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 XP_013630357.1
Organism
Brassica oleracea
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family B3
Protein Properties Length: 780aa    MW: 85509.5 Da    PI: 7.0499
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013630357.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.72.2e-18292391198
                     EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                     f+k+l+ sd+++ grlvlpk +ae++   +++ e++ l+++d +g++W++++++  +++s++yvl+ G     ++  L++gD+v+F++++  +++
  XP_013630357.1 292 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRVD-PGGK 384
                     99**************************666678889***************9989999999***9.********************765.8888 PP

                     .EEEEE- CS
              B3  92 lvvkvfr 98 
                     l +++++
  XP_013630357.1 385 LIMGARK 391
                     8877765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.104.6E-28289393IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.62E-19289387IPR015300DNA-binding pseudobarrel domain
CDDcd100171.54E-23290391No hitNo description
PfamPF023627.9E-16292391IPR003340B3 DNA binding domain
SMARTSM010196.5E-22292393IPR003340B3 DNA binding domain
PROSITE profilePS5086310.673292393IPR003340B3 DNA binding domain
PROSITE profilePS5105013.466535585IPR011124Zinc finger, CW-type
PfamPF074966.1E-8541582IPR011124Zinc 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: 780 aa     Download sequence    Send to blast
MFEVKTGSKV CMNASCGSTS TVEWKKGWPL RSGSLADLCF RCGSAYETSL FCETFHLEQS  60
GWRDCYLCNK RLHCGCIASK LMVEFMDYGG VGCTSCTNCH QLNLNKRGEN PVVFSRLAMN  120
SQHTNGESGI SSIRSEADLF SQPLVPGDDK REEFMAQRGF ANFMKPDNNN AGEMHEPSST  180
PSQPSLNMAL ATLPYSPSFA TPVVDGKTLM GAASQSQSHI GQCSASSILQ KPSKSVPGTP  240
PGTSKSAQAR IGRPPVEGRG KGHLLPRYWP KYTDKELQQI SGNLNLNIVP LFEKTLSASD  300
AGRIGRLVLP KACAEAYFPP ISQSEGIPLK IQDVRGKEWT FQFRFWPNNN SRMYVLEGVT  360
PCIQSMMLQA GDTVTFSRVD PGGKLIMGAR KAAYTVDMQG CGLTNGTSNE DTSSSGVTEN  420
PTSINASSCP SQTPEELKGL PEHLSLKKSE MNGGRICDDP SRVKDKKRTR TIGAKNKRLL  480
LHSEELRVTW EEAQELLRPS PNAKPTVVVV EDHEFEEFDE PPVFGKRTII TSRPSGEQER  540
WASCDDCTKW RRLPVDALLP AKWTCSDNVW DVSRCSCCAP EESLKDLENV LRAGKEYKKR  600
RIQAAKTEEE PSGLDALASA ASAAVLGDAL GGDSEVATTT RHPRHRVGCS CIVCIQPPSG  660
KGRHKPTCGC TVCSTVKRRF KTLMMRRKKK QLERDEIAAA AEAYEEHNNK EAAEQGETDE  720
NNGEKEGRID LNCDPYNRED VEAVKEESKR RECSGVADDV LGLTELGGEA ASCEELKAAT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A6e-842704002132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1676688KRRFKTLMMRRKK
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
PlantRegMapXP_013630357.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3535020.0AK353502.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-47-G20.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013630357.10.0PREDICTED: B3 domain-containing transcription repressor VAL1-like
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A0D3B4850.0A0A0D3B485_BRAOL; Uncharacterized protein
STRINGBo3g024640.10.0(Brassica oleracea)
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]