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

Solyc12g014140.1.1

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: 395aa MW: 42877.5 Da PI: 6.9634

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc12g014140.1.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	113.5	3e-35	61	167	3	88
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

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	2.3E-31	61	188	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	32.855	62	120	IPR017887	Transcription 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*

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

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	2e-19	67	120	1	54	Putative transcription factor PCF6
5zkt_B	2e-19	67	120	1	54	Putative transcription factor PCF6
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.17049	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	Solyc12g014140.1.1

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	AC209584	0.0	Solanum 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
Refseq	NP_001234367.2	0.0	TCP transcription factor 3
Swissprot	Q8LPR5	1e-93	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A0A3Q7J4J5	0.0	A0A3Q7J4J5_SOLLC; Uncharacterized protein
STRING	Solyc12g014140.1.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA3207	23	49
Representative plant	OGRP180	15	163

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G15030.3	5e-81	TCP family protein

Link Out ? help Back to Top
Phytozome	Solyc12g014140.1.1
Entrez Gene	100037513

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] 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] 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]