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 Thhalv10009354m
Common NameEUTSA_v10009354mg
Organism
Eutrema salsugineum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Eutremeae; Eutrema
Family C3H
Protein Properties Length: 673aa    MW: 79045 Da    PI: 7.6295
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thhalv10009354mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.31.1e-07246265625
                      -SGGGGTS--TTTTT-SS-S CS
          zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                      C+f+++tG C++G+rC++ H
  Thhalv10009354m 246 CPFHLKTGACRFGPRCSRVH 265
                      ******************99 PP
2zf-CCCH29.11.7e-09375402126
                      --S---SGGGGTS..--TTTTT-SS-SS CS
          zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                      +k ++C  ++++   tC++G+ C+F+H+
  Thhalv10009354m 375 WKVAICGEYMKSRlkTCSRGSACNFIHC 402
                      899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.681240268IPR000571Zinc finger, CCCH-type
SMARTSM003561.1241267IPR000571Zinc finger, CCCH-type
PfamPF006421.4E-5245265IPR000571Zinc finger, CCCH-type
PRINTSPR018485.5E-36246265IPR009145U2 auxiliary factor small subunit
PRINTSPR018485.5E-36265285IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3307.0E-25271370IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501028.842272372IPR000504RNA recognition motif domain
CDDcd125403.48E-46273371No hitNo description
SMARTSM003610.0025294368IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018485.5E-36301316IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549283.76E-16304372IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018485.5E-36329351IPR009145U2 auxiliary factor small subunit
PRINTSPR018485.5E-36356380IPR009145U2 auxiliary factor small subunit
SMARTSM003560.021374403IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.319374404IPR000571Zinc finger, CCCH-type
PfamPF006423.2E-7375402IPR000571Zinc finger, CCCH-type
PRINTSPR018485.5E-36394406IPR009145U2 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: 673 aa     Download sequence    Send to blast
MEQQNDKEEG ERPEEAAGGK EGFEENKEKA AEMSRKEKRK AMKKLKRKQV RKEIAAKERE  60
EAEAKLNDPA EQERLKAIEE EEARMREKEL KEFEESERAW REAMEIKRKK EEEEEAKREE  120
EERRWKDLDE LRKLEASGND ECGEDRDGES QYIEEGPPEI IFQGNEIILK KNKVRVPKKS  180
IPQVDGNKSS NVEFVLQIAD RPTSNPLFPG SEAFPIVHNV SSAQQILDNV AQEVPNFGTE  240
QDKAHCPFHL KTGACRFGPR CSRVHFYPDK SCTLLMKNMY NGPGTAWEQD EGLEYTDEEA  300
ERCYEEFYED VHTEFLKYGE LINFKVCRNG SFHLKGNVYV QYRSLESAIL AYESVNGRYF  360
AKNQVKCEFV NISRWKVAIC GEYMKSRLKT CSRGSACNFI HCFRNPGGDY EWADHDKPPP  420
GFWIQKMTAL FGYSDEYLKH MEREYSGSLH DFRSDQPTDS HRQPSRRSRS RDSYRSHKNH  480
GDTRDSTRGY KLGRHDENCH GGDYSPSSTR GGSLEREKYR ERRYAKETSR HESKWSEYSP  540
GHRVIRKRIH GRYSDDDSPD GDDDYSRMEF GRKRKARRGT DSEVREEMDD EKNIQTHRSS  600
RKHKKEGSST DPDSDRSRRG KRRRRSSRNG IGNGKRENES SDEESSDREE THRERRHRHE  660
RRRSRHSHDQ TPK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A2e-312374019167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1655664RHRHERRRSR
Cis-element ? help Back to Top
SourceLink
PlantRegMapThhalv10009354m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2266840.0AK226684.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL07-54-F13.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024008229.10.0zinc finger CCCH domain-containing protein 5
SwissprotQ9SY740.0C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLV4L0J40.0V4L0J4_EUTSA; Uncharacterized protein (Fragment)
STRINGXP_006417479.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM59752025
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.10.0C3H 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. 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]