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 Carubv10002748m
Common NameCARUB_v10002748mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family TALE
Protein Properties Length: 395aa    MW: 45303.2 Da    PI: 6.5104
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10002748mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox28.62.4e-093203552055
                      HHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
         Homeobox  20 eknrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                      +k +yps++e+  LA+++gL+++q+ +WF N+R ++
  Carubv10002748m 320 YKWPYPSESEKVALAESTGLDQKQINNWFINQRKRH 355
                      5679*****************************885 PP
2ELK35.91.6e-12275296122
              ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                      ELK++Ll+KYsgyL+sLkqE+s
  Carubv10002748m 275 ELKNHLLKKYSGYLSSLKQELS 296
                      9*******************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012557.6E-23128172IPR005540KNOX1
PfamPF037902.3E-22129170IPR005540KNOX1
SMARTSM012562.4E-30180231IPR005541KNOX2
PfamPF037916.6E-26185230IPR005541KNOX2
PfamPF037897.8E-10275296IPR005539ELK domain
SMARTSM011881.0E-6275296IPR005539ELK domain
PROSITE profilePS5121311.243275295IPR005539ELK domain
PROSITE profilePS5007113.021295358IPR001356Homeobox domain
SuperFamilySSF466891.41E-19296370IPR009057Homeodomain-like
SMARTSM003894.0E-13297362IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.601.9E-27300361IPR009057Homeodomain-like
CDDcd000861.05E-11307359No hitNo description
PfamPF059201.2E-16315354IPR008422Homeobox KN domain
PROSITE patternPS000270333356IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0001708Biological Processcell fate specification
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010051Biological Processxylem and phloem pattern formation
GO:0010089Biological Processxylem development
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 395 aa     Download sequence    Send to blast
MEEYQHDSSS TPHRVSFLYS PISSSSNKND NTSDTNNNNN NSNNYGPGYN NTNNNHQQQH  60
HQHMLFPHMS SLLPQTTENC FRSDHDQPNN PSVKSEASSS RINHYSMLMR AIHNTQDATN  120
NDNVADVEAM KAKIIAHPHY STLLQAYLDC QKIGAPPEVV DRITAARQDF EARQQRSTPS  180
LSTSSKDPEL DQFMEAYCDM LVKYREELTR PIQEAMEFIR RIESQLSMLC QGPIHILNNP  240
DGKSEGMGSS DEEQENNSGG ETELPEIDPR AEDRELKNHL LKKYSGYLSS LKQELSKKKK  300
KGKLPKEARQ KLLTWWELHY KWPYPSESEK VALAESTGLD QKQINNWFIN QRKRHWKPSE  360
DMQFMVMDGL QHPHHAALYM DGHYMGDGPY RLGP*
Functional Description ? help Back to Top
Source Description
UniProtMay play a role in meristem function, and may be involved in maintaining cells in an undifferentiated, meristematic state, and its expression disappears at the same time the shoot apex undergoes the transition from vegetative to reproductive development (PubMed:11934861). Positive regulator of LATERAL ORGAN BOUNDARIES (LOB) (PubMed:11934861). Probably binds to the DNA sequence 5'-TGAC-3' (PubMed:11934861). Able to traffic from the L1 to the L2/L3 layers of the meristem, presumably through plasmodesmata (PubMed:12900451). {ECO:0000269|PubMed:11934861, ECO:0000269|PubMed:12900451, ECO:0000269|PubMed:7866029}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10002748m
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by ASYMMETRIC LEAVES1 (AS1) and ASYMMETRIC LEAVES2 (AS2).
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankATU141740.0U14174.1 Arabidopsis thaliana clone KNAT1 knotted-like homeobox protein gene, partial cds.
GenBankAY0808340.0AY080834.1 Arabidopsis thaliana putative KNAT1 homeobox protein (At4g08150) mRNA, complete cds.
GenBankAY1139820.0AY113982.1 Arabidopsis thaliana putative KNAT1 homeobox protein (At4g08150) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006289279.10.0homeobox protein knotted-1-like 1 isoform X2
SwissprotP466390.0KNAT1_ARATH; Homeobox protein knotted-1-like 1
TrEMBLR0FIH20.0R0FIH2_9BRAS; Uncharacterized protein
STRINGXP_006289279.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM65662335
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G08150.10.0KNOTTED-like from Arabidopsis thaliana
Publications ? help Back to Top
  1. dela Paz JS, et al.
