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 Cc06_g05170
Common NameGSCOC_T00043050001
Organism
Coffea canephora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
Family C3H
Protein Properties Length: 251aa    MW: 28813.8 Da    PI: 11.3986
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cc06_g05170genomeCGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH19.81.4e-064063226
                 -S---SGGGGTS--TTTTT-SS-SS CS
      zf-CCCH  2 ktelCrffartGtCkyGdrCkFaHg 26
                 +++ Cr + +   C++G+ C+F+H 
  Cc06_g05170 40 REATCRQYEE-NVCNRGGYCNFMHL 63
                 6789**9999.*************6 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PRINTSPR018481.0E-102044IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010310.4653865IPR000571Zinc finger, CCCH-type
PfamPF006422.1E-44063IPR000571Zinc finger, CCCH-type
PRINTSPR018481.0E-105567IPR009145U2 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:0003723Molecular FunctionRNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 251 aa     Download sequence    Send to blast
MNGDLICFVL QYTVHLLGSF TWICGGRPII VDFSPVTDFR EATCRQYEEN VCNRGGYCNF  60
MHLKKISREL RRQLFGRSKR RRSRSRSRSA SPQRQFNYGE RPRGGRGFPR RGDHLAHERS  120
RRPRSRSPGR RGGRSRSPGG RRNRSPIREG SIERRAMIEQ WNKEREQDGG FTKSYNSSPG  180
ERRNRSPTRE GSAERRAMIE QWNREKEQAD SAKGSSSFVT NNGSGGGGKT EHSSNDEYQK  240
HQEEDGNHGY *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A1e-122774132179Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
17987RRRSRSRSR
Functional Description ? help Back to Top
Source Description
UniProtNecessary for the splicing of pre-mRNA. {ECO:0000250}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEF1475753e-33EF147575.1 Populus trichocarpa clone WS0123_J01 unknown mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_027070872.11e-158splicing factor U2af small subunit B-like
RefseqXP_027070873.11e-158splicing factor U2af small subunit B-like
RefseqXP_027070874.11e-158splicing factor U2af small subunit B-like
SwissprotQ9ZQW82e-31U2AFA_ORYSJ; Splicing factor U2af small subunit A
TrEMBLA0A068V3I30.0A0A068V3I3_COFCA; Uncharacterized protein
STRINGSolyc10g083640.1.17e-57(Solanum lycopersicum)
STRINGPGSC0003DMT4000726402e-57(Solanum tuberosum)
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  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]