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 GSBRNA2T00048551001
Common NameGSBRNA2T00048551001
Organism
Brassica napus
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: 788aa    MW: 85837.5 Da    PI: 7.6955
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00048551001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B360.52.8e-19291390198
                          EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                          f+k+l+ sd+++ grlvlpk +ae++   +++ e++ l+++d +g++W++++++  +++s++yvl+ G     ++ +L++gD+v+F++++
  GSBRNA2T00048551001 291 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKVQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMRLQAGDTVTFSRVD 379
                          99**************************666678889***************9989999999***9.********************766 PP

                          SSEE..EEEEE- CS
                   B3  87 rsefelvvkvfr 98 
                            +++l +++++
  GSBRNA2T00048551001 380 -PGGKLIMGARK 390
                          .88888888776 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-29288391IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.83E-20288386IPR015300DNA-binding pseudobarrel domain
CDDcd100171.25E-24289390No hitNo description
PROSITE profilePS5086310.884291392IPR003340B3 DNA binding domain
PfamPF023622.1E-16291390IPR003340B3 DNA binding domain
SMARTSM010199.5E-23291392IPR003340B3 DNA binding domain
PROSITE profilePS5105013.624539589IPR011124Zinc finger, CW-type
PfamPF074963.0E-9545586IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 788 aa     Download sequence    Send to blast
MFEVKMGSKV CMNASCGSTS SVEWKKGWPL RSGALADLCF RCGSAYETSR FCETFHMEQS  60
GWRECYLCNK RLHCGCIASK LVVEFMDYGG VGCSTCTNSH SKRGENPGVF SRLPMNMQQT  120
NGEIRSEANL FSQPLVSGDD KREEFTPHRG FGNLMKQDNN VTTTGYTHES SSSSPAQPSL  180
NMALATLPYS PSFATPVVDG NKLMGAGGGG VASSQSHLFQ CSASSILQKP SKSVLGTPPP  240
GTSKSAQARI GRPPVEGRGK GHLLPRYWPK YTDKELQQIS GNLNLNIVPL FEKTLSASDA  300
GRIGRLVLPK ACAEAYFPPI SQSEGIPLKV QDVRGKEWTF QFRFWPNNNS RMYVLEGVTP  360
CIQSMRLQAG DTVTFSRVDP GGKLIMGARK ATYTVDMQGC GFANGASNED TSSSGVTENL  420
TSINAPSCPS QMLEGLPEHL GSPHGGNGLK KSEINGGDDP SRGKEKKRTR TLGAKNKRLL  480
LHSEESMELR VTWEEAQELL RPSANAKPTV VVIEEHEFEE FEEPPVFGKR TIVVTSRPSG  540
EQERWGSCDD CSKWRRLPVD ALLPAKWTCS DNVWDSSRCS CSAPEESLKE LENVLRAGKE  600
YKKKRIGVSQ TARNEQEPSG LDALASAAVL GDALDESEVA TTTRHPRHRV GCSCIVCIQP  660
PSGKGRHKPT CGCTVCSTVK RRFKTLMMRR KKKQLERDGT AAVDEENKEG VEPEKNEGEK  720
EGRIDLNSDP YNREDAEAVA VEKREESKKS EGGVSWGVSQ GGGVLGETEV GGGEAEKTTS  780
EEQKVTS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A9e-822693992132B3 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
PlantRegMapGSBRNA2T00048551001
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_009144302.10.0PREDICTED: B3 domain-containing transcription repressor VAL1-like
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A078FF660.0A0A078FF66_BRANA; BnaA05g11980D protein
STRINGBra018313.1-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. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]
  9. 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]
  10. 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]
  11. 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]