PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Sme2.5_00142.1_g00013.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
Family NAC
Protein Properties Length: 884aa    MW: 98869.1 Da    PI: 4.5439
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sme2.5_00142.1_g00013.1genomeEGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM164.24.8e-51251521128
                      NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLp..kkvkaeekewyfFskrdkkyatgkrknratksgyWk 84 
                              l+pGfrFhPtdeelv +yL++k+ gk +++ e+++e+d+yk+ePw+L+  +++k+++ ewyfFs+ d+ky +g+r nrat +gyWk
  Sme2.5_00142.1_g00013.1  25 LAPGFRFHPTDEELVRYYLRRKACGKLFRF-EAVAEIDVYKSEPWELKvySALKTRDLEWYFFSPVDRKYGNGSRLNRATGQGYWK 109
                              579************************999.89**************95336777888**************************** PP

                      NAM  85 atgkdkevlskkgelvglkktLvfykgrapkgektdWvmheyrl 128
                              atgkd++v + + +++g+kktLvf++grap+g++t+Wvmheyrl
  Sme2.5_00142.1_g00013.1 110 ATGKDRPVRH-NAKTIGMKKTLVFHNGRAPDGQRTNWVMHEYRL 152
                              **********.999****************************98 PP

2NAM106.14.5e-3337547833128
                      NAM  33 v.ikevdiykvePwdLpk.......kvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlskkgelvglkktLvfyk 110
                              +  +++d+++ e +dL++       ++k+++ ewyfFs  dkky +g r+nrat++gyWk+tgkd++v+++k+e+vg+kktLv++ 
  Sme2.5_00142.1_g00013.1 375 IlQSRIDLLNKENEDLRRlvrggmsRLKTRDLEWYFFSVLDKKYGNGARTNRATEKGYWKTTGKDRAVHRNKSEVVGMKKTLVYHI 460
                              31456699999999998557787777777888****************************************************** PP

