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 GSBRNA2T00015087001
Common NameGSBRNA2T00015087001
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: 755aa    MW: 88563.8 Da    PI: 7.94
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00015087001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.11.3e-07229248625
                          -SGGGGTS--TTTTT-SS-S CS
              zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                          C+f+++tG C++G+rC++ H
  GSBRNA2T00015087001 229 CPFHLKTGACRFGPRCSRVH 248
                          ******************99 PP
2zf-CCCH291.9e-09358385126
                          --S---SGGGGTS..--TTTTT-SS-SS CS
              zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                          +k ++C  ++++   tC++G+ C+F+H+
  GSBRNA2T00015087001 358 WKVAICGEYMKSRlkTCSRGSACNFIHC 385
                          899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.681223251IPR000571Zinc finger, CCCH-type
SMARTSM003561.1224250IPR000571Zinc finger, CCCH-type
PfamPF006421.5E-5228248IPR000571Zinc finger, CCCH-type
PRINTSPR018483.5E-37229248IPR009145U2 auxiliary factor small subunit
PRINTSPR018483.5E-37248268IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3305.1E-26254353IPR012677Nucleotide-binding alpha-beta plait domain
CDDcd125401.15E-49256354No hitNo description
SMARTSM003613.3E-4277351IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018483.5E-37284299IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549281.75E-16287355IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.405292355IPR000504RNA recognition motif domain
PRINTSPR018483.5E-37312334IPR009145U2 auxiliary factor small subunit
PRINTSPR018483.5E-37339363IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010311.319357387IPR000571Zinc finger, CCCH-type
SMARTSM003560.021357386IPR000571Zinc finger, CCCH-type
PfamPF006423.7E-7358385IPR000571Zinc finger, CCCH-type
PRINTSPR018483.5E-37377389IPR009145U2 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: 755 aa     Download sequence    Send to blast
MEPQNEKAEE GDRLEEATGE KEFVEESKEK AAEMSRKEKR KAMKKLKRKQ VRKEIASKER  60
EDAEAKLNDP AEQEKLKAIE EEEARKREKE LREFEESERA WREAMEIKRK KEEEEERRWK  120
ELEELRKLEA SRDGECGEDG EYEYIEEGPP EIIFKGNEII LRKNKVRVPK KSVPQVEGNE  180
IADRPTSNPL PPGTEALPKY QNVSSAQQIL DSVAQEVPNF GTEQDKAHCP FHLKTGACRF  240
GPRCSRVHFY PDKSCTILMK NMYNGPGIAW EHDEGLEYTD EEAEHCYEEF YEDVHTEFLK  300
YGELINFKVC RNGSFHLKGN VYVHYRSLES AVLAYQSING RYFAGKQVNC EFVNISRWKV  360
AICGEYMKSR LKTCSRGSAC NFIHCFRNPG GDYEWADFDK PPPRFWIRKM TALFGYSDEY  420
LRHMEREYSG SLRDCRSDQL TDSQRQPSRR SRSRDHDHVN VGSKPSYRSR DSSRGHRHSR  480
HEENHHGGDG SPNSTRDGSL EREIYKEPRH GKETSRHESK WSEHSPTHRV PRKRIHERYS  540
DDDSGDDDGR GETSHKRKSS RRYPRRGSDS EVQEQLDDQE ESRTHWSSSE RRSRKEDDRE  600
GSSASQEESR AHDRVHAVGD KSQRQRSSSR YSHERDSSES RHRRHRGSYD GENDRRRSVE  660
TSPRDKDRDK SKQRHSYNKT GDPDSSNRGR KGKQGRESQE VKRNASGSSS DEEREERHKE  720
RSHSSHRKRR RSSQHSSHEQ TPKEPDEIER WRPM*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A8e-312203849167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1662667PRDKDR
2726730RKRRR
3726731RKRRRS
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00015087001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2266840.0AK226684.1 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_013657757.10.0zinc finger CCCH domain-containing protein 5-like
SwissprotQ9SY740.0C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLA0A078G7F00.0A0A078G7F0_BRANA; BnaA08g25830D protein
STRINGBra018446.1-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
AT1G10320.10.0C3H 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]