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 AT5G16540.3
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: 354aa    MW: 39158.1 Da    PI: 8.2405
Description zinc finger nuclease 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G16540.3genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH29.99.9e-102447326
                 S---SGGGGTS--TTTTT-SS-SS CS
      zf-CCCH  3 telCrffartGtCkyGdrCkFaHg 26
                 ++ C ++ rtG C++G++C+F+H+
  AT5G16540.3 24 EPDCAYYIRTGLCRFGSTCRFNHP 47
                 789********************8 PP
2zf-CCCH37.73.5e-126993327
                 S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH  3 telCrffartGtCkyGdrCkFaHgp 27
                 +++C f+++tGtCk+G +CkF+H++
  AT5G16540.3 69 QPECEFYLKTGTCKFGVTCKFHHPR 93
                 799********************96 PP
3zf-CCCH36.96e-12115139327
                  S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   3 telCrffartGtCkyGdrCkFaHgp 27 
                  +  C++f+r G+Ck+G++CkF+H++
  AT5G16540.3 115 EDDCSYFLRIGQCKFGGTCKFNHPQ 139
                  578********************97 PP
4zf-CCCH37.34.5e-12223249127
                  --S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHgp 27 
                  +++++C+f+++tG Ck+G  CkF+H++
  AT5G16540.3 223 PGQPECQFYMKTGDCKFGTVCKFHHPR 249
                  5789*********************96 PP
5zf-CCCH38.42e-12269295127
                  --S---SGGGGTS--TTTTT-SS-SSS CS
      zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHgp 27 
                  ++++lC f++r+G+Ck+G++CkF H++
  AT5G16540.3 269 PGEPLCVFYSRYGICKFGPSCKFDHPM 295
                  589**********************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.8682149IPR000571Zinc finger, CCCH-type
SMARTSM003560.00672148IPR000571Zinc finger, CCCH-type
PfamPF006421.5E-62447IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.18E-52549IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.105.2E-42748IPR000571Zinc finger, CCCH-type
SMARTSM003562.6E-56693IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.2116694IPR000571Zinc finger, CCCH-type
PfamPF006421.1E-96993IPR000571Zinc finger, CCCH-type
SuperFamilySSF902294.58E-67095IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.7E-47293IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.202112140IPR000571Zinc finger, CCCH-type
SMARTSM003561.1E-4112139IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.44E-5112140IPR000571Zinc finger, CCCH-type
PfamPF006422.1E-9115139IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.108.7E-4118138IPR000571Zinc finger, CCCH-type
SMARTSM003561.6E-5222249IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.22222250IPR000571Zinc finger, CCCH-type
PfamPF006421.8E-8224249IPR000571Zinc finger, CCCH-type
SuperFamilySSF902296.02E-6226252IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.101.9E-4228250IPR000571Zinc finger, CCCH-type
SMARTSM003561.4E-7268295IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.234268296IPR000571Zinc finger, CCCH-type
PfamPF006423.6E-9270295IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.31E-5271295IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.105.3E-4273293IPR000571Zinc 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: 354 aa     Download sequence    Send to blast
MWQMNLGSDD TMGVDGSYPE RHGEPDCAYY IRTGLCRFGS TCRFNHPHDR KLVIATARIK  60
GEYPERIGQP ECEFYLKTGT CKFGVTCKFH HPRNKAGIDG SVSVNVLSYP LRPNEDDCSY  120
FLRIGQCKFG GTCKFNHPQT QSTNLMVSVR GSPVYSALQS LTGQPSYSWS RTSFVANPPR  180
LQDPSGFASG SQGGLFSSGF HSGNSVPLGF YALPRENVFP ERPGQPECQF YMKTGDCKFG  240
TVCKFHHPRD RQTPPPDCVL SSVGLPLRPG EPLCVFYSRY GICKFGPSCK FDHPMRVFTY  300
NNNTASPSPS SSLHQETAIT TELRNLLVSS SVEAKPTSLP ETTSAKDTIV DAQH
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
PlantRegMapAT5G16540.3
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)
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]