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_00273.1_g00037.1
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: 751aa    MW: 87759.5 Da    PI: 8.325
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00273.1_g00037.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.11.2e-07222241625
                              -SGGGGTS--TTTTT-SS-S CS
                  zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                              C+f+++tG C++G+rC++ H
  Rsa1.0_00273.1_g00037.1 222 CPFHLKTGACRFGPRCSRVH 241
                              ******************99 PP
2zf-CCCH291.9e-09377404126
                              --S---SGGGGTS..--TTTTT-SS-SS CS
                  zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                              +k ++C  ++++   tC++G+ C+F+H+
  Rsa1.0_00273.1_g00037.1 377 WKVAICGEYMKSRlkTCSRGSACNFIHC 404
                              899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.681216244IPR000571Zinc finger, CCCH-type
SMARTSM003561.1217243IPR000571Zinc finger, CCCH-type
PfamPF006421.5E-5221241IPR000571Zinc finger, CCCH-type
PRINTSPR018482.7E-32222241IPR009145U2 auxiliary factor small subunit
PRINTSPR018482.7E-32241261IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3302.6E-24247372IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.576269374IPR000504RNA recognition motif domain
SMARTSM003617.6E-5301370IPR003954RNA recognition motif domain, eukaryote
SuperFamilySSF549281.49E-16304374IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018482.7E-32331353IPR009145U2 auxiliary factor small subunit
PRINTSPR018482.7E-32358382IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010311.319376406IPR000571Zinc finger, CCCH-type
SMARTSM003560.021376405IPR000571Zinc finger, CCCH-type
PfamPF006423.6E-7377404IPR000571Zinc finger, CCCH-type
PRINTSPR018482.7E-32396408IPR009145U2 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: 751 aa     Download sequence    Send to blast
MTEPQSEKPE EGERLEESME ESKEKSAEMS RKEKRKAMKK LKRKQVRKEI ASKEREEAEA  60
KLNDPAEQEK LKAIEEEEAR KREKELKEFE ESERAWREAM EIKRKKVEEE ERRWKELEES  120
RKLLEASKDE DDDEYEYIEE GPPEIIFKGN EIILRKNKVR VPKKTVAQAD VNEIADRPTS  180
NPLPPGTEAL SKSQNVSSAQ QILDSVAQEV PNFGTEQDKA HCPFHLKTGA CRFGPRCSRV  240
HFYPDKSCTI LMKNMYNGPG TAWEQDEGLE VYIDGFTSVE VLDYNLGWVG VAVHFSYTEE  300
EAEHCYEEFY EDVHTEFLKF GELINFKVCR NGSLHLKGNV YVHYRSLESA LLAYQSINGR  360
YFAGKQVNCE FVNISRWKVA ICGEYMKSRL KTCSRGSACN FIHCFRNPGG DYEWADYDKP  420
PPRFWIRKMT ALFGYSDEYL KHMEREYSGS LSSDQPTDSQ RQPSRRSRSR EHDRESVGSR  480
PPYRSRTNHS DTRDGSRGHK LSRHEENRHG GDGSPSSTRD GSVEREIYKK PRYAKETSRQ  540
ESKWSEHSPG HRVTRKRIHE RYSEDDDGRG ETSHKRKSSR RYGRRGSDSE VQEGLDDEEN  600
TRIRRSSSDR RSRKEDDREG SSADQQESHA HDRVGDKLQR ERSRSRYSHE GDSSEGRHRP  660
HKDRDKSKHR RRYKTGDPDS DRSRKGKQGR ESQEVKRESG SGSSSGKESS EREGEERQKE  720
RSGSRHRKRR RSHEQTPPKG PEEEIERWRP I
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A3e-262134039167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1726730RKRRR
2726731RKRRRS
3727732KRRRSH
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00273.1_g00037.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2266841e-127AK226684.1 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
SwissprotQ9SY740.0C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLM4DPK50.0M4DPK5_BRARP; Uncharacterized 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. 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]