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 Araha.4736s0006.1.p
Organism
Arabidopsis halleri
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: 639aa    MW: 74189.8 Da    PI: 7.2714
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.4736s0006.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.41e-07111130625
                          -SGGGGTS--TTTTT-SS-S CS
              zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                          C+f+++tG C++G+rC++ H
  Araha.4736s0006.1.p 111 CPFHLKTGACRFGPRCSRVH 130
                          ******************99 PP
2zf-CCCH29.21.6e-09240267126
                          --S---SGGGGTS..--TTTTT-SS-SS CS
              zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                          +k ++C  ++++   tC++G+ C+F+H+
  Araha.4736s0006.1.p 240 WKVAICGEYMKSRlkTCSRGSACNFIHC 267
                          899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.681105133IPR000571Zinc finger, CCCH-type
SMARTSM003561.1106132IPR000571Zinc finger, CCCH-type
PfamPF006421.3E-5110130IPR000571Zinc finger, CCCH-type
PRINTSPR018481.2E-37111130IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.2E-37130150IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3302.0E-26136235IPR012677Nucleotide-binding alpha-beta plait domain
CDDcd125405.57E-50138236No hitNo description
SMARTSM003616.6E-5159233IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018481.2E-37166181IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549281.22E-16169237IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.371174237IPR000504RNA recognition motif domain
PRINTSPR018481.2E-37194216IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.2E-37221245IPR009145U2 auxiliary factor small subunit
SMARTSM003560.021239268IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.319239269IPR000571Zinc finger, CCCH-type
PfamPF006423.0E-7240267IPR000571Zinc finger, CCCH-type
PRINTSPR018481.2E-37259271IPR009145U2 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: 639 aa     Download sequence    Send to blast
ASGNDECGED EDGEYEYIEE GPPQIIFQGN EIILKKNKVR VPKKSVVQVD GNESFNVEFV  60
LQISDRPTSN PLPPGSEACA NYQNVSSAQQ ILESVAQEVP NFGTEQDKAH CPFHLKTGAC  120
RFGPRCSRVH FYPNKSCTIL MKNMYNGPGI AWEQDEGLEY TDEEAEHCYE EFYEDVHTEF  180
LKYGELINFK VCRNGSFHLK GNVYVHYRSL ESAILAYQSI NGRYFAGKQV NCEFVNISRW  240
KVAICGEYMK SRLKTCSRGS ACNFIHCFRN PGGDYEWADH DRPPPRFWIH KMTSLFGYSD  300
EKYMEHESSG SLNDSRSDLS TDLLRQPSIR PRSRDHDHAN VGSTPSYRSS KYHGDTRDSS  360
REDKLNRHAE NCHDGDDSPS RDGSLEREMY KERRYAKDTL HRDSRWSEHS PGHWVIRKRI  420
HVRYSDDESP DGRRETGHKQ KSRRRTDSKV EEQTDDEKDR KTHRSSRKYS RERSSADQEE  480
SHEHDRVCTV SDKSQREGSK HGHERSSSRY SHAEDSTESR HHPHKGSDLR VKGENDRRRS  540
VETSPKEHQS EKDRDKSKQR DRYKTQDPDC DRSRKGKRRG RSSGNGVSGL SSEESSDRET  600
HKERPHRHRK RRRSQNSDDQ TPNFAEEVEE EIERWRPV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A3e-321022669167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1608612RKRRR
2608613RKRRRS
Cis-element ? help Back to Top
SourceLink
PlantRegMapAraha.4736s0006.1.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_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]