PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc12g014140.1.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family TCP
Protein Properties Length: 395aa    MW: 42877.5 Da    PI: 6.9634
Description TCP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc12g014140.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1TCP113.53e-3561167388
                 TCP   3 gkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt............................ 65 
                         g+kdrhsk++T++g+RdRRvRl a++a++f+d+qd+LG+d++sk+++WL+++ak++i+el+++                            
  Solyc12g014140.1.1  61 GRKDRHSKVCTAKGPRDRRVRLAAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKASIDELAELppwkptttgvdhalqddidvgtastiml 151
                         89*************************************************************8877777766666666654433333333 PP

                 TCP  66 .ssssaseceaesssssasnsssg 88 
                          +        ++s sss++n +++
  Solyc12g014140.1.1 152 gQ--------NNSASSSGENVNAN 167
                         21........22222222211111 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF036342.3E-3161188IPR005333Transcription factor, TCP
PROSITE profilePS5136932.85562120IPR017887Transcription factor TCP subgroup
Sequence ? help Back to Top
Protein Sequence    Length: 395 aa     Download sequence    Send to blast
MYEDLDTIKQ QQEQARSKKR SFFPPPPPRP SCSKQKGVTS SKFGCGEIVE VQGGHIIRSI  60
GRKDRHSKVC TAKGPRDRRV RLAAHTAIQF YDVQDRLGYD RPSKAVDWLI KKAKASIDEL  120
AELPPWKPTT TGVDHALQDD IDVGTASTIM LGQNNSASSS GENVNANTKA DGSFMPHSLD  180
SDAISDTIKS FFPMGGSGSN EGNSFQSFQQ HNLMSRSQDL KLSLQSFQDP QAQFEASNFF  240
TGFDASVWPQ HQQQPVELGR LAAARGDIGG GAIAGAGSYL FNSQPAPPLL QQLFTQNQFL  300
SQRGPLQSSY SPSIRAWIDP SAIAIATADP IHQNQNHHQA VFPMYSTSLS GIGFASELGG  360
FSGFRIPTRI QGEIEEEHDG VSDKPSSASS DSRH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5zkt_A2e-1967120154Putative transcription factor PCF6
5zkt_B2e-1967120154Putative transcription factor PCF6
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.170490.0leaf
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in cotyledons during embryogenesis. Expressed during ovule development (PubMed:25378179). {ECO:0000269|PubMed:25378179}.
UniprotTISSUE SPECIFICITY: Expressed in cotyledons, particularly in the vascular region, in leaves, roots, buds, flowers and immature siliques. {ECO:0000269|PubMed:17307931}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc12g014140.1.1
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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2095840.0Solanum lycopersicum DNA sequence from clone LE_HBa-21L2 on chromosome 12, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001234367.20.0TCP transcription factor 3
SwissprotQ8LPR51e-93TCP4_ARATH; Transcription factor TCP4
TrEMBLA0A3Q7J4J50.0A0A3Q7J4J5_SOLLC; Uncharacterized protein
STRINGSolyc12g014140.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA32072349
Representative plantOGRP18015163
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G15030.35e-81TCP family protein
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. Ori N, et al.
    Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato.
    Nat. Genet., 2007. 39(6): p. 787-91
    [PMID:17486095]
  3. Schommer C, et al.
    Control of jasmonate biosynthesis and senescence by miR319 targets.
    PLoS Biol., 2008. 6(9): p. e230
    [PMID:18816164]
  4. 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]
  5. 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]
  6. Alvarez JP,Furumizu C,Efroni I,Eshed Y,Bowman JL
    Active suppression of a leaf meristem orchestrates determinate leaf growth.
    Elife, 2017.
    [PMID:27710768]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]