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_009115339.1
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: 372aa    MW: 41069.5 Da    PI: 9.9591
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009115339.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP239.81.1e-1268116155
             AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                     s++kGV   + +grW A+I++      ++r++lg+f  +eeAa+ ++ a+++++g
  XP_009115339.1  68 SKFKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAAASYDIAARRFRG 116
                     79****9888.8*********3.....5*************************98 PP
2B3101.35.4e-32196305195
                     EEEE-..-HHHHTT-EE--HHH.HTT...............---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh...............ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 
                     f+k+ tpsdv+k++rlv+pk++ae+h                 ++++++ + led++g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v
  XP_009115339.1 196 FEKAVTPSDVGKLNRLVIPKQHAEKHfplpamttatvvtamTPSPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVV 290
                     89****************************999999999985567799*********************************************** PP

                     EEEE-SSSEE..EEE CS
              B3  81 vFkldgrsefelvvk 95 
                      F+++   +++l++ 
  XP_009115339.1 291 CFERSTGPDRQLYID 305
                     ***876677767665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000181.50E-2468123No hitNo description
SuperFamilySSF541713.33E-1668124IPR016177DNA-binding domain
PfamPF008478.4E-768116IPR001471AP2/ERF domain
PROSITE profilePS5103219.45469124IPR001471AP2/ERF domain
SMARTSM003806.5E-2869130IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.101.5E-1969124IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.103.3E-40190312IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.58E-31194300IPR015300DNA-binding pseudobarrel domain
CDDcd100171.34E-28195295No hitNo description
SMARTSM010191.1E-24196310IPR003340B3 DNA binding domain
PROSITE profilePS5086313.803196310IPR003340B3 DNA binding domain
PfamPF023621.1E-28196305IPR003340B3 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: 372 aa     Download sequence    Send to blast
MDNSCIDDST SNTSGSLSTS TLSAKKKLSP PPPPPATMRL YRMGSGGSSV VLDSENGVET  60
ESRKLPSSKF KGVVPQPNGR WGAQIYEKHQ RVWLGTFNEE EEAAASYDIA ARRFRGRDAV  120
TNFKSPALDG TDAESAFLEA HSKAEIVDML RKHTYADELQ QSKRKFLDGN GKRCGSGTAA  180
MSKGNDGVSR AREVLFEKAV TPSDVGKLNR LVIPKQHAEK HFPLPAMTTA TVVTAMTPSP  240
TKGVLINLED RTGKVWRFRY SYWNSSQSYV LTKGWSRFVK EKNLRAGDVV CFERSTGPDR  300
QLYIDWKVQS GKEEITPVQS VVRLFGVNIF NETTNAKPND VAVECGGKKR SREVDLFALG  360
CSKKQTMMIN AL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A2e-5719331311121DNA-binding protein RAV1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.55170.0leaf| 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00024PBMTransfer from AT1G25560Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009115339.1
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_009115339.10.0PREDICTED: AP2/ERF and B3 domain-containing transcription repressor TEM1-like
SwissprotQ9C6M50.0RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLM4E7I00.0M4E7I0_BRARP; Uncharacterized protein
STRINGBra024735.1-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]