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 676729170
Organism
Sisymbrium irio
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Sisymbrieae; Sisymbrium
Family B3
Protein Properties Length: 852aa    MW: 93227.7 Da    PI: 7.9712
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
676729170genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B345.51.4e-14303385180
                EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EE CS
         B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfv 80 
                f+k+l+ sd+++ grlvlpk +ae++   +++ e++ l+++d +g++W++++++  +++s++yvl+ G     ++  L++gD+ 
  676729170 303 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMMLQAGDTA 385
                99**************************666678889***************9989999999***9.***************85 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.35E-15300384IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.2E-23300384IPR015300DNA-binding pseudobarrel domain
CDDcd100177.85E-19301384No hitNo description
SMARTSM010195.7E-13303406IPR003340B3 DNA binding domain
PfamPF023625.4E-12303385IPR003340B3 DNA binding domain
PROSITE profilePS508639.333303416IPR003340B3 DNA binding domain
PROSITE profilePS5105014.044583633IPR011124Zinc finger, CW-type
PfamPF074962.7E-11589630IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010030Biological Processpositive regulation of seed germination
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:2000034Biological Processregulation of seed maturation
GO:0005634Cellular Componentnucleus
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 852 aa     Download sequence    Send to blast
MGSKMCMNAS CGSTSTVEWK KGWPLRSGAL ADLCYRCGSA YETSLFCETF HMDQSGWREC  60
YLCNKRLHCG CIASKLMVEF MDYGGVGCTT CTNCHQLNLN KRGENPGVFN RLPMKALGDR  120
QHTNGESGMS IDGVVRSEAD LFAQPQRCDS QPLVPGDDKR EELMAQRGFG NLMKPESNAT  180
AGYRLDAGEM HESLTPSQPS LNMALAVLPY SPSFATPVDG KKLMVASQSH IVQCSASSIL  240
QKPSKSVLAT PPGTSKSAQA RIGRPPVEGR GKGHLLPRYW PKYTDKELQQ ISGNLNLNIV  300
PLFEKTLSAS DAGRIGRLVL PKACAEAYFP PISQSEGIPL KIQDVRGKEW TFQFRFWPNN  360
NSRMYVLEGV TPCIQSMMLQ AGDTATRLGE YILGFLHSLI VWSSSSPFVV SVTFSRVDPG  420
GKLIMGYRKA VYTGDMQGCG LTNGTSNEDT SSSGVTENPT SINASSCPSQ IPEELKGLPE  480
HLSSPYGVTS FKKSEMNGGR ICDDPSRVKE KKRTRTIGAK NKRLLLHSEE SMELRLTWEE  540
AQDLIRPAPN AKPTIVVIEE HEFEEFDEPP VFGKRTIITA KPSGEQDRWA SCDDCSKWRR  600
LPIDALLPAK WTCSDNVWDE SRSSCSAPEE SLRELENVLR AGKEFKRRRT GVTKSEQEPS  660
GLDALASAAS AAVLGDALGE PEAATTTRHP RHRVGCSCIV CIQPPSGKGR HKPACGCTVC  720
STVKRRFKTL MMRRKKKQLE RDATAAAAEA ADRGNKEARK EGEPDKSKVE KDGKTGRIDL  780
NSDPYNKEEV ESVAVVKQDE SQKREVGQCS GLAQGGDVIG ATELGGDAEK IREEPKVASC  840
DGEDKNAKLI AT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A7e-782814382132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1723735KRRFKTLMMRRKK
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
PlantRegMap676729170
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006410148.10.0B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLV4NXH20.0V4NXH2_EUTSA; Uncharacterized protein
STRINGXP_006410148.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69232440
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]