PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Solyc07g053410.2.1

Organism

Solanum lycopersicum

Taxonomic ID

4081

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: 245aa MW: 27601.6 Da PI: 9.9162

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc07g053410.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	113.3	3.4e-35	22	124	2	99
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt.....ssssaseceaesssssasnsss 87 +g+kdrhsk++T++g+RdRRvRl a++a++f+d+qd+LG+d++sk+++WL+++ak ai++l ++ ++++ + +ea++ + +++ ++ Solyc07g053410.2.1 22 TGRKDRHSKVYTAKGPRDRRVRLAAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKNAIDKLDELppwnpNQIPGNTTEADALVLKQQ-PEY 111 79**************************************************************88887444444444444444444.222 PP TCP 88 g.kaaksaakskk 99 + +++ +++++++ Solyc07g053410.2.1 112 QlQRELEENNQSR 124 2111111111111 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	1.5E-31	22	109	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	31.964	24	82	IPR017887	Transcription factor TCP subgroup

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009965	Biological Process	leaf morphogenesis
GO:0030154	Biological Process	cell differentiation
GO:0045962	Biological Process	positive regulation of development, heterochronic

Sequence ? help Back to Top
Protein Sequence Length: 245 aa Download sequence Send to blast
MKSATGGGEI VQVEGGHILR STGRKDRHSK VYTAKGPRDR RVRLAAHTAI QFYDVQDRLG 60 YDRPSKAVDW LIKKAKNAID KLDELPPWNP NQIPGNTTEA DALVLKQQPE YQLQRELEEN 120 NQSRVNNSSN SYLMQGGSGG GGGGGEVQQQ SLGDTMKAFF PMNLGTSLMN FQNYPHEIMP 180 RSSLQNEDLV IIMRMTILPF SQIKILKQII QEWLVGIYYH KHFSIKMLIM HLLKGNPFSP 240 IFHI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	2e-22	29	82	1	54	Putative transcription factor PCF6
5zkt_B	2e-22	29	82	1	54	Putative transcription factor PCF6
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.23319	0.0	leaf

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in cotyledons during embryogenesis. Expressed during ovule development (PubMed:25378179). {ECO:0000269\|PubMed:25378179}.
Uniprot	TISSUE 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
UniProt	Transcription 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
Source	Link
PlantRegMap	Solyc07g053410.2.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: 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
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	GQ496328	0.0	Solanum lycopersicum TCP transcription factor 10 (TCP10) mRNA, complete cds

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001234576.1	1e-128	TCP transcription factor 10
Swissprot	Q8LPR5	3e-53	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A0A3Q7HEI0	1e-127	A0A3Q7HEI0_SOLLC; Uncharacterized protein
STRING	Solyc07g053410.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA6607	22	34
Representative plant	OGRP180	15	163

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G15030.3	3e-50	TCP family protein

Link Out ? help Back to Top
Phytozome	Solyc07g053410.2.1

Publications ? help Back to Top
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] Schommer C, et al. Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol., 2008. 6(9): p. e230 [PMID:18816164] 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] 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] Alvarez JP,Furumizu C,Efroni I,Eshed Y,Bowman JL Active suppression of a leaf meristem orchestrates determinate leaf growth. Elife, 2017. [PMID:27710768] 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] 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] 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] 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] 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] 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] 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]