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

evm_27.model.AmTr_v1.0_scaffold00058.98

Common Name

AMTR_s00058p00136280, LOC18434770, nam

Organism

Amborella trichopoda

Taxonomic ID

13333

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella

Family

NAC

Protein Properties

Length: 337aa MW: 37417.9 Da PI: 7.8554

Description

NAC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00058.98	genome	TAGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NAM	181	2.9e-56	15	142	1	128
NAM 1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvkaeekewyfFskrdkkyat 70 lppGfrFhPtdeel+++yL+kkv + +++ ++i+evd++k+ePw+Lp+k+k +ekewyfFs rd+ky+t evm_27.model.AmTr_v1.0_scaffold00058.98 15 LPPGFRFHPTDEELITYYLRKKVLDGGFTA-RAIAEVDLNKCEPWELPEKAKMGEKEWYFFSLRDRKYPT 83 79***********************999.89***********99999************* PP NAM 71 gkrknratksgyWkatgkdkevlsk.kgelvglkktLvfykgrapkgektdWvmheyrl 128 g r+nrat++gyWkatgkd+e++++ + +lvg+kktLvfykgrapkgek++Wvmheyrl evm_27.model.AmTr_v1.0_scaffold00058.98 84 GLRTNRATEAGYWKATGKDREIYCSrTCSLVGMKKTLVFYKGRAPKGEKSNWVMHEYRL 142 *******************9855667*************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101941	2.75E-63	13	167	IPR003441	NAC domain
PROSITE profile	PS51005	60.251	15	167	IPR003441	NAC domain
Pfam	PF02365	4.8E-29	16	142	IPR003441	NAC domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009908	Biological Process	flower development
GO:0010072	Biological Process	primary shoot apical meristem specification
GO:0010160	Biological Process	formation of organ boundary
GO:0010223	Biological Process	secondary shoot formation
GO:0048366	Biological Process	leaf development
GO:0048504	Biological Process	regulation of timing of organ formation
GO:0051782	Biological Process	negative regulation of cell division
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 337 aa Download sequence Send to blast
MDGGFGHLEK VEGQLPPGFR FHPTDEELIT YYLRKKVLDG GFTARAIAEV DLNKCEPWEL 60 PEKAKMGEKE WYFFSLRDRK YPTGLRTNRA TEAGYWKATG KDREIYCSRT CSLVGMKKTL 120 VFYKGRAPKG EKSNWVMHEY RLDGKLSYHY LSRSTKDEWV VSRVFQKSNG GKKGRGSYTE 180 AGSPSLPALL EERESCCSYE SESGGGGPPS RDHVSCFSTP VSHSNPIHQN QGQSQMHFSE 240 VAAHYLHHSI APPLLAEPPR FNRGGVAAFP SLRSLQENLH IPFFFGGESS GGNDAGLSSG 300 SGGAMQWGVA EQKVVVAEAG QQHGGELDCM WTYRYD*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ut4_A	2e-52	15	173	17	171	NO APICAL MERISTEM PROTEIN
1ut4_B	2e-52	15	173	17	171	NO APICAL MERISTEM PROTEIN
1ut7_A	2e-52	15	173	17	171	NO APICAL MERISTEM PROTEIN
1ut7_B	2e-52	15	173	17	171	NO APICAL MERISTEM PROTEIN
4dul_A	2e-52	15	173	17	171	NAC domain-containing protein 19
4dul_B	2e-52	15	173	17	171	NAC domain-containing protein 19
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator of STM and KNAT6. Involved in molecular mechanisms regulating shoot apical meristem (SAM) formation during embryogenesis and organ separation. Required for the fusion of septa of gynoecia along the length of the ovaries. Activates the shoot formation in callus in a STM-dependent manner. Controls leaf margin development and required for leaf serration. Involved in axillary meristem initiation and separation of the meristem from the main stem. Regulates the phyllotaxy throughout the plant development. Seems to act as an inhibitor of cell division. {ECO:0000269\|PubMed:10079219, ECO:0000269\|PubMed:10750709, ECO:0000269\|PubMed:12163400, ECO:0000269\|PubMed:12492830, ECO:0000269\|PubMed:12610213, ECO:0000269\|PubMed:15202996, ECO:0000269\|PubMed:15294871, ECO:0000269\|PubMed:15500463, ECO:0000269\|PubMed:15723790, ECO:0000269\|PubMed:16798887, ECO:0000269\|PubMed:17098808, ECO:0000269\|PubMed:17122068, ECO:0000269\|PubMed:17251269, ECO:0000269\|PubMed:17287247, ECO:0000269\|PubMed:9212461}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00562	DAP	Transfer from AT5G53950	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By BRM and SYD, at the chromatin level, and conferring a very specific spatial expression pattern. Precise spatial regulation by post-transcriptional repression directed by the microRNA miR164. {ECO:0000269\|PubMed:15202996, ECO:0000269\|PubMed:15294871, ECO:0000269\|PubMed:15723790, ECO:0000269\|PubMed:16854978, ECO:0000269\|PubMed:17251269, ECO:0000269\|PubMed:17287247}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	FR668080	0.0	FR668080.1 Amborella trichopoda mRNA for NAM protein.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001292765.1	0.0	uncharacterized protein LOC18434770
Refseq	XP_020523105.1	0.0	uncharacterized protein LOC18434770 isoform X1
Refseq	XP_020523106.1	0.0	uncharacterized protein LOC18434770 isoform X1
Swissprot	O04017	1e-104	NAC98_ARATH; Protein CUP-SHAPED COTYLEDON 2
TrEMBL	G0LD32	0.0	G0LD32_AMBTC; NAM protein
STRING	ERN06571	0.0	(Amborella trichopoda)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP17	15	800