    Chromosome fragile sites in Arabidopsis harbor matrix attachment regions that may be associated with ancestral chromosome rearrangement events.
    PLoS Genet., 2012. 8(12): p. e1003136
    [PMID:23284301]
  2. Liu C, et al.
    Phosphatidylserine synthase 1 is required for inflorescence meristem and organ development in Arabidopsis.
    J Integr Plant Biol, 2013. 55(8): p. 682-95
    [PMID:23931744]
  3. Liu B, et al.
    NEVERSHED and INFLORESCENCE DEFICIENT IN ABSCISSION are differentially required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana.
    J. Exp. Bot., 2013. 64(17): p. 5345-57
    [PMID:23963677]
  4. Simonini S,Kater MM
    Class I BASIC PENTACYSTEINE factors regulate HOMEOBOX genes involved in meristem size maintenance.
    J. Exp. Bot., 2014. 65(6): p. 1455-65
    [PMID:24482368]
  5. Scofield S,Dewitte W,Murray JA
    STM sustains stem cell function in the Arabidopsis shoot apical meristem and controls KNOX gene expression independently of the transcriptional repressor AS1.
    Plant Signal Behav, 2018.
    [PMID:24776954]
  6. Lee JE,Lampugnani ER,Bacic A,Golz JF
    SEUSS and SEUSS-LIKE 2 coordinate auxin distribution and KNOXI activity during embryogenesis.
    Plant J., 2014. 80(1): p. 122-35
    [PMID:25060324]
  7. Rast-Somssich MI, et al.
    Alternate wiring of a KNOXI genetic network underlies differences in leaf development of A. thaliana and C. hirsuta.
    Genes Dev., 2015. 29(22): p. 2391-404
    [PMID:26588991]
  8. Duplat-Bermúdez L,Ruiz-Medrano R,Landsman D,Mariño-Ramírez L,Xoconostle-Cázares B
    Transcriptomic analysis of Arabidopsis overexpressing flowering locus T driven by a meristem-specific promoter that induces early flowering.
    Gene, 2016. 587(2): p. 120-31
    [PMID:27154816]
  9. Li Z, et al.
    Transcription factors AS1 and AS2 interact with LHP1 to repress KNOX genes in Arabidopsis.
    J Integr Plant Biol, 2016. 58(12): p. 959-970
    [PMID:27273574]
  10. Lozano-Sotomayor P, et al.
    Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana.
    Plant J., 2016. 88(3): p. 437-451
    [PMID:27402171]
  11. Frangedakis E,Saint-Marcoux D,Moody LA,Rabbinowitsch E,Langdale JA
    Nonreciprocal complementation of KNOX gene function in land plants.
    New Phytol., 2017. 216(2): p. 591-604
    [PMID:27886385]
  12. Woerlen N, et al.
    Repression of BLADE-ON-PETIOLE genes by KNOX homeodomain protein BREVIPEDICELLUS is essential for differentiation of secondary xylem in Arabidopsis root.
    Planta, 2017. 245(6): p. 1079-1090
    [PMID:28204875]
  13. Douglas SJ,Li B,Kliebenstein DJ,Nambara E,Riggs CD
    A novel Filamentous Flower mutant suppresses brevipedicellus developmental defects and modulates glucosinolate and auxin levels.
    PLoS ONE, 2017. 12(5): p. e0177045
    [PMID:28493925]
  14. Wang X, et al.
    Overexpressed BRH1, a RING finger gene, alters rosette leaf shape in Arabidopsis thaliana.
    Sci China Life Sci, 2018. 61(1): p. 79-87
    [PMID:28887625]
  15. Simonini S,Stephenson P,Østergaard L
    A molecular framework controlling style morphology in Brassicaceae.
    Development, 2018.
    [PMID:29440299]
  16. Felipo-Benavent A, et al.
    Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction.
    Development, 2019.
    [PMID:30389856]