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 XP_009135417.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family TCP
Protein Properties Length: 407aa    MW: 44472.9 Da    PI: 8.0355
Description TCP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009135417.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1TCP115.66.5e-36501532112
             TCP   2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt..............ssssaseceaesssssa 82 
                     +g+kdrhsk++T++g+RdRRvRlsa++a +f+d+qd+LGfd++sk+++WL+++ak++i+el+++              +                
  XP_009135417.1  50 TGRKDRHSKVCTAKGPRDRRVRLSAHTASQFYDVQDRLGFDRPSKAVDWLIKKAKTSIDELAQLppwdpadairnaaaN---------------- 128
                     79**************************************************************644443333322220................ PP

             TCP  83 snsssgkaaksaakskksqksaasalnlak 112
                         ++++ +++   + s++++ ++l+++ 
  XP_009135417.1 129 ---AKPRRTAAK--ARVSPSPPPQQLQFSG 153
                     ...222111111..1111111111122322 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF036345.7E-3250155IPR005333Transcription factor, TCP
PROSITE profilePS5136933.18852110IPR017887Transcription factor TCP subgroup
Sequence ? help Back to Top
Protein Sequence    Length: 407 aa     Download sequence    Send to blast
MAEDDEAHRF LHPPAPPSSS SMRRRATSEV ANGGCGEIVE VQGGHIVRST GRKDRHSKVC  60
TAKGPRDRRV RLSAHTASQF YDVQDRLGFD RPSKAVDWLI KKAKTSIDEL AQLPPWDPAD  120
AIRNAAANAK PRRTAAKARV SPSPPPQQLQ FSGGTAVGFA GATERRSNDN NQSSFLPPSM  180
DSDSIADTIK SFFPVVGSTA EAPPHQLMHN YHHHHPPDLL SRTNSQNQDL RLSLQPFPDG  240
PPSLLHHHHH SVAEPVLFYG QSNPLGYDTS TGGWEQQSIQ RLVAWNSGGA NDTGNGGGGG  300
GFLFAPPPNH PTSTTSFQPV LGQSQLYSQR GPLQSSYSPM IRAWFDPTHH HHQSISTDDL  360
NHHHHHMPPP IASGEFSSGF RVPARFQGQE EEQHDGLNNK PSSASRH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5zkt_A3e-1957110154Putative transcription factor PCF6
5zkt_B3e-1957110154Putative transcription factor PCF6
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.41503e-71bud| flower| leaf
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
PlantRegMapXP_009135417.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009135418.10.0PREDICTED: transcription factor TCP4-like
RefseqXP_009135419.10.0PREDICTED: transcription factor TCP4-like
SwissprotQ8LPR50.0TCP4_ARATH; Transcription factor TCP4
TrEMBLM4CBJ90.0M4CBJ9_BRARP; Uncharacterized protein
STRINGBra001579.1-P0.0(Brassica rapa)
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
AT3G15030.31e-169TCP 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]