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 Solyc05g055480.2.1
Common NameLOC101265545
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; Lycopersicon
Family NAC
Protein Properties Length: 387aa    MW: 43469 Da    PI: 5.2676
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc05g055480.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM166.49.6e-52171441128
                 NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLp..kkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkd 89 
                         l+pGfrFhPtdeelv +yL++kv gk++++ ++++e+d+yk+eP dL   ++vk+++ ewyfFs+ dkky +g+r nrat +gyWkatgkd
  Solyc05g055480.2.1  17 LAPGFRFHPTDEELVRYYLRRKVCGKPFRF-QAVTEIDVYKSEPCDLAgySSVKSRDMEWYFFSPVDKKYCNGSRLNRATGQGYWKATGKD 106
                         579*************************99.88**************85448888999********************************* PP

                 NAM  90 kevlskkgelvglkktLvfykgrapkgektdWvmheyrl 128
                         +++ + k++++g+kktLvf++grap+g++t+Wvmheyrl
  Solyc05g055480.2.1 107 RHISH-KSQAIGMKKTLVFHSGRAPDGKRTNWVMHEYRL 144
                         ****9.999****************************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019411.7E-6011167IPR003441NAC domain
PROSITE profilePS5100556.41617167IPR003441NAC domain
PfamPF023652.0E-2819144IPR003441NAC 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: 387 aa     Download sequence    Send to blast
MEQEGSKGAV TVAPTSLAPG FRFHPTDEEL VRYYLRRKVC GKPFRFQAVT EIDVYKSEPC  60
DLAGYSSVKS RDMEWYFFSP VDKKYCNGSR LNRATGQGYW KATGKDRHIS HKSQAIGMKK  120
TLVFHSGRAP DGKRTNWVMH EYRLADKELE KAGIVQDSFV LCRIFQKSGL GPPTGDRYAP  180
FIEEEWDDDS AVLPGGETED DAVNGVDARV ESNDLDQDAP PKIACDNENV IELRSLPFAC  240
KRERSEEPEL LSLSQNKKPK HDVPSSSRAN GSEDSTITSK DPENMMTTKD YPLALLGFPL  300
LESFEPKDPQ PSNPLTFDSS NLEKSVPPGY LKFISNLETE ILNVSMERET LKIEVMRAQA  360
MINVLQSRID LLTKENEDMR KLVRGG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ut4_A5e-501616716165NO APICAL MERISTEM PROTEIN
1ut4_B5e-501616716165NO APICAL MERISTEM PROTEIN
1ut7_A5e-501616716165NO APICAL MERISTEM PROTEIN
1ut7_B5e-501616716165NO APICAL MERISTEM PROTEIN
3swm_A5e-501616719168NAC domain-containing protein 19
3swm_B5e-501616719168NAC domain-containing protein 19
3swm_C5e-501616719168NAC domain-containing protein 19
3swm_D5e-501616719168NAC domain-containing protein 19
3swp_A5e-501616719168NAC domain-containing protein 19
3swp_B5e-501616719168NAC domain-containing protein 19
3swp_C5e-501616719168NAC domain-containing protein 19
3swp_D5e-501616719168NAC domain-containing protein 19
4dul_A5e-501616716165NAC domain-containing protein 19
4dul_B5e-501616716165NAC domain-containing protein 19
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.58200.0flower| fruit| leaf| trichome
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Mostly expressed in floral organs, and, at low levels, in other organs. {ECO:0000269|PubMed:25578968}.
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
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc05g055480.2.1
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
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0146260.0Lycopersicon esculentum clone 134129R, mRNA sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004239709.10.0NAC domain containing protein 50
SwissprotQ9SQY01e-105NAC52_ARATH; NAC domain containing protein 52
TrEMBLA0A0V0I4D10.0A0A0V0I4D1_SOLCH; Putative NAC domain-containing protein 78-like
STRINGSolyc05g055480.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA31402448
Representative plantOGRP1087158
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G10490.12e-95NAC domain containing protein 52
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. 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]
  3. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  4. 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]
  5. 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]
  6. Elmayan T, et al.
    Arabidopsis mutants impaired in cosuppression.
    Plant Cell, 1998. 10(10): p. 1747-58
    [PMID:9761800]