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 Carubv10020536m
Common NameCARUB_v10020536mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family RAV
Protein Properties Length: 361aa    MW: 40499.9 Da    PI: 9.9599
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10020536mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP242.22e-1368116155
              AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                      s+ykGV   + +grW A+I++      ++r++lg+f   eeAa+ ++ a+++++g
  Carubv10020536m  68 SKYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEQEEAARSYDIAALRFRG 116
                      89****9888.8*********3.....5*************************98 PP
2B3102.81.9e-32194293193
                      EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                      f+k+ tpsdv+k++rlv+pk++ae+h        ++ ++++ + +ed +g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v+F+++  
  Carubv10020536m 194 FEKAVTPSDVGKLNRLVIPKQHAEKHfplpsksPSSVTKGVLINFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVTFERSTG 287
                      89***************************998844456999*************************************************7655 PP

                      SEE..E CS
               B3  88 sefelv 93 
                       +++l+
  Carubv10020536m 288 LDRQLY 293
                      555555 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF008471.7E-868116IPR001471AP2/ERF domain
CDDcd000182.40E-2668123No hitNo description
SuperFamilySSF541717.19E-1768125IPR016177DNA-binding domain
SMARTSM003803.9E-3169130IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.102.2E-2069124IPR001471AP2/ERF domain
PROSITE profilePS5103220.73269124IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.102.9E-41188300IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.35E-32191294IPR015300DNA-binding pseudobarrel domain
CDDcd100174.59E-29193285No hitNo description
PfamPF023621.2E-29194296IPR003340B3 DNA binding domain
PROSITE profilePS5086314.254194300IPR003340B3 DNA binding domain
SMARTSM010194.5E-27194300IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 361 aa     Download sequence    Send to blast
MDSSCIEEIS SSTSESFSTT TAKKLSPPPP PPPPATALRL YRMGSGGSSI VLDPDNGVET  60
ESRKLPSSKY KGVVPQPNGR WGAQIYEKHQ RVWLGTFNEQ EEAARSYDIA ALRFRGRDAV  120
VNFKTLLEDG DLAFLEVHSK AEIVDMLRKH TYADELEQNN KRRLFVSLDA NGTQRNGSSM  180
VTNDNVLKTR EVLFEKAVTP SDVGKLNRLV IPKQHAEKHF PLPSKSPSSV TKGVLINFED  240
VNGKVWRFRY SYWNSSQSYV LTKGWSRFVK EKNLRAGDVV TFERSTGLDR QLYIDWKVRS  300
GPRETPVQVV VRLFGVDIFN VNTVKPNDVV ALCGRKRSRD DADDMFGLRC SKKQAIINAL  360
*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A5e-6219130111119DNA-binding protein RAV1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). Transcriptional repressor of flowering time on long day plants. Acts directly on FT expression by binding 5'-CAACA-3' and 5'-CACCTG-3 sequences (Probable). Functionally redundant with TEM1. {ECO:0000250, ECO:0000269|PubMed:18718758, ECO:0000305}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00025PBMTransfer from AT1G68840Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10020536m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0116650.0AC011665.8 Arabidopsis thaliana chromosome 1 BAC T6L1 genomic sequence, complete sequence.
GenBankAC0119140.0AC011914.9 Arabidopsis thaliana chromosome 1 BAC F14K14 genomic sequence, complete sequence.
GenBankAF3603120.0AF360312.1 Arabidopsis thaliana putative DNA-binding protein(RAV2 (At1g68840) mRNA, complete cds.
GenBankAY0563610.0AY056361.1 Arabidopsis thaliana putative DNA-binding protein RAV2 (At1g68840) mRNA, complete cds.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006302450.10.0AP2/ERF and B3 domain-containing transcription repressor RAV2
SwissprotP822800.0RAV2_ARATH; AP2/ERF and B3 domain-containing transcription repressor RAV2
TrEMBLR0IF200.0R0IF20_9BRAS; Uncharacterized protein
STRINGXP_006302450.10.0(Capsella rubella)
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
AT1G68840.20.0related to ABI3/VP1 2
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. Sun YW, et al.
    Attenuation of Histone Methyltransferase KRYPTONITE-mediated transcriptional gene silencing by Geminivirus.
    Sci Rep, 2015. 5: p. 16476
    [PMID:26602265]
  4. Mittal A,Jiang Y,Ritchie GL,Burke JJ,Rock CD
    AtRAV1 and AtRAV2 overexpression in cotton increases fiber length differentially under drought stress and delays flowering.
    Plant Sci., 2015. 241: p. 78-95
    [PMID:26706061]
  5. 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]
  6. Li P, et al.
    The Arabidopsis UGT87A2, a stress-inducible family 1 glycosyltransferase, is involved in the plant adaptation to abiotic stresses.
    Physiol Plant, 2017. 159(4): p. 416-432
    [PMID:27747895]