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 Lj1g3v4117200.1
Organism
Lotus japonicus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
Family B3
Protein Properties Length: 853aa    MW: 94478.5 Da    PI: 7.4253
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lj1g3v4117200.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B358.51.2e-18274374199
                      EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 
                      f+kvl+ sd+++ grlvlpk +ae++   +++ e+  l ++d +g++W++++++  +++s++yvl+ G     ++ +L++gD+v+F++++  ++
  Lj1g3v4117200.1 274 FEKVLSASDAGRIGRLVLPKACAEAYfpTISHSEGLPLHVQDVKGNEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLCAGDTVTFSRID-PGG 365
                      99**************************555556667***************9989999999***9.********************887.788 PP

                      ..EEEEE-S CS
               B3  91 elvvkvfrk 99 
                      +lv++++++
  Lj1g3v4117200.1 366 KLVMGFRKA 374
                      888887765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.9E-29270379IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019368.11E-20272376IPR015300DNA-binding pseudobarrel domain
CDDcd100173.34E-21272373No hitNo description
PfamPF023622.2E-15274373IPR003340B3 DNA binding domain
SMARTSM010195.4E-22274375IPR003340B3 DNA binding domain
PROSITE profilePS5086310.278274375IPR003340B3 DNA binding domain
PROSITE profilePS5105014.296538588IPR011124Zinc finger, CW-type
PfamPF074962.1E-11543585IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 853 aa     Download sequence    Send to blast
MCFRSSYESS VFCNKFHRQE TGWKDCKFCN KPIHCGCIVS RSLFEYLDFG GIACVSCVNT  60
SLLNMMRNHE HPNWSISFAQ TSTMDRHSAH FDCRLFTGSV DEGNLMQLCR VVEASESSLW  120
NNRSTRDITS ISSNNMKPSV QSLTFAALEN SRSTRDMTSI HESTAQPSLG MYLGNPSGSK  180
SVPHSAGENV EGRLEGKTSP PFHQGQRSRP ILPKLLKTGN VETDKGTFSQ SRVARPPAEG  240
RGKNQLLPRY WPRITDQELE RLSGDLKSTV VPLFEKVLSA SDAGRIGRLV LPKACAEAYF  300
PTISHSEGLP LHVQDVKGNE WTFQFRFWPN NNSRMYVLEG VTPCIQSMQL CAGDTVTFSR  360
IDPGGKLVMG FRKASISIDA QDASTSALSN GISAKGTDFS GGTENLPSGS NSTDLLNSTK  420
GNGDSQLNGH PENLHLGTGA ADLLKTENCE MTKNHSLQQQ ISVLEKKRAR NIGPKSKRLL  480
IDNEDSMELR LTWEEAQDLL RPPPSVKPSI VTIEDQVFEE YDEPPVFGKR TIFSACSSGG  540
KEQWAQCDDC SKWRKLPVDA LLPPKWTCSE NVWDTSRSSC STPQELRSGE VENLLKTNKD  600
SKKRRVVENG KPLQEHEPSG LDALASAAVF GENFVDPAES SAGATTKHPR HRPGCSCIVC  660
IQPPSGKGRH KPTCTCNVCM TVKRRFKTLM LRKKKRREAD AAAAASAAQK DHSHQIDESD  720
TNGAPQRDDT SHLEKEEGLN KGQSEVGESS AGQIDLNSHP NREDMQMDIT GLGMSSHHLE  780
TRSNPVRENI DQNGLRSFSS ELQNGHHSSL LTHSNGEGQR HFSDERCFPS RVWNQERRDE  840
VYNHPNQSQN SLS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A3e-652523812131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1682693KRRFKTLMLRKK
2682695KRRFKTLMLRKKKR
3682696KRRFKTLMLRKKKRR
4692696KKKRR
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in flowers and at lower levels in roots, stems and leaves. {ECO:0000269|PubMed:15894743}.
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
PlantRegMapLj1g3v4117200.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0150382e-52AP015038.1 Vigna angularis var. angularis DNA, chromosome 5, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_027334061.10.0B3 domain-containing transcription repressor VAL1 isoform X1
RefseqXP_027334062.10.0B3 domain-containing transcription repressor VAL1 isoform X1
RefseqXP_027334064.10.0B3 domain-containing transcription repressor VAL1 isoform X1
RefseqXP_027334065.10.0B3 domain-containing transcription repressor VAL1 isoform X1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A445I4E50.0A0A445I4E5_GLYSO; Uncharacterized protein
STRINGGLYMA11G31234.10.0(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF103233039
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G30470.10.0high-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]