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 AT1G25560.1
Common NameAtTEM1, EDF1, F2J7.3, TEM1
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: 361aa    MW: 40557.7 Da    PI: 9.7148
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G25560.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP237.94.5e-1270118155
          AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                  s+ykGV   + +grW A+I++      ++r++lg+f  +eeAa  ++ a ++++g
  AT1G25560.1  70 SKYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAASSYDIAVRRFRG 118
                  89****9888.8*********3.....5************************998 PP

2B3104.74.8e-33195302196
                  EEEE-..-HHHHTT-EE--HHH.HTT............---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh............ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                  f+k+ tpsdv+k++rlv+pk++ae+h            + ++++++ + led++g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v F+++ 
  AT1G25560.1 195 FEKTVTPSDVGKLNRLVIPKQHAEKHfplpamttamgmNPSPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCFERST 292
                  99*********************************988666789***************************************************886 PP

                  SSEE..EEEE CS
           B3  87 rsefelvvkv 96 
                    +++l++++
  AT1G25560.1 293 GPDRQLYIHW 302
                  6888888876 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000181.51E-2470125No hitNo description
SuperFamilySSF541713.86E-1670126IPR016177DNA-binding domain
PfamPF008473.4E-670118IPR001471AP2/ERF domain
PROSITE profilePS5103219.67871126IPR001471AP2/ERF domain
SMARTSM003806.1E-2871132IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.108.3E-2071126IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.101.1E-40190307IPR015300DNA-binding pseudobarrel domain
CDDcd100173.77E-30194301No hitNo description
SuperFamilySSF1019361.44E-32194303IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086314.212195306IPR003340B3 DNA binding domain
SMARTSM010191.3E-26195306IPR003340B3 DNA binding domain
PfamPF023628.9E-30195302IPR003340B3 DNA binding 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:0048573Biological Processphotoperiodism, flowering
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:0025281anatomypollen
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: 361 aa     Download sequence    Send to blast
MEYSCVDDSS TTSESLSIST TPKPTTTTEK KLSSPPATSM RLYRMGSGGS SVVLDSENGV  60
ETESRKLPSS KYKGVVPQPN GRWGAQIYEK HQRVWLGTFN EEEEAASSYD IAVRRFRGRD  120
AVTNFKSQVD GNDAESAFLD AHSKAEIVDM LRKHTYADEF EQSRRKFVNG DGKRSGLETA  180
TYGNDAVLRA REVLFEKTVT PSDVGKLNRL VIPKQHAEKH FPLPAMTTAM GMNPSPTKGV  240
LINLEDRTGK VWRFRYSYWN SSQSYVLTKG WSRFVKEKNL RAGDVVCFER STGPDRQLYI  300
HWKVRSSPVQ TVVRLFGVNI FNVSNEKPND VAVECVGKKR SREDDLFSLG CSKKQAIINI  360
L
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A7e-5719230611118DNA-binding protein RAV1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.173180.0flower| leaf| root| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible255742_at0.0
Expression AtlasAT1G25560-
AtGenExpressAT1G25560-
ATTED-IIAT1G25560-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in leaves. {ECO:0000269|PubMed:18718758}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the RAV transcription factor family that contains AP2 and B3 binding domains. Involved in the regulation of flowering under long days. Loss of function results in early flowering. Overexpression causes late flowering and repression of expression of FT. Novel transcriptional regulator involved in ethylene signaling. Promoter bound by EIN3. EDF1 in turn, binds to promoter elements in ethylene responsive genes.
UniProtTranscriptional repressor of flowering time on long day plants. Acts directly on FT expression by binding 5'-CAACA-3' and 5'-CACCTG-3 sequences. Functionally redundant with TEM2. {ECO:0000269|PubMed:18718758}.
Function -- GeneRIF ? help Back to Top
  1. TEMPRANILLO genes (TEM1 and TEM2) act as novel direct Flowering locus T repressors.
    [PMID: 18718758]
  2. TEMPRANILLO genes link photoperiod and gibberellin pathways to control flowering.
    [PMID: 22549837]
  3. 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]
  4. Data show that TEMPRANILLO (TEM) acts as a link between gibberellins (GAs) and cytokinin signaling in the epidermis by negatively regulating downstream genes of both trichome formation pathways.
