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 XP_009116467.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family NAC
Protein Properties Length: 303aa    MW: 33951.5 Da    PI: 7.4928
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009116467.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM174.53.1e-54211481128
             NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlsk 95 
                     +ppGfrFhPtdeel+++yL kkv ++++++  +i++vd++k+ePw+Lp+k+k +ekewyfF+ rd+ky+tg r+nrat++gyWkatgkd+e++s+
  XP_009116467.1  21 MPPGFRFHPTDEELITYYLLKKVLDSSFTC-AAISQVDLNKSEPWELPEKAKLGEKEWYFFTLRDRKYPTGLRTNRATEAGYWKATGKDREIKSS 114
                     79**************************99.88***************99999****************************************98 PP

             NAM  96 .kgelvglkktLvfykgrapkgektdWvmheyrl 128
                      +++l g+kktLvfykgrapkgek+ Wvmheyrl
  XP_009116467.1 115 kTKSLLGMKKTLVFYKGRAPKGEKSCWVMHEYRL 148
                     56677***************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019411.05E-6015173IPR003441NAC domain
PROSITE profilePS5100557.3721173IPR003441NAC domain
PfamPF023651.1E-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: 303 aa     Download sequence    Send to blast
MDMDVFSGWE RSSRYEDETI MPPGFRFHPT DEELITYYLL KKVLDSSFTC AAISQVDLNK  60
SEPWELPEKA KLGEKEWYFF TLRDRKYPTG LRTNRATEAG YWKATGKDRE IKSSKTKSLL  120
GMKKTLVFYK GRAPKGEKSC WVMHEYRLDG KFSYQYLTSS VKDEWVLSKV SLKSSVVVGR  180
EQTKLLSSST ASVAGEVSSS APIIDAFATE HVSCFSNTSA AAHADTSFPT YLPAPPLSLP  240
RQPRRIGGDD VAFGQFMDMG SSGQFNVDEA ATFLPYLPPT VLHPPQTFEL YGGSALSCWP  300
FAL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ut4_A1e-482117517167NO APICAL MERISTEM PROTEIN
1ut4_B1e-482117517167NO APICAL MERISTEM PROTEIN
1ut7_A1e-482117517167NO APICAL MERISTEM PROTEIN
1ut7_B1e-482117517167NO APICAL MERISTEM PROTEIN
3swm_A1e-482117520170NAC domain-containing protein 19
3swm_B1e-482117520170NAC domain-containing protein 19
3swm_C1e-482117520170NAC domain-containing protein 19
3swm_D1e-482117520170NAC domain-containing protein 19
3swp_A1e-482117520170NAC domain-containing protein 19
3swp_B1e-482117520170NAC domain-containing protein 19
3swp_C1e-482117520170NAC domain-containing protein 19
3swp_D1e-482117520170NAC domain-containing protein 19
3ulx_A1e-4881752170Stress-induced transcription factor NAC1
4dul_A1e-482117517167NAC domain-containing protein 19
4dul_B1e-482117517167NAC domain-containing protein 19
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First observed in young embryonic SAM. Later confined to the boundaries between cotyledon primordia and the SAM. In mature embryos, localized around first leaves primordia. Only weakly present in vegetative SAM. In inflorescence, observed at the boundaries between floral organ primordia. In callus, expressed during transition to shoot development, with a progressive restriction to specific areas corresponding to future shoot apex. {ECO:0000269|PubMed:11245578, ECO:0000269|PubMed:12492830}.
UniprotTISSUE SPECIFICITY: Expressed in inflorescence stems, rosette leaves, aerial parts of seedlings, flowers, floral buds and roots. {ECO:0000269|PubMed:11245578}.
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
PlantRegMapXP_009116467.1
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
GenBankKC9667540.0KC966754.1 Brassica napus NAC transcription factor 54-1 (NAC54-1.1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009116467.10.0PREDICTED: protein CUP-SHAPED COTYLEDON 1-like
SwissprotQ9FRV41e-145NAC54_ARATH; Protein CUP-SHAPED COTYLEDON 1
TrEMBLA0A078G6430.0A0A078G643_BRANA; BnaA01g28990D protein
TrEMBLM4DYJ60.0M4DYJ6_BRARP; Uncharacterized protein
STRINGBra021592.1-P0.0(Brassica rapa)
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-139NAC 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]