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 XP_009148359.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C3H
Protein Properties Length: 162aa    MW: 18275.2 Da    PI: 7.7246
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009148359.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH25.81.8e-087695625
                    -SGGGGTS--TTTTT-SS-S CS
         zf-CCCH  6 CrffartGtCkyGdrCkFaH 25
                    C+f+++tG C++G+rC++ H
  XP_009148359.1 76 CPFHLKTGACRFGPRCSRVH 95
                    ******************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.5127098IPR000571Zinc finger, CCCH-type
PfamPF006422.2E-67595IPR000571Zinc finger, CCCH-type
PRINTSPR018483.3E-117695IPR009145U2 auxiliary factor small subunit
PRINTSPR018483.3E-1195115IPR009145U2 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:0003723Molecular FunctionRNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 162 aa     Download sequence    Send to blast
MEGGPPDIIF KGNEIILRKN KVKVPKKPVA AQVDVNEIVD RPTSNPLPPG IEAFSKYQNF  60
SSAQQILDTE QDKAHCPFHL KTGACRFGPR CSRVHFHPDK SCTILMKNMC NGPGIAWEQD  120
EGLEVCTRCH LVMLTLMDSL QWRCMITTWT GLELQFTSLY PT
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009148359.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2266844e-96AK226684.1 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_018440617.12e-69PREDICTED: zinc finger CCCH domain-containing protein 5
SwissprotQ9SY748e-61C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLA0A178W6J58e-92A0A178W6J5_ARATH; Uncharacterized protein
STRINGBra019944.1-P2e-87(Brassica rapa)
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
AT1G10320.19e-54C3H 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]