PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT1G53910.1

Common Name

ERF074, RAP2-12, RAP2.12, T18A20.14

Organism

Arabidopsis thaliana

Taxonomic ID

3702

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: 358aa MW: 39801 Da PI: 4.9538

Description

related to AP2 12

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G53910.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	64.7	1.8e-20	124	173	2	55
AP2 2 gykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 +y+G+r+++ +g+W+AeIrdp+e +r++lg+f taeeAa+a++aa+++++g AT1G53910.1 124 QYRGIRQRP-WGKWAAEIRDPRE---GARIWLGTFKTAEEAARAYDAAARRIRG 173 69*****.******965...3***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00380	2.1E-37	124	187	IPR001471	AP2/ERF domain
CDD	cd00018	7.74E-18	124	182	No hit	No description
PROSITE profile	PS51032	24.395	124	181	IPR001471	AP2/ERF domain
SuperFamily	SSF54171	2.29E-22	124	182	IPR016177	DNA-binding domain
Gene3D	G3DSA:3.30.730.10	1.0E-32	124	183	IPR001471	AP2/ERF domain
PRINTS	PR00367	1.1E-11	125	136	IPR001471	AP2/ERF domain
Pfam	PF00847	3.9E-13	125	173	IPR001471	AP2/ERF domain
PRINTS	PR00367	1.1E-11	147	163	IPR001471	AP2/ERF domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009873	Biological Process	ethylene-activated signaling pathway
GO:0070483	Biological Process	detection of hypoxia
GO:0005634	Cellular Component	nucleus
GO:0005886	Cellular Component	plasma membrane
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025195	anatomy	pollen tube cell
PO:0025281	anatomy	pollen
PO:0001016	developmental stage	L mature pollen stage
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 358 aa Download sequence Send to blast
MCGGAIISDF IPPPRSRRVT SEFIWPDLKK NLKGSKKSSK NRSNFFDFDA EFEADFQGFK 60 DDSSIDCDDD FDVGDVFADV KPFVFTSTPK PAVSAAAEGS VFGKKVTGLD GDAEKSANRK 120 RKNQYRGIRQ RPWGKWAAEI RDPREGARIW LGTFKTAEEA ARAYDAAARR IRGSKAKVNF 180 PEENMKANSQ KRSVKANLQK PVAKPNPNPS PALVQNSNIS FENMCFMEEK HQVSNNNNNQ 240 FGMTNSVDAG CNGYQYFSSD QGSNSFDCSE FGWSDQAPIT PDISSAVINN NNSALFFEEA 300 NPAKKLKSMD FETPYNNTEW DASLDFLNED AVTTQDNGAN PMDLWSIDEI HSMIGGVF

Sequence ? help Back to Top

Protein Sequence Length: 358 aa Download sequence Send to blast

MCGGAIISDF IPPPRSRRVT SEFIWPDLKK NLKGSKKSSK NRSNFFDFDA EFEADFQGFK  60
DDSSIDCDDD FDVGDVFADV KPFVFTSTPK PAVSAAAEGS VFGKKVTGLD GDAEKSANRK  120
RKNQYRGIRQ RPWGKWAAEI RDPREGARIW LGTFKTAEEA ARAYDAAARR IRGSKAKVNF  180
PEENMKANSQ KRSVKANLQK PVAKPNPNPS PALVQNSNIS FENMCFMEEK HQVSNNNNNQ  240
FGMTNSVDAG CNGYQYFSSD QGSNSFDCSE FGWSDQAPIT PDISSAVINN NNSALFFEEA  300
NPAKKLKSMD FETPYNNTEW DASLDFLNED AVTTQDNGAN PMDLWSIDEI HSMIGGVF

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1gcc_A	5e-23	124	181	2	60	ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.21295	0.0	bud\| cell culture\| flower\| leaf\| root\| seed\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145336723	0.0
Genevisible	262197_at	0.0
Expression Atlas	AT1G53910	-
AtGenExpress	AT1G53910	-
ATTED-II	AT1G53910	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in seedlings, leaves, flowers, siliques and germinating seeds. {ECO:0000269\|PubMed:22020282}.

Functional Description ? help Back to Top
Source	Description
TAIR	encodes 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.
UniProt	Transcription 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
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] 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] RAP2.2, RAP2.3 and RAP2.12 play a role in modulating oxidative and osmotic stress tolerance during submergence acclimation. [PMID: 25847219] 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] 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] 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] 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
MP00204	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G53910.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by hypoxia but not by ethylene. {ECO:0000269\|PubMed:22020282}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G77120(A)

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q9SSA8

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G53910

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK316980	0.0	AK316980.1 Arabidopsis thaliana AT1G53910 mRNA, complete cds, clone: RAFL16-70-F02.
GenBank	AY037260	0.0	AY037260.1 Arabidopsis thaliana At1g53910/T18A20_14 mRNA, complete cds.
GenBank	AY057545	0.0	AY057545.1 Arabidopsis thaliana At1g53910/T18A20_14 mRNA, complete cds.
GenBank	AY113051	0.0	AY113051.1 Arabidopsis thaliana At1g53910/T18A20_14 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001031185.1	0.0	related to AP2 12
Refseq	NP_175794.1	0.0	related to AP2 12
Swissprot	Q9SSA8	0.0	RA212_ARATH; Ethylene-responsive transcription factor RAP2-12
TrEMBL	B9DG10	0.0	B9DG10_ARATH; AT1G53910 protein
STRING	AT1G53910.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM10	28	1650
Representative plant	OGRP6	16	1718

Link Out ? help Back to Top
Phytozome	AT1G53910.1
Entrez Gene	841829
iHOP	AT1G53910
wikigenes	AT1G53910

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] 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 [PMID:16151182] 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] 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 [PMID:16920880] 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 [PMID:16937017] 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 [PMID:18441225] 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 [PMID:18775970] 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 [PMID:18805951] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] 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 [PMID:22020282] Bailey-Serres J, et al. Making sense of low oxygen sensing. Trends Plant Sci., 2012. 17(3): p. 129-38 [PMID:22280796] 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 [PMID:22530619] 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 [PMID:22639648] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Weits DA, et al. Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway. Nat Commun, 2014. 5: p. 3425 [PMID:24599061] Giuntoli B, et al. A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in Arabidopsis. PLoS Biol., 2014. 12(9): p. e1001950 [PMID:25226037] 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 [PMID:25438831] 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 [PMID:25750178] 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 [PMID:25847219] 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 [PMID:26025519] 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 [PMID:26668304] Gonzali S, et al. Universal stress protein HRU1 mediates ROS homeostasis under anoxia. Nat Plants, 2015. 1: p. 15151 [PMID:27251529] 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 [PMID:27372243] Shahzad Z, et al. A Potassium-Dependent Oxygen Sensing Pathway Regulates Plant Root Hydraulics. Cell, 2016. 167(1): p. 87-98.e14 [PMID:27641502] 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 [PMID:28164334] 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 [PMID:28487707] Yao Y,Chen X,Wu AM ERF-VII members exhibit synergistic and separate roles in Arabidopsis. Plant Signal Behav, 2017. 12(6): p. e1329073 [PMID:28537474] 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 [PMID:28698356] 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 [PMID:28741696] 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 [PMID:9192694]