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

Sopim07g062680.0.1

Organism

Solanum pimpinellifolium

Taxonomic ID

4084

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: 401aa MW: 43397.7 Da PI: 6.8442

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sopim07g062680.0.1	genome	CSHL	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	114.3	1.6e-35	28	168	2	89
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt..........ssssaseceaesssssa 82 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LG+d++sk+++WL+++akpai+el+++ s+ +a++++ e+++ ++ Sopim07g062680.0.1 28 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKPAIDELAELpawkptigtaSAAAATNTNLEQEQAQK 118 79**************************************************************999988864322222222222222222 PP TCP 83 snsssg...........................................k 89 +++ ++ Sopim07g062680.0.1 119 QQEDNNfafqqgnvslfdnvagpsskraiesntasflppslesdaiadtI 168 22222245666666666665555555555555555555555555554441 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	1.3E-31	28	200	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.543	30	88	IPR017887	Transcription factor TCP subgroup

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009793	Biological Process	embryo development ending in seed dormancy
GO:0009965	Biological Process	leaf morphogenesis
GO:0030154	Biological Process	cell differentiation
GO:0045962	Biological Process	positive regulation of development, heterochronic
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 401 aa Download sequence Send to blast
MAETSRLGIR NTVGEIVEVQ GGHIVRSTGR KDRHSKVCTA KGPRDRRVRL SAHTAIQFYD 60 VQDRLGYDRP SKAVDWLIKK AKPAIDELAE LPAWKPTIGT ASAAAATNTN LEQEQAQKQQ 120 EDNNFAFQQG NVSLFDNVAG PSSKRAIESN TASFLPPSLE SDAIADTIKS FFPMGSSTSA 180 NSSAMQFHSF QEPHMLSRAN SQNQDLSLSL QFQDPILLHH QNQQAQHHNQ TNHREQEQVQ 240 GQAPAHFGGN TPLGFDTSGW SMHQRLRSWS DSREIGPGGS GGAVTGPGGY LFNSPPAPAL 300 LQQLFGQNQF FSQRGPLQSS NTSSVRAWMD PSAIAIASGD PSNHHQAALS MYPSTIPGYG 360 FASEVGGFSG FRIPARIQGE EEEHDGISDK PSSASSDSRH *

Sequence ? help Back to Top

Protein Sequence Length: 401 aa Download sequence Send to blast

MAETSRLGIR NTVGEIVEVQ GGHIVRSTGR KDRHSKVCTA KGPRDRRVRL SAHTAIQFYD  60
VQDRLGYDRP SKAVDWLIKK AKPAIDELAE LPAWKPTIGT ASAAAATNTN LEQEQAQKQQ  120
EDNNFAFQQG NVSLFDNVAG PSSKRAIESN TASFLPPSLE SDAIADTIKS FFPMGSSTSA  180
NSSAMQFHSF QEPHMLSRAN SQNQDLSLSL QFQDPILLHH QNQQAQHHNQ TNHREQEQVQ  240
GQAPAHFGGN TPLGFDTSGW SMHQRLRSWS DSREIGPGGS GGAVTGPGGY LFNSPPAPAL  300
LQQLFGQNQF FSQRGPLQSS NTSSVRAWMD PSAIAIASGD PSNHHQAALS MYPSTIPGYG  360
FASEVGGFSG FRIPARIQGE EEEHDGISDK PSSASSDSRH *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	2e-20	35	88	1	54	Putative transcription factor PCF6
5zkt_B	2e-20	35	88	1	54	Putative transcription factor PCF6
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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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00009	PBM	Transfer from 929286	Download

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}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	EF091571	0.0	EF091571.1 Solanum lycopersicum lanceolate mRNA, complete cds.
GenBank	EF091573	0.0	EF091573.1 Solanum lycopersicum lanceolate gene, complete cds.
GenBank	HG975519	0.0	HG975519.1 Solanum lycopersicum chromosome ch07, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001234335.2	0.0	cycloidea
Swissprot	Q8LPR5	1e-101	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A2I5C7	0.0	A2I5C7_SOLLC; Lanceolate
STRING	Solyc07g062680.1.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA3207	23	49

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G15030.3	3e-88	TCP family protein

Publications ? help Back to Top
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]