                      NAM 111 grapkgektdWvmheyrl 128
                              grapkg++t+Wvmheyrl
  Sme2.5_00142.1_g00013.1 461 GRAPKGQRTNWVMHEYRL 478
                              ****************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019412.35E-5919175IPR003441NAC domain
PROSITE profilePS5100557.42425175IPR003441NAC domain
PfamPF023651.7E-2727152IPR003441NAC domain
PROSITE profilePS5100536.791337501IPR003441NAC domain
PfamPF023652.2E-15396478IPR003441NAC domain
SuperFamilySSF1019414.05E-38399501IPR003441NAC domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009555Biological Processpollen development
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0005730Cellular Componentnucleolus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 884 aa     Download sequence    Send to blast
MEQEGVLVLK PAPARAVAAA PPTSLAPGFR FHPTDEELVR YYLRRKACGK LFRFEAVAEI  60
DVYKSEPWEL KVYSALKTRD LEWYFFSPVD RKYGNGSRLN RATGQGYWKA TGKDRPVRHN  120
AKTIGMKKTL VFHNGRAPDG QRTNWVMHEY RLADEELELA GVVQDAFVLC RIFQKSGLGP  180
PNGDRYAPFI EEEWDDDDTT HLVPGGAAEV DVAIGDEARI EGNDLDQDAR GKAPCQSENL  240
LEARALSFVC KRERSEEELE PLSLAQSKRS KHDDPSSSHA NGSEDSTTSQ QDPPTTMMTT  300
NYSPPLLTFP LLESLEPKEA QPSNSLNFDS SNLEKSVPPG YLKFISNLEN EILNVSMERE  360
TAKIEVMRAQ AMINILQSRI DLLNKENEDL RRLVRGGMSR LKTRDLEWYF FSVLDKKYGN  420
GARTNRATEK GYWKTTGKDR AVHRNKSEVV GMKKTLVYHI GRAPKGQRTN WVMHEYRLID  480
EALDRAGIPQ DAFVLCRVFQ KSGAGPKNGE QYGAPFIEEE WEDDDVQVLP KDEAAEEFVF  540
GDDIHLDANE LDQILGTGTA VAGAAHPSDY SWDENGSTEE TNNSSDAQNW VKQPGELKPI  600
DLAVQQKFDA PDQVNHEYIG ESSKNMNSED GDYLLNEPIV NGTDDLQFSD EAFLEANDLS  660
NPVEVDRSGF DMLEEYLTYF DANDDFQNMS FDPSVFFGND DQISDQALPP EKDIGEATQQ  720
FIAPSEGLGE DTNDLAASSK LVPTKPGSDC QYLFMKKASQ MLGNIHAPPA FASEFPTKEA  780
TLRLNLPSQS VSSVQFTADL VQIRDMSAAG NEMGWPLGKH SDYNIILSFG LSRGGSDDSG  840
MESFHSIHPG KTASAIFRGW FYYLFFSFLM LLMSIRIGTM ISAS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3swm_A1e-472450719174NAC domain-containing protein 19
3swm_B1e-472450719174NAC domain-containing protein 19
3swm_C1e-472450719174NAC domain-containing protein 19
3swm_D1e-472450719174NAC domain-containing protein 19
3swp_A1e-472450719174NAC domain-containing protein 19
3swp_B1e-472450719174NAC domain-containing protein 19
3swp_C1e-472450719174NAC domain-containing protein 19
3swp_D1e-472450719174NAC domain-containing protein 19
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor that binds to the motif 5'-(C/T)A(C/A)G-3' in the promoter of target genes (PubMed:25578968). Binds also to the 5'-CTTGNNNNNCAAG-3' consensus sequence in chromatin (PubMed:26617990). Can bind to the mitochondrial dysfunction motif (MDM) present in the upstream regions of mitochondrial dysfunction stimulon (MDS) genes involved in mitochondrial retrograde regulation (MRR) (PubMed:24045019). Together with NAC050 and JMJ14, regulates gene expression and flowering time by associating with the histone demethylase JMJ14, probably by the promotion of RNA-mediated gene silencing (PubMed:25578968, PubMed:26617990). Regulates siRNA-dependent post-transcriptional gene silencing (PTGS) through SGS3 expression modulation (PubMed:28207953). Required during pollen development (PubMed:19237690). {ECO:0000269|PubMed:19237690, ECO:0000269|PubMed:24045019, ECO:0000269|PubMed:25578968, ECO:0000269|PubMed:26617990, ECO:0000269|PubMed:28207953}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00612ChIP-seqTransfer from AT3G10490Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by type III effector proteins (TTEs) secreted by the pathogenic bacteria P.syringae pv. tomato DC3000 during basal defense. {ECO:0000269|PubMed:16553893}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMap-Retrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0137470.0BT013747.1 Lycopersicon esculentum clone 132610F, mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006361710.10.0PREDICTED: NAC domain-containing protein 53-like
SwissprotQ9SQY01e-101NAC52_ARATH; NAC domain containing protein 52
TrEMBLA0A3Q7JIC20.0A0A3Q7JIC2_SOLLC; Uncharacterized protein
STRINGPGSC0003DMT4000797890.0(Solanum tuberosum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA31402448
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G10500.13e-96NAC domain containing protein 53
Publications ? help Back to Top
  1. Higgins JD,Ferdous M,Osman K,Franklin FC
    The RecQ helicase AtRECQ4A is required to remove inter-chromosomal telomeric connections that arise during meiotic recombination in Arabidopsis.
    Plant J., 2011. 65(3): p. 492-502
    [PMID:21265901]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. Zhang S, et al.
    C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association.
    Cell Discov, 2019.
    [PMID:26617990]
  4. Butel N,Le Masson I,Bouteiller N,Vaucheret H,Elmayan T
    sgs1: a neomorphic nac52 allele impairing post-transcriptional gene silencing through SGS3 downregulation.
    Plant J., 2017. 90(3): p. 505-519
    [PMID:28207953]
  5. Elmayan T, et al.
    Arabidopsis mutants impaired in cosuppression.
    Plant Cell, 1998. 10(10): p. 1747-58
    [PMID:9761800]