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 897773
Common NameARALYDRAFT_897773
Organism
Arabidopsis lyrata
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 TCP
Protein Properties Length: 453aa    MW: 49827.7 Da    PI: 7.3386
Description TCP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
897773genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1TCP117.22.1e-36751812109
     TCP   2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt.......................ssssaseceaesssss 81 
             +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak +i+el+++                       +               
  897773  75 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGFDRPSKAVDWLIKKAKSSIDELAELppwnpadairlaaanakprrttaK--------------- 162
             79**************************************************************766555555555544443332110............... PP

     TCP  82 asnsssgkaaksaakskksqksaasaln 109
                     + + +++++++q++++  l+
  897773 163 -------TQISLSPPPQQQQQQQQ--LH 181
             .......22222222222222222..22 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF036342.1E-3275181IPR005333Transcription factor, TCP
PROSITE profilePS5136934.14877135IPR017887Transcription factor TCP subgroup
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0009965Biological Processleaf morphogenesis
GO:0030154Biological Processcell differentiation
GO:0045962Biological Processpositive regulation of development, heterochronic
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 453 aa     Download sequence    Send to blast
MATLDSSPSY DDHRRRRRRL DEDADLPQYA RPVADDQYLH PPPPSSMRHR ATSEAADGGC  60
GEIVEVQGGH IVRSTGRKDR HSKVCTAKGP RDRRVRLSAH TAIQFYDVQD RLGFDRPSKA  120
VDWLIKKAKS SIDELAELPP WNPADAIRLA AANAKPRRTT AKTQISLSPP PQQQQQQQQL  180
HFGAGFDRGG AEHPSNESSF LPPSMDSDSI ADTIKSFFPV VGSSTEAPPN HQLMHNYHHH  240
PPDLLSRTNS QNQDLRLSLQ SFPDGPPSLL HHNHHHHTSA SASEPVLFYG QSNPLGFDTS  300
NSVSWEQQSS EFGRIQRLVA WNSGGGGAAD TGNGGGFVFA PPPSTASFQP VLGQSQQLYS  360
QRGPLQSSYS PMIRAWFDPH HHHQSISTDD INHHHHHHLP PPVHQSAIPG IGFASGEFSS  420
GFRIPARFQG QEEEQHDGLT HKPSSASSIS RH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5zkt_A2e-1982135154Putative transcription factor PCF6
5zkt_B2e-1982135154Putative transcription factor PCF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
11318RRRRRR
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor playing a pivotal role in the control of morphogenesis of shoot organs by negatively regulating the expression of boundary-specific genes such as CUC genes, probably through the induction of miRNA (e.g. miR164) (PubMed:12931144, PubMed:17307931). Required during early steps of embryogenesis (PubMed:15634699). Participates in ovule develpment (PubMed:25378179). Activates LOX2 expression by binding to the 5'-GGACCA-3' motif found in its promoter (PubMed:18816164). {ECO:0000269|PubMed:12931144, ECO:0000269|PubMed:15634699, ECO:0000269|PubMed:17307931, ECO:0000269|PubMed:18816164, ECO:0000269|PubMed:25378179}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00009PBM25215497Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMap897773
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by the miRNA miR-JAW/miR319 (PubMed:12931144, PubMed:18816164). {ECO:0000269|PubMed:12931144, ECO:0000269|PubMed:18816164}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3167040.0AK316704.1 Arabidopsis thaliana AT3G15030 mRNA, complete cds, clone: RAFL06-89-F15.
GenBankAP0003700.0AP000370.1 Arabidopsis thaliana genomic DNA, chromosome 3, TAC clone:K15M2.
GenBankAY0944440.0AY094444.1 Arabidopsis thaliana AT3g15030/K15M2_17 mRNA, complete cds.
GenBankCP0026860.0CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020887933.10.0transcription factor TCP4
SwissprotQ8LPR50.0TCP4_ARATH; Transcription factor TCP4
TrEMBLD7L3Y20.0D7L3Y2_ARALL; Uncharacterized protein
STRINGscaffold_301743.10.0(Arabidopsis lyrata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM24082771
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G15030.30.0TCP family protein
Publications ? help Back to Top
  1. Schommer C, et al.
    Control of jasmonate biosynthesis and senescence by miR319 targets.
    PLoS Biol., 2008. 6(9): p. e230
    [PMID:18816164]
  2. Ju Y, et al.
    Arabidopsis JINGUBANG Is a Negative Regulator of Pollen Germination That Prevents Pollination in Moist Environments.
    Plant Cell, 2016. 28(9): p. 2131-2146
    [PMID:27468890]
  3. Challa KR,Aggarwal P,Nath U
    Activation of YUCCA5 by the Transcription Factor TCP4 Integrates Developmental and Environmental Signals to Promote Hypocotyl Elongation in Arabidopsis.
    Plant Cell, 2016. 28(9): p. 2117-2130
    [PMID:27597774]
  4. Alvarez JP,Furumizu C,Efroni I,Eshed Y,Bowman JL
    Active suppression of a leaf meristem orchestrates determinate leaf growth.
    Elife, 2017.
    [PMID:27710768]
  5. Li J, et al.
    RABBIT EARS regulates the transcription of TCP4 during petal development in Arabidopsis.
    J. Exp. Bot., 2016. 67(22): p. 6473-6480
    [PMID:27838638]
  6. Sun X, et al.
    Activation of secondary cell wall biosynthesis by miR319-targeted TCP4 transcription factor.
    Plant Biotechnol. J., 2017. 15(10): p. 1284-1294
    [PMID:28233945]
  7. Kubota A, et al.
    TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis.
    PLoS Genet., 2017. 13(6): p. e1006856
    [PMID:28628608]
  8. Koyama T,Sato F,Ohme-Takagi M
    Roles of miR319 and TCP Transcription Factors in Leaf Development.
    Plant Physiol., 2017. 175(2): p. 874-885
    [PMID:28842549]
  9. Bresso EG,Chorostecki U,Rodriguez RE,Palatnik JF,Schommer C
    Spatial Control of Gene Expression by miR319-Regulated TCP Transcription Factors in Leaf Development.
    Plant Physiol., 2018. 176(2): p. 1694-1708
    [PMID:29133375]
  10. Vadde BVL,Challa KR,Nath U
    The TCP4 transcription factor regulates trichome cell differentiation by directly activating GLABROUS INFLORESCENCE STEMS in Arabidopsis thaliana.
    Plant J., 2018. 93(2): p. 259-269
    [PMID:29165850]
  11. Challa KR,Rath M,Nath U
    The CIN-TCP transcription factors promote commitment to differentiation in Arabidopsis leaf pavement cells via both auxin-dependent and independent pathways.
    PLoS Genet., 2019. 15(2): p. e1007988
    [PMID:30742619]