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 AT1G13260.1
Common NameEDF4, RAV1, T6J4.2
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 RAV
Protein Properties Length: 344aa    MW: 38597.1 Da    PI: 9.8902
Description related to ABI3/VP1 1
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G13260.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP2392e-1260107154
          AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkle 54 
                  s+ykGV   + +grW A+I++      ++r++lg+f  ++eAa+a++ a  +++
  AT1G13260.1  60 SKYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEDEAARAYDVAVHRFR 107
                  89****9888.8*********3.....5**********99*********99987 PP

2B3102.81.8e-32188291199
                  EEEE-..-HHHHTT-EE--HHH.HTT.....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93 
                  f+k+ tpsdv+k++rlv+pk++ae+h     ++++ +++ l +ed +g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v F++++ ++++l+
  AT1G13260.1 188 FEKAVTPSDVGKLNRLVIPKHHAEKHfplpsSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLY 285
                  89****************************9888889***************************************************9877999999 PP

                  EEEE-S CS
           B3  94 vkvfrk 99 
                  +++ ++
  AT1G13260.1 286 IGWKSR 291
                  999776 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF008471.2E-760106IPR001471AP2/ERF domain
CDDcd000184.51E-2560118No hitNo description
SuperFamilySSF541711.83E-1660116IPR016177DNA-binding domain
PROSITE profilePS5103219.63861116IPR001471AP2/ERF domain
SMARTSM003805.2E-2661122IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.109.2E-2061117IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.106.2E-42181294IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.8E-33186294IPR015300DNA-binding pseudobarrel domain
CDDcd100171.84E-28187279No hitNo description
SMARTSM010192.0E-26188292IPR003340B3 DNA binding domain
PfamPF023621.7E-29188291IPR003340B3 DNA binding domain
PROSITE profilePS5086314.551188292IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009741Biological Processresponse to brassinosteroid
GO:0009873Biological Processethylene-activated signaling pathway
GO:0009910Biological Processnegative regulation of flower development
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048366Biological Processleaf development
GO:0048527Biological Processlateral root development
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:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
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: 344 aa     Download sequence    Send to blast
MESSSVDEST TSTGSICETP AITPAKKSSV GNLYRMGSGS SVVLDSENGV EAESRKLPSS  60
KYKGVVPQPN GRWGAQIYEK HQRVWLGTFN EEDEAARAYD VAVHRFRRRD AVTNFKDVKM  120
DEDEVDFLNS HSKSEIVDML RKHTYNEELE QSKRRRNGNG NMTRTLLTSG LSNDGVSTTG  180
FRSAEALFEK AVTPSDVGKL NRLVIPKHHA EKHFPLPSSN VSVKGVLLNF EDVNGKVWRF  240
RYSYWNSSQS YVLTKGWSRF VKEKNLRAGD VVSFSRSNGQ DQQLYIGWKS RSGSDLDAGR  300
VLRLFGVNIS PESSRNDVVG NKRVNDTEML SLVCSKKQRI FHAS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A3e-7918429810124DNA-binding protein RAV1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.205580.0cell culture| leaf| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO425620370.0
Genevisible259364_at0.0
Expression AtlasAT1G13260-
AtGenExpressAT1G13260-
ATTED-IIAT1G13260-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in all tissues examined: Roots, rosette leaves, cauline leaves, inflorescence stems, flowers and siliques. Highest expression in roots and rosette leaves. Very low expression in flowers. {ECO:0000269|PubMed:9862967}.
Functional Description ? help Back to Top
Source Description
TAIREncodes an AP2/B3 domain transcription factor which is upregulated in response to low temperature. It contains a B3 DNA binding domain. It has circadian regulation and may function as a negative growth regulator.
UniProtBinds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3'. May function as negative regulator of plant growth and development. {ECO:0000269|PubMed:15040885, ECO:0000269|PubMed:9862967}.
Function -- GeneRIF ? help Back to Top
  1. The RAV1 B3 binding domain consists of a seven-stranded open beta-barrel and two alpha-helices located at the ends of the barrel and is similar to the structure of the noncatalytic DNA binding domain of the restriction enzyme EcoRII.
    [PMID: 15548737]
  2. Arabidopsis transcription factors, RAV1 and RAV2, are regulated by touch-related stimuli in a dose-dependent and biphasic manner.
