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 AT5G25220.1
Common NameF21J6.18, KNAT3
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 TALE
Protein Properties Length: 431aa    MW: 47599.8 Da    PI: 6.2658
Description KNOTTED1-like homeobox gene 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G25220.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox23.41e-073684012154
                  HSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
     Homeobox  21 knrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                  k +yp++e++++L +++gL+ +q+ +WF N+R +
  AT5G25220.1 368 KWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 401
                  469*****************************87 PP
2ELK28.82.8e-10322343122
          ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                  ELKh+L+++Y+++++++++E++
  AT5G25220.1 322 ELKHELKQGYKEKIVDIREEIL 343
                  9*******************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012551.6E-19157201IPR005540KNOX1
PfamPF037901.1E-17160200IPR005540KNOX1
SMARTSM012562.5E-29213268IPR005541KNOX2
PfamPF037912.8E-21217267IPR005541KNOX2
PROSITE profilePS512139.969322342IPR005539ELK domain
SMARTSM011886.1E-4322343IPR005539ELK domain
PfamPF037891.0E-6322343IPR005539ELK domain
PROSITE profilePS5007111.726342405IPR001356Homeobox domain
SMARTSM003892.4E-11344409IPR001356Homeobox domain
SuperFamilySSF466895.13E-16344408IPR009057Homeodomain-like
CDDcd000866.49E-12345406No hitNo description
Gene3DG3DSA:1.10.10.603.6E-25349406IPR009057Homeodomain-like
PfamPF059201.2E-17362401IPR008422Homeobox KN domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009416Biological Processresponse to light stimulus
GO:0009722Biological Processdetection of cytokinin stimulus
GO:0071345Biological Processcellular response to cytokine stimulus
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000005anatomycultured plant cell
PO:0000013anatomycauline leaf
PO:0000017anatomyvascular leaf primordium
PO:0000035anatomycotyledon vascular system
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000258anatomyroot cortex
PO:0000293anatomyguard cell
PO:0004709anatomyaxillary bud
PO:0004724anatomyhypocotyl-root junction
PO:0005059anatomyroot endodermis
PO:0006036anatomyroot epidermis
PO:0006203anatomypericycle
PO:0006332anatomyseed funicle
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:0009062anatomygynoecium
PO:0009066anatomyanther
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020135anatomyroot differentiation zone
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
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: 431 aa     Download sequence    Send to blast
MAFHHNHLSQ DLSFNHFTDQ HQPPPPQPPP PPPQQQQHFQ EAPPPNWLNT ALLRSSDNNN  60
NFLNLHTATA NTTTASSSDS PSSAAAAAAA NQWLSRSSSF LQRNNNNNAS IVGDGIDDVT  120
GGADTMIQGE MKTGGGENKN DGGGATAADG VVSWQNARHK AEILSHPLYE QLLSAHVACL  180
RIATPVDQLP RIDAQLAQSQ HVVAKYSALG AAAQGLVGDD KELDQFMTHY VLLLCSFKEQ  240
LQQHVRVHAM EAVMACWEIE QSLQSLTGVS PGEGMGATMS DDEDEQVESD ANMFDGGLDV  300
LGFGPLIPTE SERSLMERVR QELKHELKQG YKEKIVDIRE EILRKRRAGK LPGDTTSVLK  360
AWWQSHSKWP YPTEEDKARL VQETGLQLKQ INNWFINQRK RNWHSNPSSS TVLKNKRKSN  420
AGDNSGRERF A
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1x2n_A2e-12345409872Homeobox protein PKNOX1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.53760.0floral meristem| flower| leaf| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO306897740.0
Genevisible246930_at0.0
Expression AtlasAT5G25220-
AtGenExpressAT5G25220-
ATTED-IIAT5G25220-
Functional Description ? help Back to Top
Source Description
TAIRA member of class II knotted1-like homeobox gene family (together with KNAT4 and KNAT5). Expressed in: hypocotyl-root boundary, anther-filament junction in flowers, ovule-funiculus and peduncle-silique boundaries, petioles and root. Light-regulated expression with differential response to red/far-red light. KNAT3 promoter activity showed cell-type specific pattern along longitudinal root axis, restricted mainly to the differentiation zone of the root, namely in the cortex and pericycle. Not detected in lateral root primordia
Function -- GeneRIF ? help Back to Top
  1. BLH1 and KNAT3 together modulate seed germination and early seedling development by directly regulating ABI3 expression.
    [PMID: 23663178]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G25220.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDcytokinin
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G26260, AT1G69120, AT1G75410
IntActSearch P48000
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G25220
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0860910.0AY086091.1 Arabidopsis thaliana clone 21240 mRNA, complete sequence.
