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

GSBRNA2T00137591001

Common Name

GSBRNA2T00137591001, LOC106439393

Organism

Brassica napus

Taxonomic ID

3708

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: 44196.7 Da PI: 8.0171

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00137591001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	117.9	1.3e-36	50	153	2	112
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt..............ssssaseceaes 77 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak++i+el+++ + GSBRNA2T00137591001 50 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGFDRPSKAVDWLIKKAKTSIDELAQLppwdpadairnaaaN----------- 128 79**************************************************************644443333322220........... PP TCP 78 ssssasnsssgkaaksaakskksqksaasalnlak 112 ++++ +++ + s++++ ++l+++ GSBRNA2T00137591001 129 --------AKPRRTAAK--ARVSPSPPPQQLQFSG 153 ........222111111..1111111111122322 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	3.2E-32	50	155	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.016	52	110	IPR017887	Transcription factor TCP subgroup

Sequence ? help Back to Top
Protein Sequence Length: 406 aa Download sequence Send to blast
MAEDDEAHRF LHPPAPPSSS SMRRRATSEA ANGGCGEIVE VQGGHIVRST GRKDRHSKVC 60 TAKGPRDRRV RLSAHTAIQF YDVQDRLGFD RPSKAVDWLI KKAKTSIDEL AQLPPWDPAD 120 AIRNAAANAK PRRTAAKARV SPSPPPQQLQ FSGGTAVGFA GATERRSNDN NQSSFLPPSM 180 DSDSIADTIK SFFPVVGSTA EAPPHQLMHN YHHHHPPDLL SRTNSQNQDL RLSLQPFPDG 240 PPSLLHHHSV AEPVLFYGQS NPLGYDTSTG GWEQQSIQRL VAWNSGGAND TGNGGGGGGF 300 LFAPPPNHPT STTSFQPVLG QSQLYSQRGP LQSSYSPMIR AWFDPTHHHH QSISTDDLNH 360 HHHHMPPPIA SGEFSSGFRV PARFQGQEEE QHDGLNNKPS SASRH*

Sequence ? help Back to Top

Protein Sequence Length: 406 aa Download sequence Send to blast

MAEDDEAHRF LHPPAPPSSS SMRRRATSEA ANGGCGEIVE VQGGHIVRST GRKDRHSKVC  60
TAKGPRDRRV RLSAHTAIQF YDVQDRLGFD RPSKAVDWLI KKAKTSIDEL AQLPPWDPAD  120
AIRNAAANAK PRRTAAKARV SPSPPPQQLQ FSGGTAVGFA GATERRSNDN NQSSFLPPSM  180
DSDSIADTIK SFFPVVGSTA EAPPHQLMHN YHHHHPPDLL SRTNSQNQDL RLSLQPFPDG  240
PPSLLHHHSV AEPVLFYGQS NPLGYDTSTG GWEQQSIQRL VAWNSGGAND TGNGGGGGGF  300
LFAPPPNHPT STTSFQPVLG QSQLYSQRGP LQSSYSPMIR AWFDPTHHHH QSISTDDLNH  360
HHHHMPPPIA SGEFSSGFRV PARFQGQEEE QHDGLNNKPS SASRH*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	4e-20	57	110	1	54	Putative transcription factor PCF6
5zkt_B	4e-20	57	110	1	54	Putative transcription factor PCF6
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.1206	1e-112	seed

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	GSBRNA2T00137591001

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_013736287.1	0.0	transcription factor TCP4
Refseq	XP_013736288.1	0.0	transcription factor TCP4
Refseq	XP_022572148.1	0.0	transcription factor TCP4
Swissprot	Q8LPR5	0.0	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A0A3P6ACC6	0.0	A0A3P6ACC6_BRACM; Uncharacterized protein
STRING	Bra001579.1-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-169	TCP family protein

Link Out ? help Back to Top
Entrez Gene	106439393

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] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] 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]