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 RrC2690_p5
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family NAC
Protein Properties Length: 310aa    MW: 34410 Da    PI: 8.4391
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC2690_p5genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM175.21.9e-54211481128
         NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlsk.kge 98 
                 +ppGfrFhPtdeel+++yL kkv ++++++  +i++vd++k+ePw+Lp+k+k +ekewyfF+ rd+ky+tg r+nrat++gyWkatgkd+e++s+ +++
  RrC2690_p5  21 MPPGFRFHPTDEELITYYLLKKVLDSNFSC-AAISQVDLNKSEPWELPEKAKMGEKEWYFFTLRDRKYPTGLRTNRATEAGYWKATGKDREIKSSkTNS 118
                 79****************************.88***************99999****************************************985667 PP

         NAM  99 lvglkktLvfykgrapkgektdWvmheyrl 128
                 l g+kktLvfykgrapkgek+ Wvmheyrl
  RrC2690_p5 119 LLGMKKTLVFYKGRAPKGEKSCWVMHEYRL 148
                 7***************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019414.45E-6116173IPR003441NAC domain
PROSITE profilePS5100557.69421173IPR003441NAC domain
PfamPF023651.4E-2822148IPR003441NAC domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0010014Biological Processmeristem initiation
GO:0010160Biological Processformation of organ boundary
GO:0010223Biological Processsecondary shoot formation
GO:0048467Biological Processgynoecium development
GO:0051782Biological Processnegative regulation of cell division
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 310 aa     Download sequence    Send to blast
MDMDVFNGWE RSSKFEDETI MPPGFRFHPT DEELITYYLL KKVLDSNFSC AAISQVDLNK  60
SEPWELPEKA KMGEKEWYFF TLRDRKYPTG LRTNRATEAG YWKATGKDRE IKSSKTNSLL  120
GMKKTLVFYK GRAPKGEKSC WVMHEYRLDG KFSYHYITSS AKDEWVLSKV CRKSSVVSRE  180
TKLNISSGGV NCSSSASSLI APMIDAAFAK EHVSCFSNTS AAHAAADASF PPTYLPAPSP  240
SLPRQPRLFG DDVAFGQFMD VGAASGQFSI DAAFLPNLPS LPPTVFTPPS HQSFGMYGGS  300
AVSSSWPFAL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ut4_A4e-502117517167NO APICAL MERISTEM PROTEIN
1ut4_B4e-502117517167NO APICAL MERISTEM PROTEIN
1ut7_A4e-502117517167NO APICAL MERISTEM PROTEIN
1ut7_B4e-502117517167NO APICAL MERISTEM PROTEIN
3swm_A5e-502117520170NAC domain-containing protein 19
3swm_B5e-502117520170NAC domain-containing protein 19
3swm_C5e-502117520170NAC domain-containing protein 19
3swm_D5e-502117520170NAC domain-containing protein 19
3swp_A5e-502117520170NAC domain-containing protein 19
3swp_B5e-502117520170NAC domain-containing protein 19
3swp_C5e-502117520170NAC domain-containing protein 19
3swp_D5e-502117520170NAC domain-containing protein 19
4dul_A4e-502117517167NAC domain-containing protein 19
4dul_B4e-502117517167NAC domain-containing protein 19
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription 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. Seems to act as an inhibitor of cell division. {ECO:0000269|PubMed:10079219, ECO:0000269|PubMed:10750709, ECO:0000269|PubMed:11245578, ECO:0000269|PubMed:12163400, ECO:0000269|PubMed:12492830, ECO:0000269|PubMed:12610213, ECO:0000269|PubMed:12787253, ECO:0000269|PubMed:14617069, ECO:0000269|PubMed:15202996, ECO:0000269|PubMed:15294871, ECO:0000269|PubMed:15500463, ECO:0000269|PubMed:15723790, ECO:0000269|PubMed:16798887, ECO:0000269|PubMed:17122068, ECO:0000269|PubMed:17287247, ECO:0000269|PubMed:9212461}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00357DAPTransfer from AT3G15170Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By BRM, at the chromatin level, and conferring a very specific spatial expression pattern. Directly induced by ESR2 in response to cytokinins. 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:17056621, ECO:0000269|PubMed:17287247}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKC9667550.0KC966755.1 Brassica napus NAC transcription factor 54-2 (NAC54-2.1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018490509.10.0PREDICTED: protein CUP-SHAPED COTYLEDON 1-like
SwissprotQ9FRV41e-147NAC54_ARATH; Protein CUP-SHAPED COTYLEDON 1
TrEMBLA0A0D3BBF70.0A0A0D3BBF7_BRAOL; Uncharacterized protein
STRINGBo3g066690.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM134811528
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G15170.11e-131NAC family protein
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Shinohara N,Ohbayashi I,Sugiyama M
    Involvement of rRNA biosynthesis in the regulation of CUC1 gene expression and pre-meristematic cell mound formation during shoot regeneration.
    Front Plant Sci, 2014. 5: p. 159
    [PMID:24808900]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]