GenBankX923920.0X92392.1 A.thaliana mRNA for KNAT3 homeobox protein.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_197904.10.0homeobox protein knotted-1-like 3
SwissprotP480000.0KNAT3_ARATH; Homeobox protein knotted-1-like 3
TrEMBLA0A178U9D10.0A0A178U9D1_ARATH; KNAT3
STRINGAT5G25220.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM44428158
Representative plantOGRP16717148
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Bellaoui M, et al.
    The Arabidopsis BELL1 and KNOX TALE homeodomain proteins interact through a domain conserved between plants and animals.
    Plant Cell, 2001. 13(11): p. 2455-70
    [PMID:11701881]
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  4. Rohde A, et al.
    Molecular phenotyping of the pal1 and pal2 mutants of Arabidopsis thaliana reveals far-reaching consequences on phenylpropanoid, amino acid, and carbohydrate metabolism.
    Plant Cell, 2004. 16(10): p. 2749-71
    [PMID:15377757]
  5. Hackbusch J,Richter K,Müller J,Salamini F,Uhrig JF
    A central role of Arabidopsis thaliana ovate family proteins in networking and subcellular localization of 3-aa loop extension homeodomain proteins.
    Proc. Natl. Acad. Sci. U.S.A., 2005. 102(13): p. 4908-12
    [PMID:15781858]
  6. Ehlting J, et al.
    Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiation.
    Plant J., 2005. 42(5): p. 618-40
    [PMID:15918878]
  7. Tan QK,Irish VF
    The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development.
    Plant Physiol., 2006. 140(3): p. 1095-108
    [PMID:16428600]
  8. Truernit E,Siemering KR,Hodge S,Grbic V,Haseloff J
    A map of KNAT gene expression in the Arabidopsis root.
    Plant Mol. Biol., 2006. 60(1): p. 1-20
    [PMID:16463096]
  9. Pagnussat GC,Yu HJ,Sundaresan V
    Cell-fate switch of synergid to egg cell in Arabidopsis eostre mutant embryo sacs arises from misexpression of the BEL1-like homeodomain gene BLH1.
    Plant Cell, 2007. 19(11): p. 3578-92
    [PMID:18055603]
  10. Di Giacomo E, et al.
    Characterization of KNOX genes in Medicago truncatula.
    Plant Mol. Biol., 2008. 67(1-2): p. 135-50
    [PMID:18274864]
  11. Magnani E,Hake S
    KNOX lost the OX: the Arabidopsis KNATM gene defines a novel class of KNOX transcriptional regulators missing the homeodomain.
    Plant Cell, 2008. 20(4): p. 875-87
    [PMID:18398054]
  12. Truernit E,Haseloff J
    A Role for KNAT Class II Genes in Root Development.
    Plant Signal Behav, 2007. 2(1): p. 10-2
    [PMID:19704797]
  13. Huang Z,Meilan R,Woeste K
    A KNAT3-like homeobox gene from Juglans nigra L., JnKNAT3-like, highly expressed during heartwood formation.
    Plant Cell Rep., 2009. 28(11): p. 1717-24
    [PMID:19787353]
  14. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  15. Klopffleisch K, et al.
    Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis.
    Mol. Syst. Biol., 2011. 7: p. 532
    [PMID:21952135]
  16. Smaczniak C, et al.
    Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(5): p. 1560-5
    [PMID:22238427]
  17. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
    [PMID:23449474]
  18. Kim D, et al.
    BLH1 and KNAT3 modulate ABA responses during germination and early seedling development in Arabidopsis.
    Plant J., 2013. 75(5): p. 755-66
    [PMID:23663178]
  19. Ferr
    Arabidopsis TRANSCURVATA1 encodes NUP58, a component of the nucleopore central channel.
    PLoS ONE, 2013. 8(6): p. e67661
    [PMID:23840761]
  20. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  21. Serikawa KA,Martinez-Laborda A,Zambryski P
    Three knotted1-like homeobox genes in Arabidopsis.
    Plant Mol. Biol., 1996. 32(4): p. 673-83
    [PMID:8980519]
  22. Serikawa KA,Martinez-Laborda A,Kim HS,Zambryski PC
    Localization of expression of KNAT3, a class 2 knotted1-like gene.
    Plant J., 1997. 11(4): p. 853-61
    [PMID:9161040]
  23. Serikawa KA,Zambryski PC
    Domain exchanges between KNAT3 and KNAT1 suggest specificity of the kn1-like homeodomains requires sequences outside of the third helix and N-terminal arm of the homeodomain.
    Plant J., 1997. 11(4): p. 863-9
    [PMID:9161041]