    [PMID: 26802039]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00024PBM25215497Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G25560.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Expressed with a circadian rhythm showing a peak at dawn. {ECO:0000269|PubMed:18718758}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G65480(R)
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G25560
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0792810.0AC079281.4 Arabidopsis thaliana chromosome 1 BAC F2J7 genomic sequence, complete sequence.
GenBankAY0910690.0AY091069.1 Arabidopsis thaliana putative DNA-binding protein RAV2 (At1g25560) mRNA, complete cds.
GenBankAY1229410.0AY122941.1 Arabidopsis thaliana putative DNA-binding protein RAV2 (At1g25560) mRNA, complete cds.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_173927.10.0AP2/B3 transcription factor family protein
SwissprotQ9C6M50.0RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLA0A178W8G80.0A0A178W8G8_ARATH; TEM1
STRINGAT1G25560.10.0(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. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  3. 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]
  4. Teige M, et al.
    The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis.
    Mol. Cell, 2004. 15(1): p. 141-52
    [PMID:15225555]
  5. Hampton CR, et al.
    Cesium toxicity in Arabidopsis.
    Plant Physiol., 2004. 136(3): p. 3824-37
    [PMID:15489280]
  6. 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]
  7. 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]
  8. Mandaokar A, et al.
    Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling.
    Plant J., 2006. 46(6): p. 984-1008
    [PMID:16805732]
  9. 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]
  10. Ma S,Bohnert HJ
    Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression.
    Genome Biol., 2007. 8(4): p. R49
    [PMID:17408486]
  11. Usadel B, et al.
    Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes.
    Plant Physiol., 2008. 146(4): p. 1834-61
    [PMID:18305208]
  12. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  13. Castillejo C,Pelaz S
    The balance between CONSTANS and TEMPRANILLO activities determines FT expression to trigger flowering.
    Curr. Biol., 2008. 18(17): p. 1338-43
    [PMID:18718758]
  14. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  15. Ikeda M,Ohme-Takagi M
    A novel group of transcriptional repressors in Arabidopsis.
    Plant Cell Physiol., 2009. 50(5): p. 970-5
    [PMID:19324928]
  16. Yant L,Mathieu J,Schmid M
    Just say no: floral repressors help Arabidopsis bide the time.
    Curr. Opin. Plant Biol., 2009. 12(5): p. 580-6
    [PMID:19695946]
  17. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
    [PMID:20736450]
  18. Chen MK, et al.
    The MADS box gene, FOREVER YOUNG FLOWER, acts as a repressor controlling floral organ senescence and abscission in Arabidopsis.
    Plant J., 2011. 68(1): p. 168-85
    [PMID:21689171]
  19. 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]
  20. Osnato M,Castillejo C,Mat
    TEMPRANILLO genes link photoperiod and gibberellin pathways to control flowering in Arabidopsis.
    Nat Commun, 2012. 3: p. 808
    [PMID:22549837]
  21. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  22. Choi D, et al.
    iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis.
    Mol Plant, 2014. 7(5): p. 792-813
    [PMID:24380880]
  23. Sgamma T,Jackson A,Muleo R,Thomas B,Massiah A
    TEMPRANILLO is a regulator of juvenility in plants.
    Sci Rep, 2014. 4: p. 3704
    [PMID:24424565]
  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. 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]
  26. 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]
  27. Marín-González E, et al.
    SHORT VEGETATIVE PHASE Up-Regulates TEMPRANILLO2 Floral Repressor at Low Ambient Temperatures.
    Plant Physiol., 2015. 169(2): p. 1214-24
    [PMID:26243615]
  28. Matías-Hernández L, et al.
    TEMPRANILLO Reveals the Mesophyll as Crucial for Epidermal Trichome Formation.
    Plant Physiol., 2016. 170(3): p. 1624-39
    [PMID:26802039]