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

AHYPO_016595-RA

Organism

Amaranthus hypochondriacus

Taxonomic ID

28502

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Amaranthaceae; Amaranthus

Family

TCP

Protein Properties

Length: 471aa MW: 50986.9 Da PI: 9.6088

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AHYPO_016595-RA	genome	BYU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	119.4	4.2e-37	81	182	1	89
TCP 1 aagkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgtssssaseceaesssssasnsssg...... 88 a+g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LG+d++sk+++WL+++ak ai+el ++++ s+s+++ ++s+ +++ + AHYPO_016595-RA 81 ATGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKNAIDELEQLPAWSPSSMNMSTSNRRRKKNDVKddmqee 174 589**************************************************************77777555222222222211111223333 PP TCP 89 .......k 89 + AHYPO_016595-RA 175 kgggsggS 182 34554330 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	9.8E-34	82	191	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.001	84	142	IPR017887	Transcription factor TCP subgroup

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009733	Biological Process	response to auxin
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: 471 aa Download sequence Send to blast
MKGNHFHHYN CKNNHHSIII KSEQPIKKRA YFPSSSSSSI PAGTEQVQQQ QKKQPGSSRT 60 SLRKAGIGEI VEVQGGHIVR ATGRKDRHSK VCTAKGPRDR RVRLSAHTAI QFYDVQDRLG 120 YDRPSKAVDW LIKKAKNAID ELEQLPAWSP SSMNMSTSNR RRKKNDVKDD MQEEKGGGSG 180 GSGERLYGGE DQQQLYNSSN VNNNSGSSLL PPSLDSDVIA DTMKSFFPMG VGGNVGPTSN 240 SSASEFQDYF HGGLLQRSGG NGRQNQDLKL SLQSFQDPIL MHSHSHHGGS AAHNEQQQAL 300 FPGAVPIGFE NPHTDWGDSQ HHPSPELGRL HRLVVGWNTQ QTGTEHHSVG TGSGSSNGGG 360 SGYVFNQPSP LLQPLFGGGQ HSQFLSQRGP LQSSNTPSIR AWLSDPSFSI SSSSEHHNHQ 420 AIQVHPQALS GLGFVSGGFS GFHIPARIQG EEEQNGDLNR PSSASSGSRH *

Sequence ? help Back to Top

Protein Sequence Length: 471 aa Download sequence Send to blast

MKGNHFHHYN CKNNHHSIII KSEQPIKKRA YFPSSSSSSI PAGTEQVQQQ QKKQPGSSRT  60
SLRKAGIGEI VEVQGGHIVR ATGRKDRHSK VCTAKGPRDR RVRLSAHTAI QFYDVQDRLG  120
YDRPSKAVDW LIKKAKNAID ELEQLPAWSP SSMNMSTSNR RRKKNDVKDD MQEEKGGGSG  180
GSGERLYGGE DQQQLYNSSN VNNNSGSSLL PPSLDSDVIA DTMKSFFPMG VGGNVGPTSN  240
SSASEFQDYF HGGLLQRSGG NGRQNQDLKL SLQSFQDPIL MHSHSHHGGS AAHNEQQQAL  300
FPGAVPIGFE NPHTDWGDSQ HHPSPELGRL HRLVVGWNTQ QTGTEHHSVG TGSGSSNGGG  360
SGYVFNQPSP LLQPLFGGGQ HSQFLSQRGP LQSSNTPSIR AWLSDPSFSI SSSSEHHNHQ  420
AIQVHPQALS GLGFVSGGFS GFHIPARIQG EEEQNGDLNR PSSASSGSRH *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	1e-20	89	142	1	54	Putative transcription factor PCF6
5zkt_B	1e-20	89	142	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

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_021743137.1	0.0	LOW QUALITY PROTEIN: transcription factor TCP4-like
Swissprot	Q8LPR5	6e-93	TCP4_ARATH; Transcription factor TCP4
TrEMBL	A0A0K9RU33	0.0	A0A0K9RU33_SPIOL; Uncharacterized protein
STRING	XP_004137216.1	1e-121	(Cucumis sativus)
STRING	XP_004172687.1	1e-121	(Cucumis sativus)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G15030.3	2e-47	TCP family protein

Link Out ? help Back to Top
Phytozome	AHYPO_016595-RA

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]