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 RrC831_p3
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: 313aa    MW: 35985.1 Da    PI: 9.5685
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC831_p3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM173.18.5e-5481362129
        NAM   2 ppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpk...kvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlskkge 98 
                ppG+rFhPtdeelv++yLk+kv+   l++ +vik+vd+yk+ePwd+++   + ++ee+ewyfFs +dkky+tg+r+nrat sg+Wkatg+dk+++s k+e
  RrC831_p3   8 PPGYRFHPTDEELVDYYLKNKVAFPGLQV-DVIKDVDLYKIEPWDIQElcgRGAGEEREWYFFSYKDKKYPTGTRTNRATGSGFWKATGRDKAIYS-KQE 105
                9****************************.99**************954554455788**************************************.999 PP

        NAM  99 lvglkktLvfykgrapkgektdWvmheyrle 129
                lvg++ktLvfykgrap+g+k+dW+mheyrle
  RrC831_p3 106 LVGMRKTLVFYKGRAPNGQKSDWIMHEYRLE 136
                *****************************85 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019414.84E-604156IPR003441NAC domain
PROSITE profilePS5100558.1987156IPR003441NAC domain
PfamPF023659.1E-288135IPR003441NAC domain
HamapMF_0050818.113211310IPR001848Ribosomal protein S10
Gene3DG3DSA:3.30.70.6006.3E-39211312IPR027486Ribosomal protein S10 domain
TIGRFAMsTIGR010461.4E-38212310IPR005729Ribosomal protein S10, eukaryotic/archaeal
SuperFamilySSF549996.54E-29213310IPR027486Ribosomal protein S10 domain
PRINTSPR009715.4E-13213226IPR001848Ribosomal protein S10
SMARTSM014031.2E-37215309IPR027486Ribosomal protein S10 domain
PfamPF003381.5E-26215309IPR027486Ribosomal protein S10 domain
PROSITE patternPS003610237252IPR018268Ribosomal protein S10, conserved site
PRINTSPR009715.4E-13248263IPR001848Ribosomal protein S10
PRINTSPR009715.4E-13270284IPR001848Ribosomal protein S10
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006412Biological Processtranslation
GO:0009620Biological Processresponse to fungus
GO:0009733Biological Processresponse to auxin
GO:0009735Biological Processresponse to cytokinin
GO:0009737Biological Processresponse to abscisic acid
GO:0009741Biological Processresponse to brassinosteroid
GO:0010981Biological Processregulation of cell wall macromolecule metabolic process
GO:0043068Biological Processpositive regulation of programmed cell death
GO:0045491Biological Processxylan metabolic process
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0048759Biological Processxylem vessel member cell differentiation
GO:0090058Biological Processmetaxylem development
GO:0005634Cellular Componentnucleus
GO:0009531Cellular Componentsecondary cell wall
GO:0015935Cellular Componentsmall ribosomal subunit
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003723Molecular FunctionRNA binding
GO:0003735Molecular Functionstructural constituent of ribosome
GO:0042803Molecular Functionprotein homodimerization activity
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 313 aa     Download sequence    Send to blast
MENLSRIPPG YRFHPTDEEL VDYYLKNKVA FPGLQVDVIK DVDLYKIEPW DIQELCGRGA  60
GEEREWYFFS YKDKKYPTGT RTNRATGSGF WKATGRDKAI YSKQELVGMR KTLVFYKGRA  120
PNGQKSDWIM HEYRLETDEN GPPHEEGWVV CRAFKKKLTP INYNNPRTMM GSSSGQDSNW  180
FPQQMDREVE NMAYAAMKPT KAGLEEPLEQ IHKIRITLSS KNVKNLEKVC ADLVRGAKDK  240
RLRTKGPVRM PTKVLKITTR KAPCGEGTNT WDRFELRVHK RVIDLFSSPD VVKQITSITI  300
EPGVEVEVTI ADS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4v3p_SJ2e-61191312512740S ribosomal protein S20
4v7e_BU2e-61191312512740S ribosomal protein S10
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that binds to the secondary wall NAC binding element (SNBE), 5'-(T/A)NN(C/T)(T/C/G)TNNNNNNNA(A/C)GN(A/C/T)(A/T)-3', and to the tracheary elements (TE) specific regulating cis-element (TERE), 5'-CTTNAAAGCNA-3', in the promoter of target genes (e.g. genes involved in secondary wall biosynthesis, cell wall modification such as xylan accumulation, and programmed cell death) (PubMed:20935069, PubMed:20952636, PubMed:20488898). Involved in xylem formation in roots and shoots, especially regulating metaxylem vessel differentiation by promoting immature xylem vessel-specific genes expression, especially genes regulating programmed cell death (PCD) and secondary wall formation in tracheary elements (TE) (PubMed:16103214, PubMed:20952636, PubMed:20488898). Can activate MYB25, MYB46, MYB58, MYB63, MYB83, MYB103, CESA4, LBD15, LBD30, ERF115, XCP1, XCP2, NAC010/SND3, KNAT7, ASL19 and ASL20 expression (PubMed:17890373, PubMed:18952777, PubMed:19088331, PubMed:19122102, PubMed:19808805, PubMed:20935069, PubMed:20952636). {ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:17890373, ECO:0000269|PubMed:18952777, ECO:0000269|PubMed:19088331, ECO:0000269|PubMed:19122102, ECO:0000269|PubMed:19808805, ECO:0000269|PubMed:20488898, ECO:0000269|PubMed:20935069, ECO:0000269|PubMed:20952636}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00578DAPTransfer from AT5G62380Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By brassinosteroids (e.g. brassinolide BL), auxin (e.g. 2,4-dichlorphenoxyacetic acid 2,4-D) and cytokinin (e.g. kinetin), with a synergistic effect (PubMed:16103214). Accumulates during infection by the soilborne fungal pathogen Verticillium longisporum, especially in tissues undergoing de novo xylem formation (PubMed:23023171). {ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:23023171}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0265100.0BT026510.1 Arabidopsis thaliana At5g62380 mRNA, complete cds.
GenBankDQ0567340.0DQ056734.1 Arabidopsis thaliana no apical meristem family protein (At5g62380) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018455145.11e-139PREDICTED: NAC domain-containing protein 101-like
RefseqXP_018455146.11e-139PREDICTED: NAC domain-containing protein 101-like
SwissprotQ9LVA11e-134NC101_ARATH; NAC domain-containing protein 101
TrEMBLA0A178UFI91e-131A0A178UFI9_ARATH; VND6
STRINGBostr.0568s0569.1.p1e-133(Boechera stricta)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM122481732
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62380.11e-136NAC-domain protein 101
Publications ? help Back to Top
  1. Heyndrickx KS,Vandepoele K
    Systematic identification of functional plant modules through the integration of complementary data sources.
    Plant Physiol., 2012. 159(3): p. 884-901
    [PMID:22589469]
  2. Tan TT, et al.
    Transcription Factors VND1-VND3 Contribute to Cotyledon Xylem Vessel Formation.
    Plant Physiol., 2018. 176(1): p. 773-789
    [PMID:29133368]