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 Rsa1.0_30475.1_g00001.1
Organism
Raphanus sativus
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: 196aa    MW: 21199.2 Da    PI: 9.7346
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_30475.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B348.22e-15115196179
                              EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-E CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDf 79 
                              f+k+l+ sd+++ grlvlpk +ae++   +++ e++ l+++d +g++W++++++  +++s++yvl+ G     ++  L++gD+
  Rsa1.0_30475.1_g00001.1 115 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLQIQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTTCIQSMMLQAGDT 196
                              99**************************666678889***************9989999999***9.**************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.8E-24112196IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.88E-16112196IPR015300DNA-binding pseudobarrel domain
CDDcd100173.71E-20113196No hitNo description
PfamPF023625.4E-13115196IPR003340B3 DNA binding domain
SMARTSM010199.4E-7115196IPR003340B3 DNA binding domain
PROSITE profilePS508639.982115196IPR003340B3 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: 196 aa     Download sequence    Send to blast
SSTPPQPSFN MALATLPYSP SFATPPVDGN KLMAAAAASQ SHIAQCSASS ILQKPSNPVL  60
ATPPGTSKSA QARVGRPPVD GRGKGHLLPR YWPKYTDKEL QQISGNLNLN IVPLFEKTLS  120
ASDAGRIGRL VLPKACAEAY FPPISQSEGI PLQIQDVRGK EWTFQFRFWP NNNSRMYVLE  180
GVTTCIQSMM LQAGDT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5yzy_C5e-71931961104B3 domain-containing transcription repressor VAL1
5yzz_C5e-71931961104B3 domain-containing transcription repressor VAL1
5z00_C5e-71931961104B3 domain-containing transcription repressor VAL1
5z00_G5e-71931961104B3 domain-containing transcription repressor VAL1
5z00_K5e-71931961104B3 domain-containing transcription repressor VAL1
5z00_M5e-71931961104B3 domain-containing transcription repressor VAL1
6j9a_A4e-71931962105B3 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_30475.1_g00001.1
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-146AK353502.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-47-G20.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018476649.11e-138PREDICTED: B3 domain-containing transcription repressor VAL1-like
SwissprotQ8W4L51e-110VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A3P6AWS31e-123A0A3P6AWS3_BRAOL; Uncharacterized protein
STRINGBo3g024640.11e-124(Brassica oleracea)
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
AT2G30470.11e-104high-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]