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_009132737.1
Organism
Brassica rapa
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: 783aa    MW: 85847.7 Da    PI: 7.2078
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009132737.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.72.2e-18290389198
                     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_009132737.1 290 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRVD-PGGK 382
                     99**************************666678889***************9989999999***9.********************765.8888 PP

                     .EEEEE- CS
              B3  92 lvvkvfr 98 
                     l +++++
  XP_009132737.1 383 LIMGARK 389
                     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-28287391IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.62E-19287385IPR015300DNA-binding pseudobarrel domain
CDDcd100171.55E-23288389No hitNo description
PROSITE profilePS5086310.673290391IPR003340B3 DNA binding domain
PfamPF023628.0E-16290389IPR003340B3 DNA binding domain
SMARTSM010196.5E-22290391IPR003340B3 DNA binding domain
PROSITE profilePS5105013.739538588IPR011124Zinc finger, CW-type
PfamPF074969.4E-10544585IPR011124Zinc 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: 783 aa     Download sequence    Send to blast
MFEVKTGSKV CMNASCGSTS TVEWKKGWPL RSGSLADLCF RCGSAYETSL FCETFHLEQS  60
GWRDCYLCNK RLHCGCIASK LMVEFMDYGG VGCTSCTNCH QLNLNKRGEN PVVFSRLAMN  120
SPHTNGESGI SIRSEADLFS QPLVNGDDKR EEFMAHRGFA NFMKPDNNTN NNNAGEMHEP  180
SQPSLNVALA TLPYSPSFAN PVGGNKLMAA ASQSHSHIGQ CSASSILQKP SKSVPGTPPG  240
TSKSAQARIG RPPVEGRGKG HLLPRYWPKY TDKELQQISG NLNLNIVPLF EKTLSASDAG  300
RIGRLVLPKA CAEAYFPPIS QSEGIPLKIQ DVRGKEWTFQ FRFWPNNNSR MYVLEGVTPC  360
IQSMMLQAGD TVTFSRVDPG GKLIMGARKA AYTVDMQGCG LTNGTSNEDT SSSGVTENPT  420
SINASSQIPE ELKGVPEHLS SPYGVGSSLK KSEMNGGRIC DDPSRVKDKK RTRTIGAKNK  480
RLLLRSEELR VTWEESQELL RPSPNAKPTV VVVEDHEFEE FDEPPVFGKR TILTSKPSGE  540
QERWASCDDC TKWRRLPIDA LLPAKWTCSD NVWDVSRCSC SAPEESLKDL ENVLRAGKEY  600
KKRRIQAAKT EEEPSGLDAL ASAASAAVLG DALGGDSEVA TTTRHPRHRV GCYCIVCIQP  660
PSGKGRHKPT CGCTVCSTVK RRFKTLMMRR KKKQLERDEI TAAAEAYEEH NNKEAAERGD  720
TDENNGEKEG RIDLNSDPYN REDVEAEKED TKGRECSGVA DEVLGLTELG GEAASCEELK  780
AAT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A9e-842683982132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1679691KRRFKTLMMRRKK
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_009132737.1
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_009132737.10.0PREDICTED: B3 domain-containing transcription repressor VAL1-like
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLM4E2010.0M4E201_BRARP; Uncharacterized protein
STRINGBra022801.1-P0.0(Brassica rapa)
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]