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 Cc00_g34180
Common NameGSCOC_T00005088001
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: 215aa    MW: 24789.7 Da    PI: 7.5825
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cc00_g34180genomeCGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH20.58.7e-07102123426
                  ---SGGGGTS--TTTTT-SS-SS CS
      zf-CCCH   4 elCrffartGtCkyGdrCkFaHg 26 
                  + Cr f +   C++G+ C+F+H+
  Cc00_g34180 102 ATCRQFEE-NNCNRGGYCNFMHV 123
                  57**9999.*************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd125391.36E-55195No hitNo description
Gene3DG3DSA:3.30.70.3307.1E-18195IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018482.0E-332540IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549281.16E-122799IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018482.0E-335375IPR009145U2 auxiliary factor small subunit
PRINTSPR018482.0E-3380104IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010311.05698125IPR000571Zinc finger, CCCH-type
PfamPF006422.0E-4102124IPR000571Zinc finger, CCCH-type
PRINTSPR018482.0E-33115127IPR009145U2 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: 215 aa     Download sequence    Send to blast
MYQRPDMITP GVDTQGQPFE PRKIQEHFED FYEDIFEELG KFDEIESLNI CDNLADHMIS  60
NVYVQFKEED QAAATLQALQ GHFYSDRPII ADFSPVTNFH EATCRQFEEN NCNRGGYCNF  120
MHVKMIGRDL RRKLFGSHIL KYRRSRSRRA VTVKGIIVQV VGGAEETSTP GMSDSSGGRR  180
RHVASPKRSK SPVREGSEER RARIEQWNQQ RKEN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A3e-37513449179Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtNecessary for the splicing of pre-mRNA (By similarity). Probably active at the 3' splice sites. {ECO:0000250}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009383225.11e-101PREDICTED: splicing factor U2af small subunit B-like
RefseqXP_009383227.11e-101PREDICTED: splicing factor U2af small subunit B-like
RefseqXP_018675612.11e-101PREDICTED: splicing factor U2af small subunit B-like
RefseqXP_018675613.11e-101PREDICTED: splicing factor U2af small subunit B-like
RefseqXP_018675614.11e-101PREDICTED: splicing factor U2af small subunit B-like
SwissprotQ9FMY54e-85U2AFB_ARATH; Splicing factor U2af small subunit B
TrEMBLA0A068VN301e-160A0A068VN30_COFCA; Uncharacterized protein
STRINGGSMUA_Achr9P12340_0011e-103(Musa acuminata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA106155
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.19e-15C3H family protein
Publications ? help Back to Top
  1. Day IS, et al.
    Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: insights into regulated splicing.
    Plant J., 2012. 71(6): p. 936-47
    [PMID:22563826]
  2. Kim DW,Jeon SJ,Hwang SM,Hong JC,Bahk JD
    The C3H-type zinc finger protein GDS1/C3H42 is a nuclear-speckle-localized protein that is essential for normal growth and development in Arabidopsis.
    Plant Sci., 2016. 250: p. 141-153
    [PMID:27457991]
  3. Park HY, et al.
    The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms.
    Plant Cell Rep., 2017. 36(7): p. 1113-1123
    [PMID:28432478]