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 Tp57577_TGAC_v2_mRNA23138
Organism
Trifolium pratense
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
Family C3H
Protein Properties Length: 279aa    MW: 32927.8 Da    PI: 10.2091
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp57577_TGAC_v2_mRNA23138genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH29.99.9e-101438226
                               -S---SGGGGTS--TTTTT-SS-SS CS
                    zf-CCCH  2 ktelCrffartGtCkyGdrCkFaHg 26
                               ++++C+f+++ G C++GdrC++ H 
  Tp57577_TGAC_v2_mRNA23138 14 DRVNCPFYFKIGACRHGDRCSRLHN 38
                               6899********************7 PP
2zf-CCCH20.96.5e-07144167226
                                -S---SGGGGTS--TTTTT-SS-SS CS
                    zf-CCCH   2 ktelCrffartGtCkyGdrCkFaHg 26 
                                +++ Cr + +   C++G+ C+F+H+
  Tp57577_TGAC_v2_mRNA23138 144 REATCRQYEE-NSCNRGGYCNFMHV 167
                                6789**9999.*************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.0651240IPR000571Zinc finger, CCCH-type
SMARTSM003560.00681339IPR000571Zinc finger, CCCH-type
PfamPF006422.6E-71438IPR000571Zinc finger, CCCH-type
PRINTSPR018483.7E-621837IPR009145U2 auxiliary factor small subunit
PRINTSPR018483.7E-623757IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3309.7E-1944138IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS5010210.41144140IPR000504RNA recognition motif domain
SMARTSM003610.006362136IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018483.7E-626984IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549285.02E-1571143IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018483.7E-6297119IPR009145U2 auxiliary factor small subunit
PRINTSPR018483.7E-62124148IPR009145U2 auxiliary factor small subunit
SMARTSM003560.021142168IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.629142169IPR000571Zinc finger, CCCH-type
PfamPF006427.9E-5144168IPR000571Zinc finger, CCCH-type
PRINTSPR018483.7E-62159171IPR009145U2 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: 279 aa     Download sequence    Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHNRP TISPTLLLSN MYQRPDIITP  60
GVDXXXXXXX HFEDFYEDIF LELSKFGYIE TLNVCDNLAD HMIGNVYVLF REEDHAAAAL  120
ASLHGRFYSG RPILADFSPV TDFREATCRQ YEENSCNRGG YCNFMHVKKI GRELRRKLFS  180
SQRSRSRSRS RSNSPRRRRR SRSRDRERRD RDYESRGRRS SDRDRDRNRD GDRERKRDSR  240
DRERDGGGGR RNGSSVREGS EERRARIEQW NREKEEKQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A2e-6911831184Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1197205RRRSRSRDR
2197207RRRSRSRDRER
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapTp57577_TGAC_v2_mRNA23138
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_009417288.21e-132PREDICTED: splicing factor U2af small subunit B-like
RefseqXP_018674048.11e-132PREDICTED: splicing factor U2af small subunit B-like
RefseqXP_018674049.11e-132PREDICTED: splicing factor U2af small subunit B-like
SwissprotQ9FMY51e-124U2AFB_ARATH; Splicing factor U2af small subunit B
TrEMBLA0A2K3M5U11e-131A0A2K3M5U1_TRIPR; Splicing factor U2af small subunit B-like protein
STRINGGSMUA_Achr9P12340_0011e-130(Musa acuminata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF1251810
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.12e-34C3H 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]