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

Sopen12g005920.1

Organism

Solanum pennellii

Taxonomic ID

28526

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: 397aa MW: 43079.7 Da PI: 6.6804

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sopen12g005920.1	genome	spenn	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	115	1e-35	60	195	3	89
TCP 3 gkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt.................ssssasec....e 74 g+kdrhsk++T++g+RdRRvRl a++a++f+d+qd+LG+d++sk+++WL+++ak++i+el+++ ++ss+s++ + Sopen12g005920.1 60 GRKDRHSKVCTAKGPRDRRVRLAAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKASIDELAELppwkptttgaleddidvGTSSKSATimlgQ 152 89*************************************************************999999999999999884444433334543 PP TCP 75 aesssssasnsssg............................k 89 ++s sss++n +++ Sopen12g005920.1 153 NNSASSSGENVNANtntdgsfmpqsldsdaisdtiksffpmgG 195 3333333333222244445555566665555555444444441 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	7.5E-31	60	181	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	32.855	61	119	IPR017887	Transcription factor TCP subgroup

Sequence ? help Back to Top
Protein Sequence Length: 397 aa Download sequence Send to blast
MYEDLDTIKQ QQQAQSKKRS FFPPLPRPSS CSKQKAGTSS KFGCGEIVEV QGGHIIRSIG 60 RKDRHSKVCT AKGPRDRRVR LAAHTAIQFY DVQDRLGYDR PSKAVDWLIK KAKASIDELA 120 ELPPWKPTTT GALEDDIDVG TSSKSATIML GQNNSASSSG ENVNANTNTD GSFMPQSLDS 180 DAISDTIKSF FPMGGSGSNE GNSSSMQFQS FQEHNLMSRS QDLKLSLQSF QDPQAQFQAS 240 NFFTGFDASV WPQHEQQPVE LGRLAAARGD IGGGAIAGAG GYLFNSQPAP PLLQQLFSQN 300 QFLSQRGPLQ SSYSPSIRAW IDPSAIAIAT ADPVHQNQNH HQAVFPMYST SVSGIGFASE 360 LGGFSGFRIP TRIQGEIEEE HDGVFDKPSS ASSDSRH

Sequence ? help Back to Top

Protein Sequence Length: 397 aa Download sequence Send to blast

MYEDLDTIKQ QQQAQSKKRS FFPPLPRPSS CSKQKAGTSS KFGCGEIVEV QGGHIIRSIG  60
RKDRHSKVCT AKGPRDRRVR LAAHTAIQFY DVQDRLGYDR PSKAVDWLIK KAKASIDELA  120
ELPPWKPTTT GALEDDIDVG TSSKSATIML GQNNSASSSG ENVNANTNTD GSFMPQSLDS  180
DAISDTIKSF FPMGGSGSNE GNSSSMQFQS FQEHNLMSRS QDLKLSLQSF QDPQAQFQAS  240
NFFTGFDASV WPQHEQQPVE LGRLAAARGD IGGGAIAGAG GYLFNSQPAP PLLQQLFSQN  300
QFLSQRGPLQ SSYSPSIRAW IDPSAIAIAT ADPVHQNQNH HQAVFPMYST SVSGIGFASE  360
LGGFSGFRIP TRIQGEIEEE HDGVFDKPSS ASSDSRH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	2e-19	66	119	1	54	Putative transcription factor PCF6
5zkt_B	2e-19	66	119	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}.

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	HG975451	0.0	HG975451.1 Solanum pennellii chromosome ch12, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015061568.1	0.0	transcription factor TCP4-like
Swissprot	Q8LPR5	8e-97	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

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G15030.3	1e-89	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]