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 RrC51470_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family B3
Protein Properties Length: 66aa    MW: 7542.55 Da    PI: 6.5255
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC51470_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B340.64.4e-139623284
                 --SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS
           B3 32 esktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkl 84
                 e++ l+++d +g +W++++++  +++s++yvl+ G    v++ +L++gD+v+F++
  RrC51470_p1  9 EGIPLKIQDVRGTEWTFQFRFwpNNNSRMYVLE-GVTACVQSMKLQAGDTVTFSR 62
                 567799*************9989999999***9.*******************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS508639.714166IPR003340B3 DNA binding domain
CDDcd100177.01E-12166No hitNo description
Gene3DG3DSA:2.40.330.109.7E-17164IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.92E-11265IPR015300DNA-binding pseudobarrel domain
PfamPF023621.1E-10963IPR003340B3 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: 66 aa     Download sequence    Send to blast
YFPPISQSEG IPLKIQDVRG TEWTFQFRFW PNNNSRMYVL EGVTACVQSM KLQAGDTVTF  60
SRVDPG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5yzy_C7e-4216648113B3 domain-containing transcription repressor VAL1
5yzz_C7e-4216648113B3 domain-containing transcription repressor VAL1
5z00_C7e-4216648113B3 domain-containing transcription repressor VAL1
5z00_G7e-4216648113B3 domain-containing transcription repressor VAL1
5z00_K7e-4216648113B3 domain-containing transcription repressor VAL1
5z00_M7e-4216648113B3 domain-containing transcription repressor VAL1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL2/HSL1. {ECO:0000269|PubMed:15894743, ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3535021e-63AK353502.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-47-G20.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018485193.12e-39PREDICTED: B3 domain-containing transcription repressor VAL1-like
RefseqXP_018485194.12e-39PREDICTED: B3 domain-containing transcription repressor VAL1-like
SwissprotQ8W4L54e-39VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A397ZB383e-37A0A397ZB38_BRACM; Uncharacterized protein
TrEMBLA0A397ZWD33e-37A0A397ZWD3_BRACM; Uncharacterized protein
TrEMBLA0A3P5YSI43e-37A0A3P5YSI4_BRACM; Uncharacterized protein
TrEMBLM4E2013e-37M4E201_BRARP; Uncharacterized protein
STRINGBra022801.1-P5e-38(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM1811179
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G30470.12e-41high-level expression of sugar-inducible gene 2
Publications ? help Back to Top
  1. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  2. Schneider A, et al.
    Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos.
    Plant J., 2016. 85(2): p. 305-19
    [PMID:26678037]
  3. Chhun T, et al.
    HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth.
    Plant Cell Physiol., 2016. 57(8): p. 1689-706
    [PMID:27335347]
  4. Qüesta JI,Song J,Geraldo N,An H,Dean C
    Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization.
    Science, 2016. 353(6298): p. 485-8
    [PMID:27471304]
  5. Yuan W, et al.
    A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis.
    Nat. Genet., 2016. 48(12): p. 1527-1534
    [PMID:27819666]
  6. Merini W, et al.
    The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development.
    Plant Physiol., 2017. 173(1): p. 627-641
    [PMID:27837089]
  7. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]
  8. Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD
    HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis.
    Plant Cell, 2018. 30(3): p. 600-619
    [PMID:29475938]
  9. Sasnauskas G,Kauneckaite K,Siksnys V
    Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
    Nucleic Acids Res., 2018. 46(8): p. 4316-4324
    [PMID:29660015]
  10. Wu B, et al.
    Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.
    Biochem. Biophys. Res. Commun., 2018. 501(2): p. 415-422
    [PMID:29733847]