PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G53910.3
Common NameRAP2.12
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: 356aa    MW: 39656.9 Da    PI: 4.9538
Description related to AP2 12
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G53910.3genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          AP2   2 gykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                  +y+G+r+++ +g+W+AeIrdp+e    +r++lg+f taeeAa+a++aa+++++g
                  69*******.**********965...3*************************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003802.1E-37122185IPR001471AP2/ERF domain
SuperFamilySSF541712.29E-22122180IPR016177DNA-binding domain
Gene3DG3DSA:3.30.730.101.0E-32122181IPR001471AP2/ERF domain
PROSITE profilePS5103224.395122179IPR001471AP2/ERF domain
CDDcd000187.45E-18122180No hitNo description
PfamPF008473.9E-13123171IPR001471AP2/ERF domain
PRINTSPR003671.1E-11123134IPR001471AP2/ERF domain
PRINTSPR003671.1E-11145161IPR001471AP2/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:0070483Biological Processdetection of hypoxia
GO:0005634Cellular Componentnucleus
GO:0005886Cellular Componentplasma membrane
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025195anatomypollen tube cell
PO:0001016developmental stageL mature pollen stage
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 356 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.212950.0bud| cell culture| flower| leaf| root| seed| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT1G53910-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in seedlings, leaves, flowers, siliques and germinating seeds. {ECO:0000269|PubMed:22020282}.
Functional Description ? help Back to Top
Source Description
TAIRencodes a member of the ERF (ethylene response factor) subfamily B-2 of ERF/AP2 transcription factor family (RAP2.12). The protein contains one AP2 domain. There are 5 members in this subfamily including RAP2.2 AND RAP2.12.
UniProtTranscription factor involved in the activation of hypoxic gene expression and in ethylene response. Partially redundant with RAP2-2. Acts as a downstream regulator in the ethylene signaling pathway. {ECO:0000269|PubMed:22020282, ECO:0000269|PubMed:22530619}.
Function -- GeneRIF ? help Back to Top
  1. identification of a conserved amino-terminal amino acid sequence of RAP2.12 to be dedicated to an oxygen-dependent sequence of post-translational modifications, which ultimately lead to degradation of RAP2.12 under aerobic conditions
    [PMID: 22020282]
  2. In Arabidopsis, an effective low oxygen-sensing response requires RAP2.12 stabilization followed by HRA1 induction to modulate the extent of the anaerobic response by negative feedback regulation of RAP2.12.
    [PMID: 25226037]
  3. RAP2.2, RAP2.3 and RAP2.12 play a role in modulating oxidative and osmotic stress tolerance during submergence acclimation.
    [PMID: 25847219]
  4. An evolutionarily conserved 12-bp cis-regulatory motif that binds to and is sufficient for activation by RAP2.2 and RAP2.12 is identified.
    [PMID: 26668304]
  5. Results show that oxygen-sensing, mediating transcription factor RAP2.12 degradation is indispensable to optimize metabolic performance, plant growth, and development under both normoxic and hypoxic conditions.
    [PMID: 27372243]
  6. ERF74 and ERF75 play a redundant role in the up-regulation of RbohD transcription and enhance the ROS burst during the early stages of the stress response. [ERF74]
    [PMID: 28164334]
  7. Hypoxic root bending is inhibited by the group VII ethylene response factor (ERFVII) RAP2.12, as rap2.12-1 seedlings show exaggerated primary root bending.
    [PMID: 28698356]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
Motif logo
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by hypoxia but not by ethylene. {ECO:0000269|PubMed:22020282}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G77120(A)
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G53910
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3169800.0AK316980.1 Arabidopsis thaliana AT1G53910 mRNA, complete cds, clone: RAFL16-70-F02.
GenBankAY0372600.0AY037260.1 Arabidopsis thaliana At1g53910/T18A20_14 mRNA, complete cds.
GenBankAY0575450.0AY057545.1 Arabidopsis thaliana At1g53910/T18A20_14 mRNA, complete cds.
GenBankAY1130510.0AY113051.1 Arabidopsis thaliana At1g53910/T18A20_14 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001077718.10.0related to AP2 12
SwissprotQ9SSA80.0RA212_ARATH; Ethylene-responsive transcription factor RAP2-12
TrEMBLA8MRC00.0A8MRC0_ARATH; Related to AP2 12
STRINGAT1G53910.10.0(Arabidopsis thaliana)
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
  2. Kim S,Soltis PS,Wall K,Soltis DE
    Phylogeny and domain evolution in the APETALA2-like gene family.
