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

Rsa1.0_23478.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

TCP

Protein Properties

Length: 235aa MW: 26008 Da PI: 9.5038

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_23478.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	118.8	6.5e-37	10	112	2	102
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt...................... 65 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak++i+el+++ Rsa1.0_23478.1_g00001.1 10 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGFDRPSKAVDWLIKKAKTSIDELAQLppwdpadairnaaanakprrta 95 79**************************************************************6444443333222222222211 PP TCP 66 .ssssaseceaesssssasnsssgkaaksaakskksqk 102 + ++a++s ++++++q+ Rsa1.0_23478.1_g00001.1 96 aK---------------------ARASPSPPPQQQPQQ 112 10.....................122222222222222 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	1.4E-32	10	114	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.016	12	70	IPR017887	Transcription factor TCP subgroup

Sequence ? help Back to Top
Protein Sequence Length: 235 aa Download sequence Send to blast
AAGGHIVRST GRKDRHSKVC TAKGPRDRRV RLSAHTAIQF YDVQDRLGFD RPSKAVDWLI 60 KKAKTSIDEL AQLPPWDPAD AIRNAAANAK PRRTAAKARA SPSPPPQQQP QQLQFCRFGG 120 VAENESSFLP PSMDSDSIAD TIKSFFPVVG SSTEAPPHQH LMHNYHHHHH HPPDLLSRTN 180 SQNQDLRLSL QPFPDGPPSL LHHNHSVAEP VLFYGQSNPL GYDASTGGWE QQSIQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	4e-20	17	70	1	54	Putative transcription factor PCF6
5zkt_B	4e-20	17	70	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_23478.1_g00001.1

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013736287.1	1e-143	transcription factor TCP4
Refseq	XP_013736288.1	1e-143	transcription factor TCP4
Refseq	XP_022572148.1	1e-143	transcription factor TCP4
Swissprot	Q8LPR5	1e-118	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A0A3P6ACC6	1e-142	A0A3P6ACC6_BRACM; Uncharacterized protein
STRING	Bo3g066540.1	1e-140	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2408	27	71

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G15030.3	8e-92	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]