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

AT1G53230.1

Common Name

F12M16.13, TCP3

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

TCP

Protein Properties

Length: 391aa MW: 43044.2 Da PI: 6.8017

Description

TEOSINTE BRANCHED 1, cycloidea and PCF transcription factor 3

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G53230.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	111.7	1.1e-34	47	154	2	111
TCP 2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt............ssssaseceaesssssasnsss 87 +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak ai++l+++ +a+++ + AT1G53230.1 47 TGRKDRHSKVCTAKGPRDRRVRLSAPTAIQFYDVQDRLGFDRPSKAVDWLITKAKSAIDDLAQLppwnpadtlrqhA--------------AAAANAK 130 79**************************************************************4333222222220..............2222222 PP TCP 88 gkaaksaakskksqksaasalnla 111 +++ k+ ++ ++q ++++++ + AT1G53230.1 131 PRKTKTLISPPPPQPEETEHHRIG 154 222222223333333333233222 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	7.9E-33	47	159	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	34.581	49	107	IPR017887	Transcription factor TCP subgroup

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009733	Biological Process	response to auxin
GO:0009965	Biological Process	leaf morphogenesis
GO:0030154	Biological Process	cell differentiation
GO:0045962	Biological Process	positive regulation of development, heterochronic
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000056	anatomy	flower bud
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009001	anatomy	fruit
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 391 aa Download sequence Send to blast
MAPDNDHFLD SPSPPLLEMR HHQSATENGG GCGEIVEVQG GHIVRSTGRK DRHSKVCTAK 60 GPRDRRVRLS APTAIQFYDV QDRLGFDRPS KAVDWLITKA KSAIDDLAQL PPWNPADTLR 120 QHAAAAANAK PRKTKTLISP PPPQPEETEH HRIGEEEDNE SSFLPASMDS DSIADTIKSF 180 FPVASTQQSY HHQPPSRGNT QNQDLLRLSL QSFQNGPPFP NQTEPALFSG QSNNQLAFDS 240 STASWEQSHQ SPEFGKIQRL VSWNNVGAAE SAGSTGGFVF ASPSSLHPVY SQSQLLSQRG 300 PLQSINTPMI RAWFDPHHHH HHHQQSMTTD DLHHHHPYHI PPGIHQSAIP GIAFASSGEF 360 SGFRIPARFQ GEQEEHGGDN KPSSASSDSR H

Sequence ? help Back to Top

Protein Sequence Length: 391 aa Download sequence Send to blast

MAPDNDHFLD SPSPPLLEMR HHQSATENGG GCGEIVEVQG GHIVRSTGRK DRHSKVCTAK  60
GPRDRRVRLS APTAIQFYDV QDRLGFDRPS KAVDWLITKA KSAIDDLAQL PPWNPADTLR  120
QHAAAAANAK PRKTKTLISP PPPQPEETEH HRIGEEEDNE SSFLPASMDS DSIADTIKSF  180
FPVASTQQSY HHQPPSRGNT QNQDLLRLSL QSFQNGPPFP NQTEPALFSG QSNNQLAFDS  240
STASWEQSHQ SPEFGKIQRL VSWNNVGAAE SAGSTGGFVF ASPSSLHPVY SQSQLLSQRG  300
PLQSINTPMI RAWFDPHHHH HHHQQSMTTD DLHHHHPYHI PPGIHQSAIP GIAFASSGEF  360
SGFRIPARFQ GEQEEHGGDN KPSSASSDSR H

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5zkt_A	4e-19	54	107	1	54	Putative transcription factor PCF6
5zkt_B	4e-19	54	107	1	54	Putative transcription factor PCF6
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Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	42562725	0.0
Genevisible	260618_at	0.0
Expression Atlas	AT1G53230	-
AtGenExpress	AT1G53230	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: First observed in the distal and middle regions of cotyledons of torpedo-shaped embryos. Later localized in bending cotyledon, and mature embryos, but no signals were detected in the presumptive shoot apical meristem (SAM) and the boundary region during embryogenesis. During flower development, first observed throughout the floral meristem. Later expressed in rapidly growing floral primordia. Detected to a lower extent in vegetative primordia. During flower development, first observed throughout the floral meristem. Expressed during ovule development (PubMed:25378179). {ECO:0000269\|PubMed:10363373, ECO:0000269\|PubMed:17307931, 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
TAIR	Encodes a member of a recently identified plant transcription factor family that includes Teosinte branched 1, Cycloidea 1, and proliferating cell nuclear antigen (PCNA) factors, PCF1 and 2. Regulated by miR319. Involved in heterchronic regulation of leaf differentiation.
UniProt	Plays 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). Participates in ovule develpment (PubMed:25378179). {ECO:0000269\|PubMed:17307931, ECO:0000269\|PubMed:25378179}.

Function -- GeneRIF ? help Back to Top
TCP3 interactions with R2R3-MYBs lead to enhanced flavonoid production, which further negatively modulates the auxin response. [PMID: 24118612]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00203	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G53230.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G04240(A), AT2G37630(A)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G53230, AT1G56650, AT1G58100, AT1G65620, AT1G66370, AT1G66380, AT1G66390, AT1G69690, AT1G71030

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G53230

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC008007	0.0	AC008007.7 Genomic sequence for Arabidopsis thaliana BAC F12M16 from chromosome I, complete sequence.
GenBank	AY099678	0.0	AY099678.1 Arabidopsis thaliana putative flower development protein cycloidea (At1g53230) mRNA, complete cds.
GenBank	BT000266	0.0	BT000266.1 Arabidopsis thaliana putative flower development protein cycloidea (At1g53230) mRNA, complete cds.
GenBank	CP002684	0.0	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001322492.1	0.0	TEOSINTE BRANCHED 1, cycloidea and PCF transcription factor 3
Refseq	NP_564624.2	0.0	TEOSINTE BRANCHED 1, cycloidea and PCF transcription factor 3
Swissprot	Q9MAH8	0.0	TCP3_ARATH; Transcription factor TCP3
TrEMBL	A0A178WDV9	0.0	A0A178WDV9_ARATH; TCP3
STRING	AT1G53230.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2408	27	71
Representative plant	OGRP180	15	163

