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_00466.1_g00013.1

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: 362aa MW: 39679 Da PI: 7.4047

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00466.1_g00013.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	114	2.1e-35	48	157	2	106
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt....ssssaseceaesssssas 83 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LG+d++sk+++WL+++a ++i+el+++ +++++ ++ +++ + +a+ Rsa1.0_00466.1_g00013.1 48 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGVDRPSKAVDWLIRKARTSIDELAQLppwdPADANAAAANAKLRRTAA 133 89**************************************************************6554222222222333333333 PP TCP 84 nsssgkaaksaa.kskksqksaas 106 + +++ + + + +++ + +++s Rsa1.0_00466.1_g00013.1 134 KTKISPSPPPPPpPQQLQFGDESS 157 333332222222244444444444 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	3.7E-31	48	136	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	32.824	50	108	IPR017887	Transcription factor TCP subgroup

Sequence ? help Back to Top
Protein Sequence Length: 362 aa Download sequence Send to blast
MADDHREAHH FLHPQPPPMR HRATSQAANG GCGEIVEVQG GHIVRCQTGR KDRHSKVCTA 60 KGPRDRRVRL SAHTAIQFYD VQDRLGVDRP SKAVDWLIRK ARTSIDELAQ LPPWDPADAN 120 AAAANAKLRR TAAKTKISPS PPPPPPPQQL QFGDESSYLP PSMDSDSIAD TMKSFFPVVG 180 SSPEAPRNQD LRLSLHSFSE GLPSLLHHHH SSASEPVLFY GQSNPFGYDT STGGWEQQSI 240 QRVVSGATDT VNGGGGCQYF APPHHPSTTS FQQVLGQSQF YSQRGPLQSS YTPMIRAWFD 300 PHHLHSISTD DLNHHHIPPP VFASGELSSG FLVPARFQGQ EEEQQDGLTN KPSSASSVSR 360 HC

Sequence ? help Back to Top

Protein Sequence Length: 362 aa Download sequence Send to blast

MADDHREAHH FLHPQPPPMR HRATSQAANG GCGEIVEVQG GHIVRCQTGR KDRHSKVCTA  60
KGPRDRRVRL SAHTAIQFYD VQDRLGVDRP SKAVDWLIRK ARTSIDELAQ LPPWDPADAN  120
AAAANAKLRR TAAKTKISPS PPPPPPPQQL QFGDESSYLP PSMDSDSIAD TMKSFFPVVG  180
SSPEAPRNQD LRLSLHSFSE GLPSLLHHHH SSASEPVLFY GQSNPFGYDT STGGWEQQSI  240
QRVVSGATDT VNGGGGCQYF APPHHPSTTS FQQVLGQSQF YSQRGPLQSS YTPMIRAWFD  300
PHHLHSISTD DLNHHHIPPP VFASGELSSG FLVPARFQGQ EEEQQDGLTN KPSSASSVSR  360
HC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	6e-19	55	108	1	54	Putative transcription factor PCF6
5zkt_B	6e-19	55	108	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00466.1_g00013.1

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_018438721.1	0.0	PREDICTED: transcription factor TCP4-like
Swissprot	Q8LPR5	1e-151	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A0A3P6F4S8	1e-180	A0A3P6F4S8_BRAOL; Uncharacterized protein
STRING	Bra021586.1-P	1e-176	(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-133	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]