    Mol. Biol. Evol., 2006. 23(1): p. 107-20
  3. Cao D,Cheng H,Wu W,Soo HM,Peng J
    Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis.
    Plant Physiol., 2006. 142(2): p. 509-25
  4. Jung J, et al.
    The barley ERF-type transcription factor HvRAF confers enhanced pathogen resistance and salt tolerance in Arabidopsis.
    Planta, 2007. 225(3): p. 575-88
  5. Papdi C, et al.
    Functional identification of Arabidopsis stress regulatory genes using the controlled cDNA overexpression system.
    Plant Physiol., 2008. 147(2): p. 528-42
  6. Wang Y, et al.
    Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
    Plant Physiol., 2008. 148(3): p. 1201-11
  7. Jakoby MJ, et al.
    Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106.
    Plant Physiol., 2008. 148(3): p. 1583-602
  8. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
  9. Licausi F, et al.
    Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization.
    Nature, 2011. 479(7373): p. 419-22
  10. Bailey-Serres J, et al.
    Making sense of low oxygen sensing.
    Trends Plant Sci., 2012. 17(3): p. 129-38
  11. Zhao Y, et al.
    Arabidopsis RAP2.2 plays an important role in plant resistance to Botrytis cinerea and ethylene responses.
    New Phytol., 2012. 195(2): p. 450-60
  12. Sobkowiak L,Karlowski W,Jarmolowski A,Szweykowska-Kulinska Z
    Non-Canonical Processing of Arabidopsis pri-miR319a/b/c Generates Additional microRNAs to Target One RAP2.12 mRNA Isoform.
    Front Plant Sci, 2012. 3: p. 46
  13. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
  14. Giuntoli B, et al.
    A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in Arabidopsis.
    PLoS Biol., 2014. 12(9): p. e1001950
  15. Kosmacz M, et al.
    The stability and nuclear localization of the transcription factor RAP2.12 are dynamically regulated by oxygen concentration.
    Plant Cell Environ., 2015. 38(6): p. 1094-103
  16. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
  17. Papdi C, et al.
    The low oxygen, oxidative and osmotic stress responses synergistically act through the ethylene response factor VII genes RAP2.12, RAP2.2 and RAP2.3.
    Plant J., 2015. 82(5): p. 772-84
  18. Bui LT,Giuntoli B,Kosmacz M,Parlanti S,Licausi F
    Constitutively expressed ERF-VII transcription factors redundantly activate the core anaerobic response in Arabidopsis thaliana.
    Plant Sci., 2015. 236: p. 37-43
  19. Gasch P, et al.
    Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis.
    Plant Cell, 2016. 28(1): p. 160-80
  20. Gonzali S, et al.
    Universal stress protein HRU1 mediates ROS homeostasis under anoxia.
    Nat Plants, 2015. 1: p. 15151
  21. Paul MV, et al.
    Oxygen Sensing via the Ethylene Response Transcription Factor RAP2.12 Affects Plant Metabolism and Performance under Both Normoxia and Hypoxia.
    Plant Physiol., 2016. 172(1): p. 141-53
  22. Shahzad Z, et al.
    A Potassium-Dependent Oxygen Sensing Pathway Regulates Plant Root Hydraulics.
    Cell, 2016. 167(1): p. 87-98.e14
  23. Yao Y, et al.
    ETHYLENE RESPONSE FACTOR 74 (ERF74) plays an essential role in controlling a respiratory burst oxidase homolog D (RbohD)-dependent mechanism in response to different stresses in Arabidopsis.
    New Phytol., 2017. 213(4): p. 1667-1681
  24. Giuntoli B,Licausi F,van Veen H,Perata P
    Functional Balancing of the Hypoxia Regulators RAP2.12 and HRA1 Takes Place in vivo in Arabidopsis thaliana Plants.
    Front Plant Sci, 2017. 8: p. 591
  25. Yao Y,Chen X,Wu AM
    ERF-VII members exhibit synergistic and separate roles in Arabidopsis.
    Plant Signal Behav, 2017. 12(6): p. e1329073
  26. Eysholdt-Derzsó E,Sauter M
    Root Bending Is Antagonistically Affected by Hypoxia and ERF-Mediated Transcription via Auxin Signaling.
    Plant Physiol., 2017. 175(1): p. 412-423
  27. Giuntoli B, et al.
    Age-dependent regulation of ERF-VII transcription factor activity in Arabidopsis thaliana.
    Plant Cell Environ., 2017. 40(10): p. 2333-2346
  28. Okamuro JK,Caster B,Villarroel R,Van Montagu M,Jofuku KD
    The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 1997. 94(13): p. 7076-81