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 mrna27171.1-v1.0-hybrid
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria
Family TCP
Protein Properties Length: 544aa    MW: 58452.9 Da    PI: 9.736
Description TCP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
mrna27171.1-v1.0-hybridgenomeGDRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1TCP116.73e-36158261189
                      TCP   1 aagkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt...............ssssas 71 
                              a+g+kdrhsk++T++g+RdRRvRl a++a++f+d+qd+LG+d++sk+++WL+++ak+ai+el ++               +     
  mrna27171.1-v1.0-hybrid 158 ATGRKDRHSKVCTAKGPRDRRVRLAAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKAAIDELDELppwnpnsisvqtsasP----- 238
                              589**************************************************************7666555554322110..... PP

                      TCP  72 ec.eaesssssasnsssg.....k 89 
                               +  + s  ++++n+ss      +
  mrna27171.1-v1.0-hybrid 239 -TaPPTSAAQETQNNSSLhfsmvE 261
                              .11111111111111111122220 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF036349.0E-30159288IPR005333Transcription factor, TCP
PROSITE profilePS5136933.273161219IPR017887Transcription 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: 544 aa     Download sequence    Send to blast
MAEPFAIRFQ KSHSTSSSRS SPSVKALGKS KAGSVEIHKP SKQKSSIVVA KNNSDRSSTS  60
SASASSSSGA AVTTVPLKAG KGNSQYPHSS TSTGEPTIEY AARKMGEQSH NNLHHHHHRA  120
TASSSSAAAR LGLGIRTTTS SSTASEIVEA RGGHIIRATG RKDRHSKVCT AKGPRDRRVR  180
LAAHTAIQFY DVQDRLGYDR PSKAVDWLIK KAKAAIDELD ELPPWNPNSI SVQTSASPTA  240
PPTSAAQETQ NNSSLHFSMV EAPSSLSANR RASMVGSGVA ELVNQNSSNF LPPSMDSDSI  300
ADTIKSFFPM GAATTAETPS FHPSYPPDLL SRTSSQSQDL RLSLHSFQDP ILLHHHQAHQ  360
HQTHHQNEQT FLTPNPLGFD SSAATWTEQH HQQQQQAELN RFQRMLAWSN AGGGDSNNNN  420
NNNSGGGGGG FTFNSLPLSQ SQSPTLQPFL FGQNQFFSSQ RGPLQSSNAP SVHAWIDHND  480
LSDHQHQMAP SMHNHHHQQS SISGMGFASG VFPGFHIPAR IQGEEEHDGI SDKPSSASSN  540
SRH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5zkt_A4e-20166219154Putative transcription factor PCF6
5zkt_B4e-20166219154Putative transcription factor PCF6
Search in ModeBase
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
MP00009PBMTransfer from 929286Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapmrna27171.1-v1.0-hybrid
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
GenBankAM4688632e-67AM468863.2 Vitis vinifera contig VV78X023076.3, whole genome shotgun sequence.
GenBankFQ3818312e-67FQ381831.1 Vitis vinifera clone SS0ABG82YF20.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004294116.10.0PREDICTED: transcription factor TCP4
SwissprotQ8LPR51e-104TCP4_ARATH; Transcription factor TCP4
TrEMBLA0A2P6QA820.0A0A2P6QA82_ROSCH; Putative transcription factor TCP family
STRINGXP_004294116.10.0(Fragaria vesca)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF116334105
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G15030.31e-100TCP 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]