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 Bostr.13671s0457.1.p
Organism
Boechera stricta
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera
Family C3H
Protein Properties Length: 768aa    MW: 90170 Da    PI: 7.2526
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bostr.13671s0457.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.11.3e-07246265625
                           -SGGGGTS--TTTTT-SS-S CS
               zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                           C+f+++tG C++G+rC++ H
  Bostr.13671s0457.1.p 246 CPFHLKTGACRFGPRCSRVH 265
                           ******************99 PP
2zf-CCCH28.91.9e-09375402126
                           --S---SGGGGTS..--TTTTT-SS-SS CS
               zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                           +k ++C  ++++   tC++G+ C+F+H+
  Bostr.13671s0457.1.p 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
PfamPF006421.6E-5245265IPR000571Zinc finger, CCCH-type
PRINTSPR018481.2E-36246265IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.2E-36265285IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3301.8E-26271370IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.644272372IPR000504RNA recognition motif domain
CDDcd125409.04E-49273371No hitNo description
SMARTSM003619.3E-6294368IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018481.2E-36301316IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549289.27E-17304371IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018481.2E-36329351IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.2E-36356380IPR009145U2 auxiliary factor small subunit
SMARTSM003560.021374403IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.319374404IPR000571Zinc finger, CCCH-type
PfamPF006423.7E-7375402IPR000571Zinc finger, CCCH-type
PRINTSPR018481.2E-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: 768 aa     Download sequence    Send to blast
MEQKNEKEEG ERHEEAAGEK ECYEESKEKA AEMSRKEKRK AMKKLKRKQV RKEIAEMERE  60
EAEAKLNDPA EQERLKAIEE EEARMREKEL KEFEESERAW REAMEIKRKK EEEEEAKREE  120
EERRWKDLDE LRKLEASGND ECGEDEDGEY EYIEEGPPEI IFQGNEIILR KNKVRVPKKS  180
VVQLDGNESS NVEYVLQISD RPTSNPLPPG TEACANYQNV SSAQQILENV SQEVPNFGTE  240
QDKAHCPFHL KTGACRFGPR CSRVHFYPNR SCTLLMKNMY NGPGIAWEQD EGLEYTDEEA  300
ERCYEEFYED VHTEFLKFGE LINFKVCRNG SFHLKGNVYV HYRSLESAIL AYQSINGRYF  360
AGKQVKCEFV NILRWKVAIC GEYMKSRLKT CSRGSACNFI HCFRNPGGDY EWADHDKPPP  420
RFWIHKMTAL FGYSDEKDME HESSGSLYDS RSDLLTDSHR QPSRRFRLRD HDHVNVGSKP  480
SYRSRKNHGD TRDSTRGDKL SRHTENFRDG DDNPSRDGSV EREMYKEQRY AKDTLHRDSR  540
WSEHSPGHQV IRKRIHGRYS DDDSPDGNDY GRRETGEKRK ARRETNSEVQ EQMDDEKGRK  600
PHRSSKKYSR EGSSADEEES HKHDRVRTVC DKSQGERLKH RHERNSSRYS HTGDSTESRI  660
NDRKRSVETS PGKYQSDKDR DKSKQRHRYT TQDPHSDRSR KGKRRGRSSG NGVSGSSSEE  720
SSDRETHKER PHRHRKRRRS QNSHDQTPKF AEESEGVKEE IERWRPV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A1e-302374019167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1734738RKRRR
2734739RKRRRS
Cis-element ? help Back to Top
SourceLink
PlantRegMapBostr.13671s0457.1.p
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_010475893.10.0PREDICTED: zinc finger CCCH domain-containing protein 5-like
SwissprotQ9SY740.0C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLR0GU420.0R0GU42_9BRAS; Uncharacterized protein
STRINGBostr.13671s0457.1.p0.0(Boechera stricta)
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]