    [PMID: 19420805]
  3. Results strongly suggest that RAV1 is sufficient to cause leaf senescence and it functions as a positive regulator in this process.
    [PMID: 20826506]
  4. Transgenic cotton (Gossypium hirsutum) expressing AtRAV1/2 and/or AtABI5 showed resistance to imposed drought stress.
    [PMID: 24483851]
  5. Arabidopsis RAV1, RAV2 and Rav1L transcription factors modulates drought and salt stress responses independent of abscisic acid.
    [PMID: 25189341]
  6. RAV1 transcription factor plays an important role in abscisic acid signaling by modulating the expression of ABI3, ABI4, and ABI5, and that its activity is negatively affected by SnRK2s.Rav1 is phosphorylated by SnRK2 kinases.
    [PMID: 25231920]
  7. Data show that FOREVER YOUNG FLOWER UP-REGULATING FACTOR1 (FUF1; At1g71450) acts as an activator in suppressing ETHYLENE RESPONSE DNA BINDING FACTORs EDF1/2/3/4 function and senescence/abscission of the flowers.
    [PMID: 26063506]
  8. AtRAV1 and AtRAV2-overexpressing cotton had approximately 5% significantly longer fibers with only marginal decreases in yields under well-watered or drought stress conditions that resulted in 40-60% yield penalties and 3-7% fiber length penalties in control plants.
    [PMID: 26706061]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00139DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G13260.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated by brassinosteroid and zeatin. {ECO:0000269|PubMed:15040885}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT4G25470 (A)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDbrassinosteroid
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G13260
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0138860.0AB013886.1 Arabidopsis thaliana mRNA for RAV1, complete cds.
GenBankAC0118100.0AC011810.8 Arabidopsis thaliana chromosome I BAC T6J4 genomic sequence, complete sequence.
GenBankAY0638550.0AY063855.1 Arabidopsis thaliana putative DNA-binding protein RAV1 (At1g13260) mRNA, complete cds.
GenBankAY0912910.0AY091291.1 Arabidopsis thaliana putative DNA-binding protein RAV1 (At1g13260) mRNA, complete cds.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_172784.10.0related to ABI3/VP1 1
SwissprotQ9ZWM90.0RAV1_ARATH; AP2/ERF and B3 domain-containing transcription factor RAV1
TrEMBLA0A178WCC50.0A0A178WCC5_ARATH; RAV1
STRINGAT1G13260.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM84827121
Representative plantOGRP36516108
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. Gutierrez RA,Ewing RM,Cherry JM,Green PJ
    Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes.
    Proc. Natl. Acad. Sci. U.S.A., 2002. 99(17): p. 11513-8
    [PMID:12167669]
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  4. Hu YX,Wang YX,Liu XF,Li JY
    Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development.
    Cell Res., 2004. 14(1): p. 8-15
    [PMID:15040885]
  5. Zhang JZ,Creelman RA,Zhu JK
    From laboratory to field. Using information from Arabidopsis to engineer salt, cold, and drought tolerance in crops.
    Plant Physiol., 2004. 135(2): p. 615-21
    [PMID:15173567]
  6. Yamasaki K, et al.
    Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1.
    Plant Cell, 2004. 16(12): p. 3448-59
    [PMID:15548737]
  7. Koroleva OA,Tomlinson ML,Leader D,Shaw P,Doonan JH
    High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions.
    Plant J., 2005. 41(1): p. 162-74
    [PMID:15610358]
  8. Fowler SG,Cook D,Thomashow MF
    Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock.
    Plant Physiol., 2005. 137(3): p. 961-8
    [PMID:15728337]
  9. Stepanova AN,Hoyt JM,Hamilton AA,Alonso JM
    A Link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis.
    Plant Cell, 2005. 17(8): p. 2230-42
    [PMID:15980261]
  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. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  12. Ikeda M,Ohme-Takagi M
    A novel group of transcriptional repressors in Arabidopsis.
    Plant Cell Physiol., 2009. 50(5): p. 970-5
    [PMID:19324928]
  13. Kagaya Y,Hattori T
    Arabidopsis transcription factors, RAV1 and RAV2, are regulated by touch-related stimuli in a dose-dependent and biphasic manner.
    Genes Genet. Syst., 2009. 84(1): p. 95-9
    [PMID:19420805]
  14. Gong W, et al.
    The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors.
