PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Sme2.5_00311.1_g00010.1
Organism
Solanum melongena
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: 381aa    MW: 43959.7 Da    PI: 9.3031
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sme2.5_00311.1_g00010.1genomeEGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH28.42.7e-091437225
                             -S---SGGGGTS--TTTTT-SS-S CS
                  zf-CCCH  2 ktelCrffartGtCkyGdrCkFaH 25
                             ++++C+f+++ G C++GdrC++ H
  Sme2.5_00311.1_g00010.1 14 DRVNCPFYFKIGACRHGDRCSRLH 37
                             6899******************** PP
2zf-CCCH192.4e-06186209226
                              -S---SGGGGTS--TTTTT-SS-SS CS
                  zf-CCCH   2 ktelCrffartGtCkyGdrCkFaHg 26 
                              +++ Cr + +   C++G+ C+F+H 
  Sme2.5_00311.1_g00010.1 186 REATCRQYEE-NVCNRGGYCNFMHL 209
                              6789**9999.*************6 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.1121240IPR000571Zinc finger, CCCH-type
SMARTSM003560.00651339IPR000571Zinc finger, CCCH-type
PfamPF006425.8E-71437IPR000571Zinc finger, CCCH-type
PRINTSPR018482.2E-441837IPR009145U2 auxiliary factor small subunit
PRINTSPR018482.2E-443757IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3304.7E-1244113IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018482.2E-447590IPR009145U2 auxiliary factor small subunit
PRINTSPR018482.2E-44166190IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010310.465184211IPR000571Zinc finger, CCCH-type
SMARTSM003560.41184210IPR000571Zinc finger, CCCH-type
PRINTSPR018482.2E-44201213IPR009145U2 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: 381 aa     Download sequence    Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHTKP SISPTLVLSN MYQRPDMITP  60
GVDPQGQPLD PRQIQRHFED FYEDLFEELS KYGEIENLNI CDNLADHMVG NVYGGRPCCK  120
CSSESYWKIL CSVSLVSTRQ LSFSSFTAFN FWRLCTILCC LLHLSVCFAH AGRPIIVDFS  180
PVTDFREATC RQYEENVCNR GGYCNFMHLK KISRELRRQL FGKSSRRRRS HSRSRSPRGN  240
RNYEERPQGG RGSGRRGGDD RYHDRGRRPR SRSPGRRSGH SRSPGGRRNR SPGREGSEER  300
RAKIEQWNRE REEAGSGRNH GGGTRREDRE GSAERRAKIE QWNREKEEAE SAKYNNFDAG  360
NGRNDGGNHY GEQFDDYPEQ Q
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A4e-5512201179Splicing 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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0140220.0BT014022.1 Lycopersicon esculentum clone 133084R, mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016543444.10.0PREDICTED: splicing factor U2af small subunit B-like
RefseqXP_016543445.10.0PREDICTED: splicing factor U2af small subunit B-like
RefseqXP_016543446.10.0PREDICTED: splicing factor U2af small subunit B-like
SwissprotQ9FMY51e-107U2AFB_ARATH; Splicing factor U2af small subunit B
TrEMBLA0A1U8EJD70.0A0A1U8EJD7_CAPAN; splicing factor U2af small subunit B-like
TrEMBLA0A2G2WE220.0A0A2G2WE22_CAPBA; Splicing factor U2af small subunit A
TrEMBLA0A2G3BGH70.0A0A2G3BGH7_CAPCH; Splicing factor U2af small subunit A
STRINGSolyc10g083640.1.10.0(Solanum lycopersicum)
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
AT3G44785.13e-29C3H 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]