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 Bostr.12659s0398.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera
Family RAV
Protein Properties Length: 359aa    MW: 40222.2 Da    PI: 9.335
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bostr.12659s0398.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP240.19.1e-1365113155
                   AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                           s+ykGV   + +grW A+I++      ++r++lg+f  +eeAa  ++ a+++++g
  Bostr.12659s0398.1.p  65 SKYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAASSYDIAARRFRG 113
                           89****9888.8*********3.....5*************************98 PP

2B3102.52.4e-32193300196
                           EEEE-..-HHHHTT-EE--HHH.HTT............---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT CS
                    B3   1 ffkvltpsdvlksgrlvlpkkfaeeh............ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkeg 77 
                           f+k+ tpsdv+k++rlv+pk++ae+h            + ++++++ + led++g++W+++++y+++s++yvltkGW++Fvk+++L++g
  Bostr.12659s0398.1.p 193 FEKAVTPSDVGKLNRLVIPKQYAEKHfplpemttatgmSPSPTKGVLINLEDTTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAG 281
                           89****************************99999988666789********************************************* PP

                           -EEEEEE-SSSEE..EEEE CS
                    B3  78 DfvvFkldgrsefelvvkv 96 
                           D+v F+++   +++l++ +
  Bostr.12659s0398.1.p 282 DVVCFERSTGPDRQLYIDW 300
                           ******8766777777765 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541711.96E-1665121IPR016177DNA-binding domain
PfamPF008474.8E-765113IPR001471AP2/ERF domain
CDDcd000187.75E-2665120No hitNo description
Gene3DG3DSA:3.30.730.103.0E-2066121IPR001471AP2/ERF domain
PROSITE profilePS5103219.96866121IPR001471AP2/ERF domain
SMARTSM003802.1E-2966127IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.106.0E-40187305IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019367.98E-32192295IPR015300DNA-binding pseudobarrel domain
CDDcd100176.16E-30192289No hitNo description
PROSITE profilePS5086314.452193304IPR003340B3 DNA binding domain
PfamPF023629.6E-29193300IPR003340B3 DNA binding domain
SMARTSM010197.8E-26193304IPR003340B3 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: 359 aa     Download sequence    Send to blast
MDYSCVDDSS TASESLSIST PKTTEKLSSP PAKTMRLYRM GSGGSSVVLD LENGVETESR  60
KLPSSKYKGV VPQPNGRWGA QIYEKHQRVW LGTFNEEEEA ASSYDIAARR FRGRDAVTNF  120
KSLTTDGDDQ NDAESAFLDA HSKAEIVDML RKHTYADELE QSKRKFVNGN GKRYGSEMTM  180
SNDAVSRARD VLFEKAVTPS DVGKLNRLVI PKQYAEKHFP LPEMTTATGM SPSPTKGVLI  240
NLEDTTGKVW RFRYSYWNSS QSYVLTKGWS RFVKEKNLRA GDVVCFERST GPDRQLYIDW  300
KVRSSPVQTV VRLFGVNIFN VTNDKPNDVA VQCGGKKRSR EDDLFSLRCS KQAIINIL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A2e-5619030411118DNA-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
PlantRegMapBostr.12659s0398.1.p
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_010460355.10.0PREDICTED: AP2/ERF and B3 domain-containing transcription repressor TEM1-like isoform X3
SwissprotQ9C6M50.0RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLA0A178W8G80.0A0A178W8G8_ARATH; TEM1
STRINGBostr.12659s0398.1.p0.0(Boechera stricta)
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]