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 AT5G16540.1
Common NameMQK4.29, ZFN3
Organism
Arabidopsis thaliana
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: 375aa    MW: 41525.7 Da    PI: 8.023
Description zinc finger nuclease 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G16540.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH29.81.1e-094568326
                 S---SGGGGTS--TTTTT-SS-SS CS
      zf-CCCH  3 telCrffartGtCkyGdrCkFaHg 26
                 ++ C ++ rtG C++G++C+F+H+
  AT5G16540.1 45 EPDCAYYIRTGLCRFGSTCRFNHP 68
                 789********************8 PP
2zf-CCCH37.63.8e-1290114327
                  S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   3 telCrffartGtCkyGdrCkFaHgp 27 
                  +++C f+++tGtCk+G +CkF+H++
  AT5G16540.1  90 QPECEFYLKTGTCKFGVTCKFHHPR 114
                  799********************96 PP
3zf-CCCH36.86.4e-12136160327
                  S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   3 telCrffartGtCkyGdrCkFaHgp 27 
                  +  C++f+r G+Ck+G++CkF+H++
  AT5G16540.1 136 EDDCSYFLRIGQCKFGGTCKFNHPQ 160
                  578********************97 PP
4zf-CCCH37.24.9e-12244270127
                  --S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHgp 27 
                  +++++C+f+++tG Ck+G  CkF+H++
  AT5G16540.1 244 PGQPECQFYMKTGDCKFGTVCKFHHPR 270
                  5789*********************96 PP
5zf-CCCH38.32.1e-12290316127
                  --S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHgp 27 
                  ++++lC f++r+G+Ck+G++CkF H++
  AT5G16540.1 290 PGEPLCVFYSRYGICKFGPSCKFDHPM 316
                  589**********************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.8684270IPR000571Zinc finger, CCCH-type
SMARTSM003560.00674269IPR000571Zinc finger, CCCH-type
PfamPF006421.6E-64568IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.27E-54670IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.105.6E-44869IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.21187115IPR000571Zinc finger, CCCH-type
SMARTSM003562.6E-587114IPR000571Zinc finger, CCCH-type
PfamPF006421.2E-990114IPR000571Zinc finger, CCCH-type
SuperFamilySSF902294.97E-691116IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.9E-493114IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.57E-5133161IPR000571Zinc finger, CCCH-type
SMARTSM003561.1E-4133160IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.202133161IPR000571Zinc finger, CCCH-type
PfamPF006422.2E-9136160IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.109.4E-4139159IPR000571Zinc finger, CCCH-type
SMARTSM003561.6E-5243270IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.22243271IPR000571Zinc finger, CCCH-type
PfamPF006422.0E-8245270IPR000571Zinc finger, CCCH-type
SuperFamilySSF902296.54E-6247273IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.0E-4249271IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.234289317IPR000571Zinc finger, CCCH-type
SMARTSM003561.4E-7289316IPR000571Zinc finger, CCCH-type
PfamPF006423.9E-9291316IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.44E-5292316IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.105.7E-4294314IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0090305Biological Processnucleic acid phosphodiester bond hydrolysis
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0004518Molecular Functionnuclease activity
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025195anatomypollen tube cell
PO:0025281anatomypollen
PO:0001016developmental stageL mature pollen stage
PO:0001017developmental stageM germinated pollen stage
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 375 aa     Download sequence    Send to blast
MDFDSISRES TFLSPLLNQN AMWQMNLGSD DTMGVDGSYP ERHGEPDCAY YIRTGLCRFG  60
STCRFNHPHD RKLVIATARI KGEYPERIGQ PECEFYLKTG TCKFGVTCKF HHPRNKAGID  120
GSVSVNVLSY PLRPNEDDCS YFLRIGQCKF GGTCKFNHPQ TQSTNLMVSV RGSPVYSALQ  180
SLTGQPSYSW SRTSFVANPP RLQDPSGFAS GSQGGLFSSG FHSGNSVPLG FYALPRENVF  240
PERPGQPECQ FYMKTGDCKF GTVCKFHHPR DRQTPPPDCV LSSVGLPLRP GEPLCVFYSR  300
YGICKFGPSC KFDHPMRVFT YNNNTASPSP SSSLHQETAI TTELRNLLVS SSVEAKPTSL  360
PETTSAKDTI VDAQH
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.217110.0flower
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible250128_at0.0
Expression AtlasAT5G16540-
AtGenExpressAT5G16540-
ATTED-IIAT5G16540-
Functional Description ? help Back to Top
Source Description
TAIREncodes a zinc finger protein.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G16540.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G16540
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0846340.0AY084634.1 Arabidopsis thaliana clone 113763 mRNA, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_851041.10.0zinc finger nuclease 3
SwissprotQ8L7N80.0C3H57_ARATH; Zinc finger CCCH domain-containing protein 57
TrEMBLA0A178USP30.0A0A178USP3_ARATH; ZFN3
STRINGAT5G16540.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM33892864
Representative plantOGRP12471750
Publications ? help Back to Top
  1. Haas BJ, et al.
    Full-length messenger RNA sequences greatly improve genome annotation.
    Genome Biol., 2002. 3(6): p. RESEARCH0029
    [PMID:12093376]
  2. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  3. Castelli V, et al.
    Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation.
    Genome Res., 2004. 14(3): p. 406-13
    [PMID:14993207]
  4. Lloyd A,Plaisier CL,Carroll D,Drews GN
    Targeted mutagenesis using zinc-finger nucleases in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2005. 102(6): p. 2232-7
    [PMID:15677315]
  5. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  6. Delaney KJ, et al.
    Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit.
    Plant Physiol., 2006. 140(4): p. 1507-21
    [PMID:16500995]
  7. Wang D, et al.
    Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.
    BMC Genomics, 2008. 9: p. 44
    [PMID:18221561]
  8. Wang Y, et al.
    Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
    Plant Physiol., 2008. 148(3): p. 1201-11
    [PMID:18775970]
  9. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  10. Xie W, et al.
    Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach.
    Front Plant Sci, 2015. 6: p. 829
    [PMID:26528302]