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 Rsa1.0_02628.1_g00006.1
Organism
Raphanus sativus
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: 34416.9 Da    PI: 8.1927
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_02628.1_g00006.1genomeRGDView 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 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvkaeekewyfFskrdkkyatgkrknratksgyWkat 86 
                              +ppGfrFhPtdeel+++yL kkv ++++++  +i++vd++k+ePw+Lp+k+k +ekewyfF+ rd+ky+tg r+nrat++gyWkat
  Rsa1.0_02628.1_g00006.1  21 MPPGFRFHPTDEELITYYLLKKVLDSNFSC-AAISQVDLNKSEPWELPEKAKMGEKEWYFFTLRDRKYPTGLRTNRATEAGYWKAT 105
                              79****************************.88***************99999********************************* PP

                      NAM  87 gkdkevlsk.kgelvglkktLvfykgrapkgektdWvmheyrl 128
                              gkd+e++s+ +++l g+kktLvfykgrapkgek+ Wvmheyrl
  Rsa1.0_02628.1_g00006.1 106 GKDREIKSSkTNSLLGMKKTLVFYKGRAPKGEKSCWVMHEYRL 148
                              *******9856677***************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019413.01E-6115173IPR003441NAC domain
PROSITE profilePS5100557.40621173IPR003441NAC 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 RSSRFEDETA MPPGFRFHPT DEELITYYLL KKVLDSNFSC AAISQVDLNK  60
SEPWELPEKA KMGEKEWYFF TLRDRKYPTG LRTNRATEAG YWKATGKDRE IKSSKTNSLL  120
GMKKTLVFYK GRAPKGEKSC WVMHEYRLDG KFSYHYITSS AKDEWVLSKV CLKSSVVSRE  180
TKLNISSGGV NCSSSASSLI APMIDAAFAK EHVSCFSNTS AAHAAADASF PPTYLPAPSP  240
SLPRQPRFFG DDVAFGQFMD VGASSGQFSI DAAFLPNLPS LPPTVFTPPS HQSFGMYGGS  300
ALSSSWPFAL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ut4_A9e-501817514167NO APICAL MERISTEM PROTEIN
1ut4_B9e-501817514167NO APICAL MERISTEM PROTEIN
1ut7_A9e-501817514167NO APICAL MERISTEM PROTEIN
1ut7_B9e-501817514167NO APICAL MERISTEM PROTEIN
3swm_A1e-491817517170NAC domain-containing protein 19
3swm_B1e-491817517170NAC domain-containing protein 19
3swm_C1e-491817517170NAC domain-containing protein 19
3swm_D1e-491817517170NAC domain-containing protein 19
3swp_A1e-491817517170NAC domain-containing protein 19
3swp_B1e-491817517170NAC domain-containing protein 19
3swp_C1e-491817517170NAC domain-containing protein 19
3swp_D1e-491817517170NAC domain-containing protein 19
4dul_A9e-501817514167NAC domain-containing protein 19
4dul_B9e-501817514167NAC 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
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_02628.1_g00006.1
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-148NAC54_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-133NAC 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]