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 471143
Common NameARALYDRAFT_471143
Organism
Arabidopsis lyrata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family C3H
Protein Properties Length: 773aa    MW: 90432.7 Da    PI: 6.8634
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
471143genomeJGIView 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
   471143 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+
   471143 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
PRINTSPR018482.7E-37246265IPR009145U2 auxiliary factor small subunit
PRINTSPR018482.7E-37265285IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3302.6E-26271370IPR012677Nucleotide-binding alpha-beta plait domain
CDDcd125405.04E-50273371No hitNo description
SMARTSM003616.6E-5294368IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018482.7E-37301316IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549281.61E-16304372IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.371309372IPR000504RNA recognition motif domain
PRINTSPR018482.7E-37329351IPR009145U2 auxiliary factor small subunit
PRINTSPR018482.7E-37356380IPR009145U2 auxiliary factor small subunit
SMARTSM003560.021374403IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.319374404IPR000571Zinc finger, CCCH-type
PfamPF006423.8E-7375402IPR000571Zinc finger, CCCH-type
PRINTSPR018482.7E-37394406IPR009145U2 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: 773 aa     Download sequence    Send to blast
MEQKNGKEEG ERHGEALGEK ESFEESKEKL AEMSRKEKRK ALKKLKRKQV RKEIAEKERE  60
EAEAKLNDPA EQERLKAIEE EEARRREKEL KEFEESERAW REAMEIKRKK EEEEEAKREE  120
EERRWKDLEE LRKLEASGHD ECGEDEDGEY EYIEEGPPEI IFQGNEIILK KNKVRVPKKS  180
VVQVDGNESS NVEFVLQISD RPTSNPLPPG SEACANYQNV SSAQQILESV SQEVPNFGTE  240
QDKAHCPFHL KTGACRFGPR CSRVHFYPNK SCTLLMKNMY NGPGIAWEQD EGLEYTDEEA  300
EHCYEEFYED VHTEFLKYGE LINFKVCRNG SFHLKGNVYV HYRSLESAIL AYQSINGRYF  360
AGKQVNCEFV NISRWKVAIC GEYMKSRLKT CSRGSACNFI HCFRNPGGDY EWADHDRPPP  420
RFWIHKMTSL FGYSDEKYME HESSGSLNNS RSDLSTDSHR QPSRRSRSRN HDHASVGSTP  480
SYRSRKYHGD TWDSTREDEL SRHAENCHDG DDSPSRDCSL EREMYKERRY AKDTLHRDSR  540
WCEHSPGHRV IRKRIHGSDD DSPDGRRDTG HKQKSRRGTD SEVQEQTDDE KDRKTHRSSR  600
KYSRERSSAD QEEGHEHDRV HTVSDKSQRE RSKHGHERSS SRYSHAEDST ESRHHPHKGS  660
DLGVKGENDR KRSVETSPKE NQSDKDRDKS KQRDRYKTQD PDCNRSRKGK RRGRSTGNGV  720
SGISSEEESS DRETHKERPH RHRKRRRSQN SDDQTPNFAE EVEEEIERWR PV*
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
1742746RKRRR
2742747RKRRRS
Cis-element ? help Back to Top
SourceLink
PlantRegMap471143
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_020867793.10.0zinc finger CCCH domain-containing protein 5
SwissprotQ9SY740.0C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLD7KKP30.0D7KKP3_ARALL; Uncharacterized protein
STRINGfgenesh2_kg.1__1097__AT1G10320.10.0(Arabidopsis lyrata)
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]