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

XP_013587208.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

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

Family

TCP

Protein Properties

Length: 404aa MW: 44277.9 Da PI: 8.3791

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013587208.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	119.9	3.1e-37	45	150	2	103
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt...................ssssaseceaes 77 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak++i+el+++ XP_013587208.1 45 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGFDRPSKAVDWLIKKAKASIDELAQLppwnpadamrnaaanakprR----------- 128 79**************************************************************64443322222222111110........... PP TCP 78 ssssasnsssg....kaaksaa..kskksqks 103 + + ++s + +++++q++ XP_013587208.1 129 ----------TaaktRISPSPPppPPSQQQQQ 150 ..........1222222222221022222221 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	2.1E-32	45	146	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.256	47	105	IPR017887	Transcription factor TCP subgroup

Sequence ? help Back to Top
Protein Sequence Length: 404 aa Download sequence Send to blast
MADEAHHFLH PPAPPPPSSM RHREAANGGC GEIVEVQGGH IVRSTGRKDR HSKVCTAKGP 60 RDRRVRLSAH TAIQFYDVQD RLGFDRPSKA VDWLIKKAKA SIDELAQLPP WNPADAMRNA 120 AANAKPRRTA AKTRISPSPP PPPPSQQQQQ QLQFGGFEGV AEHRGNESSF LPPSMDSDSI 180 ADTIKSFFPV VGSTTEAPPP NQLMHSNYHH HPPNLLSRTN SHNQDLRLSL HSFPDGPPSL 240 LQHHHSASAS TAEPVLFYGQ SNPLGYDTST GGWEQQSIQR LVAWNSGGAT ETGNGGGGGF 300 LFAPPAATSF QPVLGQSQLY SQRGPLQSSY SPMIRAWFDP HHHHHQSIST DDLNHHHHHI 360 PQPVHQGEFS SGFRIPARFQ GQEEEQHDGL SNKPSSASSI SRHR

Sequence ? help Back to Top

Protein Sequence Length: 404 aa Download sequence Send to blast

MADEAHHFLH PPAPPPPSSM RHREAANGGC GEIVEVQGGH IVRSTGRKDR HSKVCTAKGP  60
RDRRVRLSAH TAIQFYDVQD RLGFDRPSKA VDWLIKKAKA SIDELAQLPP WNPADAMRNA  120
AANAKPRRTA AKTRISPSPP PPPPSQQQQQ QLQFGGFEGV AEHRGNESSF LPPSMDSDSI  180
ADTIKSFFPV VGSTTEAPPP NQLMHSNYHH HPPNLLSRTN SHNQDLRLSL HSFPDGPPSL  240
LQHHHSASAS TAEPVLFYGQ SNPLGYDTST GGWEQQSIQR LVAWNSGGAT ETGNGGGGGF  300
LFAPPAATSF QPVLGQSQLY SQRGPLQSSY SPMIRAWFDP HHHHHQSIST DDLNHHHHHI  360
PQPVHQGEFS SGFRIPARFQ GQEEEQHDGL SNKPSSASSI SRHR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	3e-20	52	105	1	54	Putative transcription factor PCF6
5zkt_B	3e-20	52	105	1	54	Putative transcription factor PCF6
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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}.

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013587208.1

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	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC189530	0.0	AC189530.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH001C24, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013587208.1	0.0	PREDICTED: transcription factor TCP4-like
Refseq	XP_013696845.1	0.0	transcription factor TCP4-like
Swissprot	Q8LPR5	0.0	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A0A0D3CK09	0.0	A0A0D3CK09_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6FFA0	0.0	A0A3P6FFA0_BRAOL; Uncharacterized protein
STRING	Bo5g127500.1	0.0	(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	1e-173	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]