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 Carubv10010429m
Common NameCARUB_v10010429mg
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 B3
Protein Properties Length: 179aa    MW: 20135.2 Da    PI: 10.5034
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10010429mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3104.46e-3314121196
                      EEEE-..-HHHHTT-EE--HHH.HTT............---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh............ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvF 82 
                      f+k+ tpsdv+k++rlv+pk++ae+h            + +++++  + led++g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v F
  Carubv10010429m  14 FEKAVTPSDVGKLNRLVIPKQHAEKHfplpamttatgmNPSPTKGLLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCF 107
                      89*********************************98866677999************************************************ PP

                      EE-SSSEE..EEEE CS
               B3  83 kldgrsefelvvkv 96 
                      +++   +++l++ +
  Carubv10010429m 108 ERSTGPDRQLYIDW 121
                      *8766777777765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.2E-417126IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.89E-3212117IPR015300DNA-binding pseudobarrel domain
CDDcd100171.07E-2813110No hitNo description
PfamPF023621.5E-2914121IPR003340B3 DNA binding domain
PROSITE profilePS5086314.05714125IPR003340B3 DNA binding domain
SMARTSM010191.1E-2514125IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 179 aa     Download sequence    Send to blast
MLNDAVSKAR EVLFEKAVTP SDVGKLNRLV IPKQHAEKHF PLPAMTTATG MNPSPTKGLL  60
INLEDRTGKV WRFRYSYWNS SQSYVLTKGW SRFVKEKNLR AGDVVCFERS TGPDRQLYID  120
WKVRSSPVQT VVRLFGVNIF NDRPNGVAVD CTGGKKRSRD DDLFSLGCSK KQTIINIL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A6e-591112511118DNA-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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10010429m
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_006304241.11e-131AP2/ERF and B3 domain-containing transcription repressor TEM1
SwissprotQ9C6M51e-115RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLR0I4E51e-129R0I4E5_9BRAS; Uncharacterized protein
STRINGXP_006304241.11e-130(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
AT1G25560.11e-118RAV 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]