Link Out ? help Back to Top
Phytozome	AT1G53230.1
Entrez Gene	841756
iHOP	AT1G53230
wikigenes	AT1G53230

Publications ? help Back to Top
Cubas P,Lauter N,Doebley J,Coen E The TCP domain: a motif found in proteins regulating plant growth and development. Plant J., 1999. 18(2): p. 215-22 [PMID:10363373] Cubas P,Vincent C,Coen E An epigenetic mutation responsible for natural variation in floral symmetry. Nature, 1999. 401(6749): p. 157-61 [PMID:10490023] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Lee HS,Chen ZJ Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. U.S.A., 2001. 98(12): p. 6753-8 [PMID:11371624] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Qin G, et al. An indole-3-acetic acid carboxyl methyltransferase regulates Arabidopsis leaf development. Plant Cell, 2005. 17(10): p. 2693-704 [PMID:16169896] Arciga-Reyes L,Wootton L,Kieffer M,Davies B UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis. Plant J., 2006. 47(3): p. 480-9 [PMID:16813578] Damerval C,Le Guilloux M,Jager M,Charon C Diversity and evolution of CYCLOIDEA-like TCP genes in relation to flower development in Papaveraceae. Plant Physiol., 2007. 143(2): p. 759-72 [PMID:17189327] Guti Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol., 2007. 8(1): p. R7 [PMID:17217541] Aguilar-Martínez JA,Poza-Carrión C,Cubas P Arabidopsis BRANCHED1 acts as an integrator of branching signals within axillary buds. Plant Cell, 2007. 19(2): p. 458-72 [PMID:17307924] Koyama T,Furutani M,Tasaka M,Ohme-Takagi M TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell, 2007. 19(2): p. 473-84 [PMID:17307931] L Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis. Plant Cell, 2008. 20(4): p. 947-68 [PMID:18424613] Efroni I,Blum E,Goldshmidt A,Eshed Y A protracted and dynamic maturation schedule underlies Arabidopsis leaf development. Plant Cell, 2008. 20(9): p. 2293-306 [PMID:18805992] Nag A,King S,Jack T miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2009. 106(52): p. 22534-9 [PMID:20007771] Koyama T,Mitsuda N,Seki M,Shinozaki K,Ohme-Takagi M TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis. Plant Cell, 2010. 22(11): p. 3574-88 [PMID:21119060] Giraud E, et al. TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana. Plant Cell, 2010. 22(12): p. 3921-34 [PMID:21183706] Liu Z,Jia L,Wang H,He Y HYL1 regulates the balance between adaxial and abaxial identity for leaf flattening via miRNA-mediated pathways. J. Exp. Bot., 2011. 62(12): p. 4367-81 [PMID:21610018] Klopffleisch K, et al. Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Mol. Syst. Biol., 2011. 7: p. 532 [PMID:21952135] Causier B,Ashworth M,Guo W,Davies B The TOPLESS interactome: a framework for gene repression in Arabidopsis. Plant Physiol., 2012. 158(1): p. 423-38 [PMID:22065421] Li Z,Li B,Shen WH,Huang H,Dong A TCP transcription factors interact with AS2 in the repression of class-I KNOX genes in Arabidopsis thaliana. Plant J., 2012. 71(1): p. 99-107 [PMID:22380849] Efroni I, et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev. Cell, 2013. 24(4): p. 438-45 [PMID:23449474] Li S,Zachgo S TCP3 interacts with R2R3-MYB proteins, promotes flavonoid biosynthesis and negatively regulates the auxin response in Arabidopsis thaliana. Plant J., 2013. 76(6): p. 901-13 [PMID:24118612] Danisman S, et al. Analysis of functional redundancies within the Arabidopsis TCP transcription factor family. J. Exp. Bot., 2013. 64(18): p. 5673-85 [PMID:24129704] Kim SH, et al. The Arabidopsis immune adaptor SRFR1 interacts with TCP transcription factors that redundantly contribute to effector-triggered immunity. Plant J., 2014. 78(6): p. 978-89 [PMID:24689742] Mar Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners. Plant Physiol., 2014. 166(2): p. 1022-32 [PMID:25118255] Wei B, et al. The molecular mechanism of sporocyteless/nozzle in controlling Arabidopsis ovule development. Cell Res., 2015. 25(1): p. 121-34 [PMID:25378179] Chen GH,Sun JY,Liu M,Liu J,Yang WC SPOROCYTELESS is a novel embryophyte-specific transcription repressor that interacts with TPL and TCP proteins in Arabidopsis. J Genet Genomics, 2014. 41(12): p. 617-25 [PMID:25527103] Wang X, et al. TCP transcription factors are critical for the coordinated regulation of isochorismate synthase 1 expression in Arabidopsis thaliana. Plant J., 2015. 82(1): p. 151-62 [PMID:25702611] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Alvarez JP,Furumizu C,Efroni I,Eshed Y,Bowman JL Active suppression of a leaf meristem orchestrates determinate leaf growth. Elife, 2017. [PMID:27710768] 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] Mazur MJ, et al. Arabidopsis TCP Transcription Factors Interact with the SUMO Conjugating Machinery in Nuclear Foci. Front Plant Sci, 2017. 8: p. 2043 [PMID:29250092]