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

Neem_2528_f_4

Organism

Azadirachta indica

Taxonomic ID

124943

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta

Family

TCP

Protein Properties

Length: 454aa MW: 50521.6 Da PI: 9.0076

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_2528_f_4	genome	NGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	103.1	4.7e-32	111	327	2	133
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt..........................ssssas 71 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LG+d++sk+++WL+++ak+ai+el+++ + Neem_2528_f_4 111 TGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKAAIDELAELppwnpetvpntaantktraaaqqnetN----- 201 79**************************************************************999987776444433333333333330..... PP TCP 72 eceaesssssasnsssg............................................................................... 88 g Neem_2528_f_4 202 ----------------Gdrnyqfpstaatiagtsndvrnlqmadnqnqsssflppsldsdsiadtiksffpmgastdtssssinfqsyppdllsrt 281 ................12333444555555555444444444444444455666666666666666666777777777777777777777777777 PP TCP 89 .kaaksaakskksqksaasalnlakesrakarararertrekmrik 133 +++++ s +s +++++ l +++++++ a+++ +++++++++++ Neem_2528_f_4 282 tSHSQDLRLSLQSFQEPSNILLPHQSHHHHAHSQVEQQQQQQHQNE 327 5444444466666777776677777666666666555555555554 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	5.8E-30	111	284	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.295	113	171	IPR017887	Transcription factor TCP subgroup

Sequence ? help Back to Top
Protein Sequence Length: 454 aa Download sequence Send to blast
MEVEILNGRA FWERQQQKKQ KNQVSVWWQL HKQQEQIRNQ KESLDTHLQQ PHKRRSCFPS 60 SSSSNFGQES IQYARKMGDS NNQAATSSRL GIRNAGGEIV EVQGGHIVRS TGRKDRHSKV 120 CTAKGPRDRR VRLSAHTAIQ FYDVQDRLGY DRPSKAVDWL IKKAKAAIDE LAELPPWNPE 180 TVPNTAANTK TRAAAQQNET NGDRNYQFPS TAATIAGTSN DVRNLQMADN QNQSSSFLPP 240 SLDSDSIADT IKSFFPMGAS TDTSSSSINF QSYPPDLLSR TTSHSQDLRL SLQSFQEPSN 300 ILLPHQSHHH HAHSQVEQQQ QQQHQNEQVQ VLFSGTNPLG YDNASAAWSE SEHQHHHSAE 360 IARFQRMMAW NSGAADTAGS ASGGAGGFVF NSQPPPPLQP LFGQNQLYNS QRGPLQSSNT 420 PSDFAFQHES KAKMRSTMAF TIGHPLLPPT LAIE

Sequence ? help Back to Top

Protein Sequence Length: 454 aa Download sequence Send to blast

MEVEILNGRA FWERQQQKKQ KNQVSVWWQL HKQQEQIRNQ KESLDTHLQQ PHKRRSCFPS  60
SSSSNFGQES IQYARKMGDS NNQAATSSRL GIRNAGGEIV EVQGGHIVRS TGRKDRHSKV  120
CTAKGPRDRR VRLSAHTAIQ FYDVQDRLGY DRPSKAVDWL IKKAKAAIDE LAELPPWNPE  180
TVPNTAANTK TRAAAQQNET NGDRNYQFPS TAATIAGTSN DVRNLQMADN QNQSSSFLPP  240
SLDSDSIADT IKSFFPMGAS TDTSSSSINF QSYPPDLLSR TTSHSQDLRL SLQSFQEPSN  300
ILLPHQSHHH HAHSQVEQQQ QQQHQNEQVQ VLFSGTNPLG YDNASAAWSE SEHQHHHSAE  360
IARFQRMMAW NSGAADTAGS ASGGAGGFVF NSQPPPPLQP LFGQNQLYNS QRGPLQSSNT  420
PSDFAFQHES KAKMRSTMAF TIGHPLLPPT LAIE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	1e-19	118	171	1	54	Putative transcription factor PCF6
5zkt_B	1e-19	118	171	1	54	Putative transcription factor PCF6
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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

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}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	GQ505958	1e-103	GQ505958.1 Citrus trifoliata cultivar Zhi TCP4 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006451744.1	1e-163	transcription factor TCP4
Refseq	XP_006485680.1	1e-163	transcription factor TCP4-like
Swissprot	Q8LPR5	6e-90	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A0A067EX66	1e-162	A0A067EX66_CITSI; Uncharacterized protein
TrEMBL	A0A2H5PZJ6	1e-162	A0A2H5PZJ6_CITUN; Uncharacterized protein
TrEMBL	V4WEK3	1e-162	V4WEK3_9ROSI; Uncharacterized protein
STRING	XP_006485680.1	1e-163	(Citrus sinensis)
STRING	XP_006451744.1	1e-163	(Citrus clementina)

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	2e-69	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]