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 RrC1796_p5
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family RAV
Protein Properties Length: 354aa    MW: 39582.4 Da    PI: 9.7833
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1796_p5genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP237.36.9e-1267115155
         AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                 s++kGV   + +grW A+I++      ++r++lg+f  +eeAa+ ++ a ++++g
  RrC1796_p5  67 SKFKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAAASYDVAVRRFRG 115
                 79****9888.8*********3.....5************************998 PP
2B3101.64.6e-32189291196
                 EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
          B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                 f+k+ tpsdv+k++rlv+pk++ae+h           ++++ + led++g++W+++++y+++s++yvltkGW++Fvk+++L++gD v F+++   +++l
  RrC1796_p5 189 FEKAVTPSDVGKLNRLVIPKQHAEKHfplpattTTAATKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKDLRAGDAVCFERSTGPDRQL 287
                 89*************************99998855556999*************************************************876677777 PP

                 EEEE CS
          B3  93 vvkv 96 
                 ++ +
  RrC1796_p5 288 YIDW 291
                 7765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541712.48E-1467124IPR016177DNA-binding domain
CDDcd000184.72E-2267123No hitNo description
PfamPF008472.3E-667115IPR001471AP2/ERF domain
SMARTSM003803.8E-2568130IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.103.1E-1868124IPR001471AP2/ERF domain
PROSITE profilePS5103219.09868124IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.102.8E-41182297IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.05E-31187289IPR015300DNA-binding pseudobarrel domain
CDDcd100171.94E-29188280No hitNo description
PROSITE profilePS5086314.438189295IPR003340B3 DNA binding domain
SMARTSM010193.1E-25189295IPR003340B3 DNA binding domain
PfamPF023627.3E-29189291IPR003340B3 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: 354 aa     Download sequence    Send to blast
MDYSCLDDNT SNNNNNSATL SMSTKKTPSP PPQAMRLYRM GSGGSSVVLD LENNGVETES  60
RKKLPSSKFK GVVPQPNGRW GAQIYEKHQR VWLGTFNEEE EAAASYDVAV RRFRGRDAAV  120
TNFKSPASDS ESAFLEAHSK AEIVDMLRKH TYADELRQSG RKFLDGDGQR RKTATTVNEN  180
DGVSREVLFE KAVTPSDVGK LNRLVIPKQH AEKHFPLPAT TTTAATKGVL INLEDRTGKV  240
WRFRYSYWNS SQSYVLTKGW SRFVKEKDLR AGDAVCFERS TGPDRQLYID WKVRSGTELI  300
NPVQNVVRLF GVNIFNAATT NAKQNDECGG EKRSREVDLF ALGCSKKQAI INAL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A1e-5918629911122DNA-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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018460371.10.0PREDICTED: AP2/ERF and B3 domain-containing transcription repressor TEM1-like
SwissprotQ9C6M50.0RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLA0A3P6BEN00.0A0A3P6BEN0_BRAOL; Uncharacterized protein
STRINGBo3g138550.10.0(Brassica oleracea)
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]