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_009146296.1

Organism

Brassica rapa

Taxonomic ID

3711

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: 406aa MW: 44035.4 Da PI: 7.5321

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009146296.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	120.6	1.8e-37	45	160	2	117
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt.ssssaseceaesssssasnsssg....... 88 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak++i+el+++ + ++ ++ ++ +++ + XP_009146296.1 45 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGFDRPSKAVDWLIKKAKASIDELAQLpP-WNPADAMRNAAANAK-----Prrtaakt 133 79**************************************************************51.222222111111111.....11222221 PP TCP 89 kaaksaakskksqksaasalnlak.esrak 117 + ++ ++ +++++++++l++ + a+ XP_009146296.1 134 RISP---SPPPPSQQQQNQLQFGGfDGAAE 160 2222...22222222222344443333333 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	1.7E-32	45	148	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.256	47	105	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: 406 aa Download sequence Send to blast
MADEAHNFLH PPAPPPPSSM SHREAANGGC GEIVEVQGGH IVRSTGRKDR HSKVCTAKGP 60 RDRRVRLSAH TAIQFYDVQD RLGFDRPSKA VDWLIKKAKA SIDELAQLPP WNPADAMRNA 120 AANAKPRRTA AKTRISPSPP PPSQQQQNQL QFGGFDGAAE HRGNENESSF LPPSMDSDSI 180 ADTIKSFFPV VGSSTEAPPP NQLIHSNYHH HHPPDLLSRT NSHNQDLRLS LHSFPDGPPS 240 LLHHHHSASA STAEPVLFYG QSNPLGYDTS TGGWEQQSIQ RLVAWNSGGA TETGNGGGGG 300 GGGFLFAPPA PSTTSFQPVL GQSPPCSPRG PLQSSYSPMI RAWFDPHHHH QSISTDDLNH 360 HIPHPVHQGE FSSGFRIPAR FQGQEEEQHD GFSNKPSSAS SISRHR

Sequence ? help Back to Top

Protein Sequence Length: 406 aa Download sequence Send to blast

MADEAHNFLH PPAPPPPSSM SHREAANGGC GEIVEVQGGH IVRSTGRKDR HSKVCTAKGP  60
RDRRVRLSAH TAIQFYDVQD RLGFDRPSKA VDWLIKKAKA SIDELAQLPP WNPADAMRNA  120
AANAKPRRTA AKTRISPSPP PPSQQQQNQL QFGGFDGAAE HRGNENESSF LPPSMDSDSI  180
ADTIKSFFPV VGSSTEAPPP NQLIHSNYHH HHPPDLLSRT NSHNQDLRLS LHSFPDGPPS  240
LLHHHHSASA STAEPVLFYG QSNPLGYDTS TGGWEQQSIQ RLVAWNSGGA TETGNGGGGG  300
GGGFLFAPPA PSTTSFQPVL GQSPPCSPRG PLQSSYSPMI RAWFDPHHHH QSISTDDLNH  360
HIPHPVHQGE FSSGFRIPAR FQGQEEEQHD GFSNKPSSAS SISRHR

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_009146296.1

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_009146296.1	0.0	PREDICTED: transcription factor TCP4
Swissprot	Q8LPR5	0.0	TCP4_ARATH; Transcription factor TCP4
TrEMBL	M4EES2	0.0	M4EES2_BRARP; Uncharacterized protein
STRING	Bra027284.1-P	0.0	(Brassica rapa)

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-172	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]