PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cagra.0834s0028.1.p
Organism
Capsella grandiflora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family NAC
Protein Properties Length: 449aa    MW: 50716.6 Da    PI: 6.0803
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.0834s0028.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM167.64.1e-52271541128
                  NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLp..kkvkaeekewyfFskrdkkyatgkrknratksgyWkatgk 88 
                          l+pGfrFhPtdeelv++yLk+kv +k++++ ++i evdiyk+ePwdL   +++k++++ewyf+s  dkky +g r nrat++gyWkatgk
  Cagra.0834s0028.1.p  27 LAPGFRFHPTDEELVSYYLKRKVLAKPVRF-DAIGEVDIYKHEPWDLAvfSRLKTRDQEWYFYSALDKKYGNGARMNRATNKGYWKATGK 115
                          579************************999.99**************8544899999********************************* PP

                  NAM  89 dkevlskkgelvglkktLvfykgrapkgektdWvmheyrl 128
                          d+e+ + + +l g+kktLvf++grap+g +t+Wvmheyrl
  Cagra.0834s0028.1.p 116 DREIRR-DIQLLGMKKTLVFHSGRAPDGLRTNWVMHEYRL 154
                          *****9.999****************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019411.14E-5821179IPR003441NAC domain
PROSITE profilePS5100556.77627178IPR003441NAC domain
PfamPF023651.5E-2629154IPR003441NAC 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: 449 aa     Download sequence    Send to blast
MGRESVAVVT APPSGTAPGT AAAATSLAPG FRFHPTDEEL VSYYLKRKVL AKPVRFDAIG  60
EVDIYKHEPW DLAVFSRLKT RDQEWYFYSA LDKKYGNGAR MNRATNKGYW KATGKDREIR  120
RDIQLLGMKK TLVFHSGRAP DGLRTNWVMH EYRLVEYETE KNGNLVQDAY VLCRVFHKNN  180
IGPPSGNRYA PFMEEEWADD VGALIPGVDV RLRVEPQPVA NGNNQMDQEI QSASKSLINI  240
NEPPRETVAM DIEPNQQNNH ESDIKPHEHN NNNAYEEDEE TLKREQTEEG ERPPPVCVLN  300
KEAPLPLLQY KRRRQNESNN NSSRNTQDHC SSTTTVDNTN TLISSSAAAT NTAISALLEF  360
SLMGISDKKE NPQQALRPHK EPSPHTPQAS PDEKVNDLQK EIHQMSVERE TFKLEMMSAE  420
AMISILQSRI DALRQENEEL KKNHASGQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ut4_A2e-472618016167NO APICAL MERISTEM PROTEIN
1ut4_B2e-472618016167NO APICAL MERISTEM PROTEIN
1ut7_A2e-472618016167NO APICAL MERISTEM PROTEIN
1ut7_B2e-472618016167NO APICAL MERISTEM PROTEIN
3swm_A2e-472618019170NAC domain-containing protein 19
3swm_B2e-472618019170NAC domain-containing protein 19
3swm_C2e-472618019170NAC domain-containing protein 19
3swm_D2e-472618019170NAC domain-containing protein 19
3swp_A2e-472618019170NAC domain-containing protein 19
3swp_B2e-472618019170NAC domain-containing protein 19
3swp_C2e-472618019170NAC domain-containing protein 19
3swp_D2e-472618019170NAC domain-containing protein 19
4dul_A2e-472618016167NAC domain-containing protein 19
4dul_B2e-472618016167NAC 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
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.0834s0028.1.p
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
GenBankAY0597950.0AY059795.1 Arabidopsis thaliana unknown protein (At3g10480) mRNA, complete cds.
GenBankAY0912620.0AY091262.1 Arabidopsis thaliana unknown protein (At3g10480) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023641095.10.0NAC domain containing protein 52 isoform X1
RefseqXP_023641096.10.0NAC domain containing protein 52 isoform X1
SwissprotQ9SQY00.0NAC52_ARATH; NAC domain containing protein 52
TrEMBLR0G4Y10.0R0G4Y1_9BRAS; Uncharacterized protein (Fragment)
STRINGCagra.0834s0028.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM17802880
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G10490.20.0NAC domain containing protein 52
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]