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G53950.1	1e-100	NAC family protein

Link Out ? help Back to Top
Phytozome	evm_27.model.AmTr_v1.0_scaffold00058.98
Entrez Gene	18434770

Publications ? help Back to Top
Vialette-Guiraud AC, et al. Insights from ANA-grade angiosperms into the early evolution of CUP-SHAPED COTYLEDON genes. Ann. Bot., 2011. 107(9): p. 1511-9 [PMID:21320879] Wang YX Characterization of a novel Medicago sativa NAC transcription factor gene involved in response to drought stress. Mol. Biol. Rep., 2013. 40(11): p. 6451-8 [PMID:24057250] Amborella Genome Project The Amborella genome and the evolution of flowering plants. Science, 2013. 342(6165): p. 1241089 [PMID:24357323] Kamiuchi Y,Yamamoto K,Furutani M,Tasaka M,Aida M The CUC1 and CUC2 genes promote carpel margin meristem formation during Arabidopsis gynoecium development. Front Plant Sci, 2014. 5: p. 165 [PMID:24817871] Gonçalves B, et al. A conserved role for CUP-SHAPED COTYLEDON genes during ovule development. Plant J., 2015. 83(4): p. 732-42 [PMID:26119568] Du Q,Wang H The role of HD-ZIP III transcription factors and miR165/166 in vascular development and secondary cell wall formation. Plant Signal Behav, 2015. 10(10): p. e1078955 [PMID:26340415] Vialette-Guiraud AC, et al. A Conserved Role for the NAM/miR164 Developmental Module Reveals a Common Mechanism Underlying Carpel Margin Fusion in Monocarpous and Syncarpous Eurosids. Front Plant Sci, 2015. 6: p. 1239 [PMID:26793217] Cui X, et al. REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Nat. Genet., 2016. 48(6): p. 694-9 [PMID:27111035] Blein T,Pautot V,Laufs P Combinations of Mutations Sufficient to Alter Arabidopsis Leaf Dissection. Plants (Basel), 2013. 2(2): p. 230-47 [PMID:27137374] Biot E, et al. Multiscale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis. Development, 2016. 143(18): p. 3417-28 [PMID:27387872] Zheng M, et al. Chloroplast Translation Initiation Factors Regulate Leaf Variegation and Development. Plant Physiol., 2016. 172(2): p. 1117-1130 [PMID:27535792] Balkunde R,Kitagawa M,Xu XM,Wang J,Jackson D SHOOT MERISTEMLESS trafficking controls axillary meristem formation, meristem size and organ boundaries in Arabidopsis. Plant J., 2017. 90(3): p. 435-446 [PMID:28161901] 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] González-Carranza ZH, et al. HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression. PLoS ONE, 2017. 12(9): p. e0185106 [PMID:28934292] Wilson-Sánchez D,Martínez-López S,Navarro-Cartagena S,Jover-Gil S,Micol JL Members of the DEAL subfamily of the DUF1218 gene family are required for bilateral symmetry but not for dorsoventrality in Arabidopsis leaves. New Phytol., 2018. 217(3): p. 1307-1321 [PMID:29139551] Gonçalves B, et al. GDP-L-fucose is required for boundary definition in plants. J. Exp. Bot., 2017. 68(21-22): p. 5801-5811 [PMID:29186469] Sha S, et al. To be serrate or pinnate: diverse leaf forms of yarrows (Achillea) are linked to differential expression patterns of NAM genes. Ann. Bot., 2018. 121(2): p. 255-266 [PMID:29267935] Maugarny-Calès A, et al. Dissecting the pathways coordinating patterning and growth by plant boundary domains. PLoS Genet., 2019. 15(1): p. e1007913 [PMID:30677017]