PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID 890147
Common NameARALYDRAFT_890147
Organism
Arabidopsis lyrata
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: 358aa    MW: 39927 Da    PI: 9.538
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
890147genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP239.71.2e-1267115155
     AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
             s+ykGV   + +grW A+I++      ++r++lg+f  +eeAa  ++ a+++++g
  890147  67 SKYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAATSYDIAARRFRG 115
             89****9888.8*********3.....5*************************98 PP
2B3103.89e-33192299196
             EEEE-..-HHHHTT-EE--HHH.HTT............---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
      B3   1 ffkvltpsdvlksgrlvlpkkfaeeh............ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
             f+k+ tpsdv+k++rlv+pk++ae+h            + ++++++ + led++g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v F+++   +++
  890147 192 FEKTVTPSDVGKLNRLVIPKQHAEKHfplpatttamgmSPSPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCFERSTGPDRQ 294
             99******************************999988666789***************************************************87667777 PP

             .EEEE CS
      B3  92 lvvkv 96 
             l++ +
  890147 295 LYIDW 299
             77765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541717.85E-1767123IPR016177DNA-binding domain
CDDcd000182.52E-2567122No hitNo description
PfamPF008474.8E-767115IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.102.7E-2068123IPR001471AP2/ERF domain
PROSITE profilePS5103219.94168123IPR001471AP2/ERF domain
SMARTSM003801.9E-2868129IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.101.8E-40187304IPR015300DNA-binding pseudobarrel domain
CDDcd100177.38E-30191288No hitNo description
SuperFamilySSF1019365.1E-32191294IPR015300DNA-binding pseudobarrel domain
PfamPF023621.5E-29192299IPR003340B3 DNA binding domain
SMARTSM010192.5E-26192303IPR003340B3 DNA binding domain
PROSITE profilePS5086314.099192303IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048573Biological Processphotoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 358 aa     Download sequence    Send to blast
MDYSCVDDSS TTSESLSIST PKPTTTTEKL SSPPATMRLY RMGSGGSSVV LDSENGVETE  60
SRKLPSSKYK GVVPQPNGRW GAQIYEKHQR VWLGTFNEEE EAATSYDIAA RRFRGRDAVT  120
NFKSQVDGNE AESAFLDAHS KAEIVDMLRK HTYADEFEQS KRKFVNGKGR HCGSETAMQG  180
NDAVLRAREV LFEKTVTPSD VGKLNRLVIP KQHAEKHFPL PATTTAMGMS PSPTKGVLIN  240
LEDRTGKVWR FRYSYWNSSQ SYVLTKGWSR FVKEKNLRAG DVVCFERSTG PDRQLYIDWK  300
VRSSPVQTVV RLFGVNIFNV SNEKPNDVAV ECGGKRSREV DLFSLGCSKK QAIINVL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A1e-5718930311118DNA-binding protein RAV1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00024PBMTransfer from AT1G25560Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMap890147
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
PlantRegMapRetrieve-
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
RefseqXP_002890683.10.0AP2/ERF and B3 domain-containing transcription repressor TEM1
SwissprotQ9C6M50.0RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLD7KQU40.0D7KQU4_ARALL; Uncharacterized protein
STRINGscaffold_102941.10.0(Arabidopsis lyrata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM84827121
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G25560.10.0RAV family protein
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]