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 Sopen05g005620.1
Organism
Solanum pennellii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family RAV
Protein Properties Length: 396aa    MW: 44450.3 Da    PI: 9.8647
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sopen05g005620.1genomespennView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP242.31.8e-1371119155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                       s+ykGV   + +grW A+I++      ++r++lg+f  ++eAa+a++ a+++++g
  Sopen05g005620.1  71 SRYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEENEAARAYDVAAQRFRG 119
                       78****9888.8*********3.....5*************************98 PP
2B3105.62.5e-33207305195
                       EEEE-..-HHHHTT-EE--HHH.HTT....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                       f+kv tpsdv+k++rlv+pk++ae+h    +g++ +++ l +ed++g++W+++++y+++s++yvltkGW++Fvk+++Lk+gD+v F+++++ +
  Sopen05g005620.1 207 FEKVVTPSDVGKLNRLVIPKQHAEKHfplqNGNNSKGVLLNFEDLNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGDIVSFQRSSSGD 299
                       99****************************778889***************************************************887777 PP

                       E..EEE CS
                B3  90 felvvk 95 
                       ++l++ 
  Sopen05g005620.1 300 KQLYID 305
                       766665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541713.27E-1771127IPR016177DNA-binding domain
CDDcd000182.55E-2671126No hitNo description
PfamPF008474.5E-971119IPR001471AP2/ERF domain
SMARTSM003802.7E-3072133IPR001471AP2/ERF domain
PROSITE profilePS5103220.27172127IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.101.4E-2072127IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.101.4E-42199312IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.32E-32205305IPR015300DNA-binding pseudobarrel domain
CDDcd100174.40E-30206298No hitNo description
PfamPF023621.5E-30207306IPR003340B3 DNA binding domain
PROSITE profilePS5086315.552207310IPR003340B3 DNA binding domain
SMARTSM010194.0E-27207310IPR003340B3 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:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 396 aa     Download sequence    Send to blast
MEGSISSIDQ ESTTSDSLSI APAASSSTMI KSSTTIKPPP ESGLCRMGSG TSVIIDAENG  60
VEAESRKLPS SRYKGVVPQP NGRWGAQIYE KHQRVWLGTF NEENEAARAY DVAAQRFRGR  120
DAVTNFKPLL ENQESDDMEI AFLNSHSKAE IVDMLRKHTY IDELEQSKRL FGFTKDGMIK  180
RKDGLVISSF FGSTNDKVNC KAREQLFEKV VTPSDVGKLN RLVIPKQHAE KHFPLQNGNN  240
SKGVLLNFED LNGKVWRFRY SYWNSSQSYV LTKGWSRFVK EKNLKAGDIV SFQRSSSGDK  300
QLYIDFKAKN VGNTSVVVTN QVQAQVQVPI VQMVRLFGVN ICKVPANVSN VVIDNNNNNN  360
NNNNMTSWSG GKRRMEMELL TFESCRKKQR VIIDAL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A5e-5620431011118DNA-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
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
GenBankHG9754440.0HG975444.1 Solanum pennellii chromosome ch05, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015074490.10.0AP2/ERF and B3 domain-containing transcription factor RAV1
SwissprotQ9C6M51e-140RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLE1U2K50.0E1U2K5_SOLLC; RAV2
STRINGSolyc05g009790.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA29582453
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G13260.11e-138related to ABI3/VP1 1
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]