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 Csa17g013200.1
Organism
Camelina sativa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina
Family C3H
Protein Properties Length: 564aa    MW: 65416.3 Da    PI: 7.0386
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa17g013200.1genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH22.91.5e-07168187625
                     -SGGGGTS--TTTTT-SS-S CS
         zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                     C+f ++tG C++G+rC++ H
  Csa17g013200.1 168 CPFQLKTGACRFGPRCTRVH 187
                     *****************999 PP
2zf-CCCH29.41.3e-09289316126
                     --S---SGGGGTS..--TTTTT-SS-SS CS
         zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                     +k ++C  ++++   tC++G+ C+F+H+
  Csa17g013200.1 289 WKVAICGEYMKSRlkTCSRGSACNFIHC 316
                     899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.164162190IPR000571Zinc finger, CCCH-type
SMARTSM003560.95163189IPR000571Zinc finger, CCCH-type
PfamPF006422.2E-5167187IPR000571Zinc finger, CCCH-type
PRINTSPR018481.2E-24168187IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.2E-24187207IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3307.6E-6193247IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018481.2E-24270294IPR009145U2 auxiliary factor small subunit
SMARTSM003560.021288317IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.319288318IPR000571Zinc finger, CCCH-type
PfamPF006422.6E-7289316IPR000571Zinc finger, CCCH-type
PRINTSPR018481.2E-24308320IPR009145U2 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: 564 aa     Download sequence    Send to blast
MEGFEERKEK AAEMSRKEMP KAMKKLKRKQ VRKEIAEKER DETEAKLNNP AEHERLKAIE  60
REGVRGDGND ECGEDEDGKY EYIEERPPEI IFQGNEIILR KNKVRVPKKP LVQVDGNQIS  120
DRPTSNPLPP GTEACASNYQ NVSSAQQILE NVAQEVPNFG TEQDKAHCPF QLKTGACRFG  180
PRCTRVHFYP NKSCTLLLKN MYNGPGIAWE QDEGLEYTDE EAERCYEEFY EDVHTKFQKY  240
GELINFKKWL IPLEGQCIRT LQILAYQPIN GRYFAGKQEK CEFVNISRWK VAICGEYMKS  300
RLKTCSRGSA CNFIHCFRNP GGDYEWADHD KPPPRFWIHK MTALFGYSDE KHLEHELLGS  360
LNNSRSDLQT DSHSVMLMCF VSMSGNLQED LYQGTMIVRM LDLSLPIGAV KIMVKLGTVL  420
METKHSRDAV NCHDGDDSPS RDGSLEREIY KERRYAKDKF HRDSRWSEHS PGHRVIRKRT  480
HGRYSDDDFP DGDDNARRET GHKRKSRRRT DSEAEEQMDD EKDRKPRRSS RKYSREGSSA  540
DQEESHEHDR VHTVCDKSQR EKV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A1e-181593159167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Cis-element ? help Back to Top
SourceLink
PlantRegMapCsa17g013200.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0054890.0AC005489.1 Genomic sequence for Arabidopsis thaliana BAC F14N23 from Chromosome 1, complete sequence.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010475893.10.0PREDICTED: zinc finger CCCH domain-containing protein 5-like
SwissprotQ9SY740.0C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLR0GU420.0R0GU42_9BRAS; Uncharacterized protein
STRINGXP_010475893.10.0(Camelina sativa)
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]