F+H+
  GSBRNA2T00117437001  96 REATCRQYEE-NNCNRGGYCNFMHV 119
                          6789**9999.*************8 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
PfamPF006422.1E-71438IPR000571Zinc finger, CCCH-type
PRINTSPR018482.0E-211837IPR009145U2 auxiliary factor small subunit
PRINTSPR018482.0E-213757IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549281.52E-562100IPR012677Nucleotide-binding alpha-beta plait domain
Gene3DG3DSA:3.30.70.3303.9E-46291IPR012677Nucleotide-binding alpha-beta plait domain
SMARTSM003560.008794120IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.69594121IPR000571Zinc finger, CCCH-type
PfamPF006421.1E-496120IPR000571Zinc 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: 245 aa     Download sequence    Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHNRP TISPTLLLSN MYQRPDMITP  60
GFKEEDQAAA ALQALQGRFY SGRPIIADFS PVTDFREATC RQYEENNCNR GGYCNFMHVK  120
LVSRELRRKL FGRSRRSYRR GSGSRSRSRS ISPRHKREYD WRDPPHREFS HRDRDGEFYR  180
HGSGKRSSER SEKGDRDGSR RRHGSPPPRR GGSPGGGREG SEERRARIEQ WNREREEKEE  240
GGGA*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A6e-4211361185Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1209217RGGSPGGGR
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.205800.0flower| leaf
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00117437001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3531711e-133AK353171.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-26-L07.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009102962.11e-113PREDICTED: LOW QUALITY PROTEIN: splicing factor U2af small subunit A-like
SwissprotQ9S7099e-91U2AFA_ARATH; Splicing factor U2af small subunit A
TrEMBLM4EMN71e-122M4EMN7_BRARP; Uncharacterized protein
STRINGBra030057.1-P1e-122(Brassica rapa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G44785.13e-29C3H 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. 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. 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]
  4. 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]