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_009116532.1

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: 350aa MW: 38203.2 Da PI: 7.3461

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009116532.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	114.5	1.4e-35	43	127	2	66
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt....................s 66 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++a+++i+el+++ + XP_009116532.1 43 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGFDRPSKAVDWLIRKAQTSIDELAQLppwspadairnakprrtaakT 127 79**************************************************************544433333322222222221 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	3.4E-31	43	108	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	33.397	45	103	IPR017887	Transcription factor TCP subgroup

Sequence ? help Back to Top
Protein Sequence Length: 350 aa Download sequence Send to blast
MADDHDEAHH FLHPQPPPPS SMRHRAASDE IVEVQGGHIV RSTGRKDRHS KVCTAKGPRD 60 RRVRLSAHTA IQFYDVQDRL GFDRPSKAVD WLIRKAQTSI DELAQLPPWS PADAIRNAKP 120 RRTAAKTKIS PSPPPPQREQ LQFGGARSGG FDGAAELPSF LPPSTDSESF FPVVGSSTEA 180 PPSQDLRLSL HSFPDGPPSL LHRHHSAPEP VLFYGQSNPF GYDGWEQQSI QRLVACNGGG 240 ATDTGNGGGG FLFAPSPTTS YQPVLGQSQL CSQRGSLQSS YTPMIRAWFD PHHHQSISTE 300 DLSHHIPPPV FASGEFSSGF RVPARFQGQE EEQQDGLTNK PSSASSVSRH

Sequence ? help Back to Top

Protein Sequence Length: 350 aa Download sequence Send to blast

MADDHDEAHH FLHPQPPPPS SMRHRAASDE IVEVQGGHIV RSTGRKDRHS KVCTAKGPRD  60
RRVRLSAHTA IQFYDVQDRL GFDRPSKAVD WLIRKAQTSI DELAQLPPWS PADAIRNAKP  120
RRTAAKTKIS PSPPPPQREQ LQFGGARSGG FDGAAELPSF LPPSTDSESF FPVVGSSTEA  180
PPSQDLRLSL HSFPDGPPSL LHRHHSAPEP VLFYGQSNPF GYDGWEQQSI QRLVACNGGG  240
ATDTGNGGGG FLFAPSPTTS YQPVLGQSQL CSQRGSLQSS YTPMIRAWFD PHHHQSISTE  300
DLSHHIPPPV FASGEFSSGF RVPARFQGQE EEQQDGLTNK PSSASSVSRH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	2e-19	50	103	1	54	Putative transcription factor PCF6
5zkt_B	2e-19	50	103	1	54	Putative transcription factor PCF6
Search in ModeBase

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009116532.1

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC189530	4e-95	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_009116532.1	0.0	PREDICTED: transcription factor TCP4-like
Refseq	XP_018512082.1	0.0	PREDICTED: transcription factor TCP4-like
Refseq	XP_018512083.1	0.0	PREDICTED: transcription factor TCP4-like
Swissprot	Q8LPR5	1e-145	TCP4_ARATH; Transcription factor TCP4
TrEMBL	M4DYJ0	0.0	M4DYJ0_BRARP; Uncharacterized protein
STRING	Bra021586.1-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-146	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]