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_009595178.1
Organism
Nicotiana tomentosiformis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
Family B3
Protein Properties Length: 862aa    MW: 94961 Da    PI: 6.3328
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009595178.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B359.94.5e-19338437198
                     EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                     f+kvl+ sd+++ grlvlpk +ae++   +++  +  ++++d +g++W++++++  +++s++yvl+ G     +  +L++gD+v+F++++  +++
  XP_009595178.1 338 FEKVLSASDAGRIGRLVLPKACAEAYfpPINQSDGLPIRIQDIKGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQNMQLQAGDTVTFSRID-PGGK 430
                     99**************************556666778***************9989999999***9.********************887.7887 PP

                     .EEEEE- CS
              B3  92 lvvkvfr 98 
                     lv+++++
  XP_009595178.1 431 LVMGFRK 437
                     8888776 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.6E-29335441IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.02E-21335438IPR015300DNA-binding pseudobarrel domain
CDDcd100176.44E-24336437No hitNo description
PfamPF023622.2E-16338437IPR003340B3 DNA binding domain
PROSITE profilePS5086311.237338439IPR003340B3 DNA binding domain
SMARTSM010193.1E-22338438IPR003340B3 DNA binding domain
PROSITE profilePS5105013.76562616IPR011124Zinc finger, CW-type
PfamPF074963.8E-10567613IPR011124Zinc 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: 862 aa     Download sequence    Send to blast
MGFLDLEILN MGSMICMNEV CRKTTSSEWK KGWSLKSGGF ANLCYNCGSA FENLSFCETF  60
HMGDSGWREC KMCGKHLHCG CIASKYLFEY LDFGGVGCIS CARCLDDHSM RPMQVPADDF  120
RDSAFGTNFI QPLHVEKGVD KTNFDKGRLP TVNNIMEISE PGQPFQSQKD ENNVSLGKTK  180
QEKVLPVGDV STCFSNLNQQ SIASLFREQD NSKPNQGVKE MYDTTNQPSL DFSLSTPVGC  240
SSSGLSFPDG GVEGREHEKT PFQQGLRTRH ILLKPLKPSP SFGSDSNKEL PSQTRIARPP  300
AEGRGGRNQL LPRYWPRITD QELCQLSGDL NSAIVPLFEK VLSASDAGRI GRLVLPKACA  360
EAYFPPINQS DGLPIRIQDI KGKEWTFQFR FWPNNNSRMY VLEGVTPCIQ NMQLQAGDTV  420
TFSRIDPGGK LVMGFRKATN SVETQDPQSS HLPDGSGSAD TSFTGLTENL NNGGRTSADS  480
VHRQVPVSEK KKTTNIGSKN KRLLMHADDA MELRITWEES QELLRPPPTT QPTILVIEDC  540
EFEAYDEPPV FGKQTIFTSR PSGDQEQWAQ CDSCSKWRRL PMHVLLPPKW TCSDNIWDSN  600
SFLYRCSCSA PEEIKAKELE AFFRVSKGHK RQKIAGKNED CEPSGLNALA TVAVLGDSIS  660
DLGEPLVGAT TKHPRHRPGC TCIVCIQPPS GKGKHQPTCK CNACLSAERR FKTLMLRKKK  720
KQSEREAEVA QAKDQVPPKD GSETDGASGA ELMMQTSHSE NERNTNGDHM EKVGAGKGQL  780
DLNCHPNRED EMLIEAAAGI SMTSLINAAD LPLDMYQTQN GLATLDKCLL SLATAGSEGQ  840
QPDNGCVRPA DAQVQENNGD NG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A5e-693164452131B3 domain-containing transcription repressor VAL1
Search in ModeBase
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}.
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_009595178.10.0PREDICTED: B3 domain-containing transcription repressor VAL1-like isoform X1
SwissprotQ6Z3U30.0Y7797_ORYSJ; B3 domain-containing protein Os07g0679700
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A1J6I6X90.0A0A1J6I6X9_NICAT; B3 domain-containing protein
STRINGXP_009595178.10.0(Nicotiana tomentosiformis)
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. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. 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]
  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]