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 XP_009109894.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family RAV
Protein Properties Length: 359aa    MW: 40279.4 Da    PI: 9.7831
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009109894.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP236.61.2e-1167113355
             AP2   3 ykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                      kGV   + +grW A+I++      ++r++lg+f  +eeAa+ ++ a+++++g
  XP_009109894.1  67 SKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAAASYDIAARRFRG 113
                     57887667.8*********3.....5*************************98 PP
2B3105.52.7e-33191293196
                     EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                     f+k+ tpsdv+k++rlv+pk++ae+h         ++++++ + led++g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v F++++  
  XP_009109894.1 191 FEKTVTPSDVGKLNRLVIPKQHAEKHfplpvtvTPSPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCFERSSGP 285
                     99*****************************996677899**************************************************98778 PP

                     EE..EEEE CS
              B3  89 efelvvkv 96 
                     +++l++ +
  XP_009109894.1 286 DRQLYIDW 293
                     88777765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000182.39E-2365120No hitNo description
PfamPF008473.3E-666113IPR001471AP2/ERF domain
SuperFamilySSF541711.57E-1566121IPR016177DNA-binding domain
SMARTSM003802.8E-2566127IPR001471AP2/ERF domain
PROSITE profilePS5103218.9466121IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.102.4E-1868121IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.103.9E-41184300IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019368.76E-33189293IPR015300DNA-binding pseudobarrel domain
CDDcd100171.02E-29190282No hitNo description
SMARTSM010198.6E-27191297IPR003340B3 DNA binding domain
PfamPF023627.7E-30191293IPR003340B3 DNA binding domain
PROSITE profilePS5086314.522191297IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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
MDYSCLDDNT SNTSETLSMS KKTPSPPLPL PPAMRLYRMG SGGSSVVLDL ENGVETESSR  60
KLPSSRSKGV VPQPNGRWGA QIYEKHQRVW LGTFNEEEEA AASYDIAARR FRGRDAVTNF  120
KSPASDAESA FLEAHSKAEV VDMLRKHTYA DELRQSERKF LDGDGNGRKR CEFSKTTVTN  180
ENDGVSREVL FEKTVTPSDV GKLNRLVIPK QHAEKHFPLP VTVTPSPTKG VLINLEDRTG  240
KVWRFRYSYW NSSQSYVLTK GWSRFVKEKN LRAGDVVCFE RSSGPDRQLY IDWKVRSGIE  300
KITPVQNVVR LFGVNIFNAT TTNANTNDVV GESGSKKRFR EVDLFALGCS KKQAIINVL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A2e-5718829811119DNA-binding protein RAV1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.55171e-144leaf| root
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
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009109894.1
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
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009109894.10.0PREDICTED: AP2/ERF and B3 domain-containing transcription repressor TEM1-like
SwissprotQ9C6M50.0RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLM4D3E80.0M4D3E8_BRARP; Uncharacterized protein
STRINGBra011002.1-P0.0(Brassica rapa)
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]