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

676784608

Organism

Sisymbrium irio

Taxonomic ID

3730

Taxonomic Lineage

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

Family

TCP

Protein Properties

Length: 439aa MW: 47964.8 Da PI: 7.3389

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
676784608	genome	VEGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	111.9	9.2e-35	54	158	2	108
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt.......................ssssaseceaess 78 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak++i+el+++ + 676784608 54 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGFDRPSKAVDWLIKKAKTSIDELAQLppwnpaeairnaaanakprrtaaK------------ 141 79**************************************************************654444443333322222221110............ PP TCP 79 sssasnsssgkaaksaakskksqksaasal 108 ++ +s +++++++++l 676784608 142 -------------TQVSPSPPPPQQQQQHL 158 .............11112222222222222 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	5.1E-31	54	161	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.016	56	114	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: 439 aa Download sequence Send to blast
MANDDDDEAH HFLHPPAPPP SLMRHRATLD AADATNGGCG EIVEVQGGHI VRSTGRKDRH 60 SKVCTAKGPR DRRVRLSAHT AIQFYDVQDR LGFDRPSKAV DWLIKKAKTS IDELAQLPPW 120 NPAEAIRNAA ANAKPRRTAA KTQVSPSPPP PQQQQQHLQF GGTRAVGFHG VAEHPSNHNE 180 SSFLPPSMDS DSIADTIKSF FPVVGSSTEA PPNQLMHSYH HHHHPPDLLS RTSSQSQDLR 240 LSLQSFPDGR PSLLHHQQQQ QHHQHSSSAS VAEPVLFYGQ SNPLGYDTST GGWEQQSSEF 300 GRIQRLVAWN SGGATDTGNG GGGFLFAPPP PPPSATSFQP VLGQSQLFSQ RGPLQSSYTP 360 MIRAWFDPHH HQSISTDDLN HHHHHIPPPV HQSAIPGIGF ASGEFSSGFR VPARFQGQEE 420 EQHDGLTNKP SSASSISRH

Sequence ? help Back to Top

Protein Sequence Length: 439 aa Download sequence Send to blast

MANDDDDEAH HFLHPPAPPP SLMRHRATLD AADATNGGCG EIVEVQGGHI VRSTGRKDRH  60
SKVCTAKGPR DRRVRLSAHT AIQFYDVQDR LGFDRPSKAV DWLIKKAKTS IDELAQLPPW  120
NPAEAIRNAA ANAKPRRTAA KTQVSPSPPP PQQQQQHLQF GGTRAVGFHG VAEHPSNHNE  180
SSFLPPSMDS DSIADTIKSF FPVVGSSTEA PPNQLMHSYH HHHHPPDLLS RTSSQSQDLR  240
LSLQSFPDGR PSLLHHQQQQ QHHQHSSSAS VAEPVLFYGQ SNPLGYDTST GGWEQQSSEF  300
GRIQRLVAWN SGGATDTGNG GGGFLFAPPP PPPSATSFQP VLGQSQLFSQ RGPLQSSYTP  360
MIRAWFDPHH HQSISTDDLN HHHHHIPPPV HQSAIPGIGF ASGEFSSGFR VPARFQGQEE  420
EQHDGLTNKP SSASSISRH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	4e-20	61	114	1	54	Putative transcription factor PCF6
5zkt_B	4e-20	61	114	1	54	Putative transcription factor PCF6
Search in ModeBase

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	676784608

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006407022.1	0.0	transcription factor TCP4
Swissprot	Q8LPR5	0.0	TCP4_ARATH; Transcription factor TCP4
TrEMBL	V4LDG9	0.0	V4LDG9_EUTSA; Uncharacterized protein
STRING	XP_006407022.1	0.0	(Eutrema salsugineum)

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-162	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]