    Mol Plant, 2008. 1(1): p. 27-41
    [PMID:19802365]
  15. Sharabi-Schwager M,Lers A,Samach A,Guy CL,Porat R
    Overexpression of the CBF2 transcriptional activator in Arabidopsis delays leaf senescence and extends plant longevity.
    J. Exp. Bot., 2010. 61(1): p. 261-73
    [PMID:19854800]
  16. Yun KY, et al.
    Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress.
    BMC Plant Biol., 2010. 10: p. 16
    [PMID:20100339]
  17. Dong CJ,Liu JY
    The Arabidopsis EAR-motif-containing protein RAP2.1 functions as an active transcriptional repressor to keep stress responses under tight control.
    BMC Plant Biol., 2010. 10: p. 47
    [PMID:20230648]
  18. Lee SC,Choi DS,Hwang IS,Hwang BK
    The pepper oxidoreductase CaOXR1 interacts with the transcription factor CaRAV1 and is required for salt and osmotic stress tolerance.
    Plant Mol. Biol., 2010. 73(4-5): p. 409-24
    [PMID:20333442]
  19. Woo HR, et al.
    The RAV1 transcription factor positively regulates leaf senescence in Arabidopsis.
    J. Exp. Bot., 2010. 61(14): p. 3947-57
    [PMID:20826506]
  20. Causier B,Ashworth M,Guo W,Davies B
    The TOPLESS interactome: a framework for gene repression in Arabidopsis.
    Plant Physiol., 2012. 158(1): p. 423-38
    [PMID:22065421]
  21. Moreno-Cort
    CsRAV1 induces sylleptic branching in hybrid poplar.
    New Phytol., 2012. 194(1): p. 83-90
    [PMID:22229950]
  22. Chen L, et al.
    Arabidopsis BPM proteins function as substrate adaptors to a cullin3-based E3 ligase to affect fatty acid metabolism in plants.
    Plant Cell, 2013. 25(6): p. 2253-64
    [PMID:23792371]
  23. Mittal A, et al.
    Related to ABA-Insensitive3(ABI3)/Viviparous1 and AtABI5 transcription factor coexpression in cotton enhances drought stress adaptation.
    Plant Biotechnol. J., 2014. 12(5): p. 578-89
    [PMID:24483851]
  24. Matías-Hernández L,Aguilar-Jaramillo AE,Marín-González E,Suárez-López P,Pelaz S
    RAV genes: regulation of floral induction and beyond.
    Ann. Bot., 2014. 114(7): p. 1459-70
    [PMID:24812253]
  25. Fu M,Kang HK,Son SH,Kim SK,Nam KH
    A subset of Arabidopsis RAV transcription factors modulates drought and salt stress responses independent of ABA.
    Plant Cell Physiol., 2014. 55(11): p. 1892-904
    [PMID:25189341]
  26. Feng CZ, et al.
    Arabidopsis RAV1 transcription factor, phosphorylated by SnRK2 kinases, regulates the expression of ABI3, ABI4, and ABI5 during seed germination and early seedling development.
    Plant J., 2014. 80(4): p. 654-68
    [PMID:25231920]
  27. 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]
  28. Chen WH,Li PF,Chen MK,Lee YI,Yang CH
    FOREVER YOUNG FLOWER Negatively Regulates Ethylene Response DNA-Binding Factors by Activating an Ethylene-Responsive Factor to Control Arabidopsis Floral Organ Senescence and Abscission.
    Plant Physiol., 2015. 168(4): p. 1666-83
    [PMID:26063506]
  29. Mittal A,Jiang Y,Ritchie GL,Burke JJ,Rock CD
    AtRAV1 and AtRAV2 overexpression in cotton increases fiber length differentially under drought stress and delays flowering.
    Plant Sci., 2015. 241: p. 78-95
    [PMID:26706061]
  30. Huang Y,Feng CZ,Ye Q,Wu WH,Chen YF
    Arabidopsis WRKY6 Transcription Factor Acts as a Positive Regulator of Abscisic Acid Signaling during Seed Germination and Early Seedling Development.
    PLoS Genet., 2016. 12(2): p. e1005833
    [PMID:26829043]
  31. Zhao Y, et al.
    ABA receptor PYL9 promotes drought resistance and leaf senescence.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(7): p. 1949-54
    [PMID:26831097]
  32. Kagaya Y,Ohmiya K,Hattori T
    RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants.
    Nucleic Acids Res., 1999. 27(2): p. 470-8
    [PMID:9862967]