PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_011080654.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Pedaliaceae; Sesamum
Family B3
Protein Properties Length: 820aa    MW: 90628 Da    PI: 6.5577
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_011080654.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B360.13.8e-19302401198
                     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++ ++++d +g++W++++++  +++s++yvl+ G     +  ++++gD+v+F++++  +++
  XP_011080654.1 302 FEKILSASDAGRIGRLVLPKACAEAYfpPINQSEGIPIRIQDIKGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQNMQVQAGDTVTFSRID-PGGQ 394
                     99**************************777788999***************9989999999***9.********************887.8888 PP

                     .EEEEE- CS
              B3  92 lvvkvfr 98 
                     lv++ ++
  XP_011080654.1 395 LVIGCRK 401
                     8888876 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.14E-19299400IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.9E-27299407IPR015300DNA-binding pseudobarrel domain
CDDcd100172.21E-23300401No hitNo description
SMARTSM010194.6E-21302402IPR003340B3 DNA binding domain
PROSITE profilePS5086310.659302403IPR003340B3 DNA binding domain
PfamPF023623.3E-16302401IPR003340B3 DNA binding domain
PROSITE profilePS5105013.046525575IPR011124Zinc finger, CW-type
PfamPF074962.7E-12532572IPR011124Zinc 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: 820 aa     Download sequence    Send to blast
MGSKNCMNEA CRGTTTSEWK KGWSLKSGGF ATLCYTCGSA YENSLFCETF HSEDSGWREC  60
RICGKRIHCG CIASRYLHEY LDFGGIGCIS CAKRLEIHAV QSIQIPGDTP NGTFATNAIR  120
DVRPVVENQI DDDKFSTERL LQLTKAIGSN DVSSALEQLK PEESMFKTRQ SSKRLLNLAQ  180
QCSSSALFKT DNSRPKEGIK DIYESLPQPS LNFSLTTPLG SPSSGLPFPG AVVEGSEQSK  240
GSFQQGQRTR HVLPKPPKPS PTAVSETNKG TQLLLPRYWP KITDQELQQL SGDLKSTIVP  300
LFEKILSASD AGRIGRLVLP KACAEAYFPP INQSEGIPIR IQDIKGKEWT FQFRFWPNNN  360
SRMYVLEGVT PCIQNMQVQA GDTVTFSRID PGGQLVIGCR KATNSTDVQE AQTPSVVNGD  420
SPGETSFSGV TDDPLSNGGR TSDDSLQRHM PISEKKKARN IKNKRLLMPS DDAMELRITW  480
EEAQELLRPS PTXXXXVVMV EDHEFEEFEE PPIFGKRTIF TSRPSGEQEQ LAQCDSCSKW  540
RRLPVHALLS AKWTCSDNIW DSKRSSCAAP EDINPRDLES FISIYKDSKK RKISDNKVPR  600
EGEPSGLDAL ATAAVLGDNI SDIAESSVGA TTRHPRHRPG CTCIVCIQPP SGKGKHEPMC  660
KCNVCLTVRR RFKTLMMRKK KRQSEREAEL AQGKDKASVK VGLEREDIAG HALLNMSHHT  720
DNERNQNGNQ TELEETNKGQ LDLNCDPHRE DDILAEAAGM SLTTLMNAAT LPLDMYLGQN  780
GVPVTGPCLV SRTAGENEEN AADEGFTSGR VDQENNREDG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A4e-712804092131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1668679RRRFKTLMMRKK
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_011080654.1
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_011080654.20.0LOW QUALITY PROTEIN: B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A2G9GBQ20.0A0A2G9GBQ2_9LAMI; Uncharacterized protein
STRINGMigut.D00818.1.p0.0(Erythranthe guttata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA14912365
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]