PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G25390.2
Common NameERF005, F18G18.130, SHN3
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family ERF
Protein Properties Length: 189aa    MW: 21254.2 Da    PI: 10.1846
Description ERF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G25390.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP258.51.6e-18555155
          AP2  1 sgykGVrwdkkrgrWvAeIrdpsengkr..krfslgkfgtaeeAakaaiaarkkleg 55
                 ++++GVr++  +g+Wv+eIr+p        +r++lg+f+tae Aa+a+++a+  ++g
  AT5G25390.2  5 KKFRGVRQRQ-WGSWVSEIRHP-----LlkRRVWLGTFDTAETAARAYDQAAVLMNG 55
                 59*****999.**********8.....334*********************977765 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000182.39E-32564No hitNo description
PfamPF008473.7E-11651IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.103.2E-32663IPR001471AP2/ERF domain
SMARTSM003801.3E-38669IPR001471AP2/ERF domain
SuperFamilySSF541717.85E-20664IPR016177DNA-binding domain
PROSITE profilePS5103221.694663IPR001471AP2/ERF domain
PRINTSPR003672.3E-10718IPR001471AP2/ERF domain
PRINTSPR003672.3E-102945IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009873Biological Processethylene-activated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000115anatomysocket cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0005059anatomyroot endodermis
PO:0009009anatomyplant embryo
PO:0009029anatomystamen
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009052anatomyflower pedicel
PO:0020123anatomyroot cap
PO:0025022anatomycollective leaf structure
PO:0001185developmental stageplant embryo globular stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 189 aa     Download sequence    Send to blast
MVHSKKFRGV RQRQWGSWVS EIRHPLLKRR VWLGTFDTAE TAARAYDQAA VLMNGQSAKT  60
NFPVIKSNGS NSLEINSALR SPKSLSELLN AKLRKNCKDQ TPYLTCLRLD NDSSHIGVWQ  120
KRAGSKTSPN WVKLVELGDK VNARPGGDIE TNKMKVRNED VQEDDQMAMQ MIEELLNWTC  180
PGSGSIAQV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5wx9_A8e-186711480Ethylene-responsive transcription factor ERF096
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.196360.0inflorescence| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible246939_at0.0
Expression AtlasAT5G25390-
AtGenExpressAT5G25390-
ATTED-IIAT5G25390-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Found in all organs, mostly in veins, epidermis and trichome bases. Specific expression in lateral root tips. {ECO:0000269|PubMed:15319479}.
Functional Description ? help Back to Top
Source Description
TAIRencodes a member of the ERF (ethylene response factor) subfamily B-6 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 12 members in this subfamily including RAP2.11.
UniProtPromotes cuticle formation by inducing the expression of enzymes involved in wax biosynthesis. Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). {ECO:0000250, ECO:0000269|PubMed:15319479}.
Function -- GeneRIF ? help Back to Top
  1. Silencing SHINE clade genes (SHN1/SHN2/SHN3) reduces flower cutin load and modifies petal cell wall structure.
    [PMID: 21637781]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00527DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G25390.2
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By wounding in cauline leaves, stems, and siliques, but not in rosette leaves. {ECO:0000269|PubMed:15319479}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Interaction ? help Back to Top
Source Intact With
IntActSearch Q3E958
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G25390
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1187800.0AK118780.1 Arabidopsis thaliana At5g25390 mRNA for putative AP2 domain containing protein, complete cds, clone: RAFL21-11-L16.
GenBankBT0054610.0BT005461.1 Arabidopsis thaliana clone U51209 putative AP2 domain containing protein (At5g25390) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_197921.11e-140Integrase-type DNA-binding superfamily protein
SwissprotQ3E9581e-141SHN3_ARATH; Ethylene-responsive transcription factor SHINE 3
TrEMBLA0A178USD71e-138A0A178USD7_ARATH; SHN3
STRINGAT5G25390.21e-139(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM83428116
Representative plantOGRP6161718
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
    [PMID:11910074]
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  4. Castelli V, et al.
    Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation.
    Genome Res., 2004. 14(3): p. 406-13
    [PMID:14993207]
  5. Rizhsky L, et al.
    When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress.
    Plant Physiol., 2004. 134(4): p. 1683-96
    [PMID:15047901]
  6. Broun P,Poindexter P,Osborne E,Jiang CZ,Riechmann JL
    WIN1, a transcriptional activator of epidermal wax accumulation in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2004. 101(13): p. 4706-11
    [PMID:15070782]
  7. Czechowski T,Bari RP,Stitt M,Scheible WR,Udvardi MK
    Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes.
    Plant J., 2004. 38(2): p. 366-79
    [PMID:15078338]
  8. Aharoni A, et al.
    The SHINE clade of AP2 domain transcription factors activates wax biosynthesis, alters cuticle properties, and confers drought tolerance when overexpressed in Arabidopsis.
    Plant Cell, 2004. 16(9): p. 2463-80
    [PMID:15319479]
  9. Nagata T,Yamada H,Du Z,Todoriki S,Kikuchi S
    Microarray analysis of genes that respond to gamma-irradiation in Arabidopsis.
    J. Agric. Food Chem., 2005. 53(4): p. 1022-30
    [PMID:15713015]
  10. Nakano T,Suzuki K,Fujimura T,Shinshi H
    Genome-wide analysis of the ERF gene family in Arabidopsis and rice.
    Plant Physiol., 2006. 140(2): p. 411-32
    [PMID:16407444]
  11. Osuna D, et al.
    Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings.
    Plant J., 2007. 49(3): p. 463-91
    [PMID:17217462]
  12. Shi JX, et al.
    SHINE transcription factors act redundantly to pattern the archetypal surface of Arabidopsis flower organs.
    PLoS Genet., 2011. 7(5): p. e1001388
    [PMID:21637781]
  13. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  14. Lisso J,Schr
    NFXL2 modifies cuticle properties in Arabidopsis.
    Plant Signal Behav, 2012. 7(5): p. 551-5
    [PMID:22516817]
  15. Li-Beisson Y, et al.
    Acyl-lipid metabolism.
    Arabidopsis Book, 2013. 11: p. e0161
    [PMID:23505340]
  16. Djemal R,Khoudi H
    Isolation and molecular characterization of a novel WIN1/SHN1 ethylene-responsive transcription factor TdSHN1 from durum wheat (Triticum turgidum. L. subsp. durum).
    Protoplasma, 2015. 252(6): p. 1461-73
    [PMID:25687296]
  17. Sadler C, et al.
    Wax and cutin mutants of Arabidopsis: Quantitative characterization of the cuticular transport barrier in relation to chemical composition.
    Biochim. Biophys. Acta, 2016. 1861(9 Pt B): p. 1336-1344
    [PMID:26965486]