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 PGSC0003DMP400035995
Organism
Solanum tuberosum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
Family C3H
Protein Properties Length: 286aa    MW: 33384.2 Da    PI: 4.7306
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400035995genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH25.13.1e-08235254625
                           -SGGGGTS--TTTTT-SS-S CS
               zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                           C+f+++tG C++G+rC++ H
  PGSC0003DMP400035995 235 CPFHLKTGACRFGSRCSRVH 254
                           ******************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.671229257IPR000571Zinc finger, CCCH-type
PfamPF006423.8E-6234254IPR000571Zinc finger, CCCH-type
PRINTSPR018484.2E-12235254IPR009145U2 auxiliary factor small subunit
PRINTSPR018484.2E-12254274IPR009145U2 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: 286 aa     Download sequence    Send to blast
MTEPISVEED DKQAPELQRR GEPISAAAEE DQICNNRKEK RKLTKKEKRK QKRKELAEKT  60
RQEEEAKLND PEELRRIQLE EEEEKERLER ERREFKERER LFLEALARKE AQEVEEEERR  120
RVEEEEEKAK QSQVALENEP DGDDEWEYVE DGPPEIIWQG NEIIVKRNKV KVKKKDPDPA  180
ILKEDPNRPT SNPLAPQSEV YADYKNASSL SAQQLLENVA VQTPNFGTEQ DKAHCPFHLK  240
TGACRFGSRC SRVHFYPDKS CTLLMKNMYC GPGFAWEQDE GLEVC*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
14452KKEKRKQKR
Cis-element ? help Back to Top
SourceLink
PlantRegMapPGSC0003DMP400035995
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2389120.0AC238912.10 Solanum lycopersicum strain Heinz 1706 chromosome 1 clone hba-164m23 map 1, complete sequence.
GenBankHG9755130.0HG975513.1 Solanum lycopersicum chromosome ch01, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006349285.10.0PREDICTED: zinc finger CCCH domain-containing protein 5 isoform X1
RefseqXP_015165012.10.0PREDICTED: zinc finger CCCH domain-containing protein 5 isoform X2
SwissprotQ9SY747e-82C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLM1BUU90.0M1BUU9_SOLTU; Uncharacterized protein
STRINGPGSC0003DMT4000533610.0(Solanum tuberosum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.12e-59C3H 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. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]
  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]