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 Cagra.11546s0001.1.p
Organism
Capsella grandiflora
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: 211aa    MW: 23631.1 Da    PI: 10.5254
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.11546s0001.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3103.89.5e-3346153196
                           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
  Cagra.11546s0001.1.p  46 FEKAVTPSDVGKLNRLVIPKQHAEKHfplpamttatgmNPSPTKGLLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAG 134
                           89*********************************98866677999******************************************* PP

                           -EEEEEE-SSSEE..EEEE CS
                    B3  78 DfvvFkldgrsefelvvkv 96 
                           D+v F+++   +++l++ +
  Cagra.11546s0001.1.p 135 DVVCFERSTGPDRQLYIDW 153
                           ******8766777777765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.106.8E-4140158IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019369.68E-3244149IPR015300DNA-binding pseudobarrel domain
CDDcd100179.35E-2945142No hitNo description
SMARTSM010191.1E-2546157IPR003340B3 DNA binding domain
PfamPF023622.4E-2946153IPR003340B3 DNA binding domain
PROSITE profilePS5086314.05746157IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 211 aa     Download sequence    Send to blast
MLRKHTYADE LQQSRRKFVN GGNGKCCGSD TAMLNGAVSK AREVLFEKAV TPSDVGKLNR  60
LVIPKQHAEK HFPLPAMTTA TGMNPSPTKG LLINLEDRTG KVWRFRYSYW NSSQSYVLTK  120
GWSRFVKEKN LRAGDVVCFE RSTGPDRQLY IDWKVRSSPV QTVVRLFGVN IFNDRPNGVA  180
VDCTGGKKRS RDDDLFSLGC SKKQTIINIL *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A1e-584315711118DNA-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
PlantRegMapCagra.11546s0001.1.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_010477910.11e-132PREDICTED: AP2/ERF and B3 domain-containing transcription repressor TEM1-like
SwissprotQ9C6M51e-130RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBLA0A178W8G81e-127A0A178W8G8_ARATH; TEM1
TrEMBLR0I4E51e-128R0I4E5_9BRAS; Uncharacterized protein
STRINGCagra.11546s0001.1.p1e-156(Capsella grandiflora)
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-132RAV 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]