PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Tp4g13000
Organism
Thellungiella parvula
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassicaceae incertae sedis; Schrenkiella
Family B3
Protein Properties Length: 808aa    MW: 88587.3 Da    PI: 8.0092
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp4g13000genomethellungiellaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B356.93.9e-18306402195
                EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEE CS
         B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvk 95 
                f+k+l+ sd+++ grlvlpk +ae++   +++ e++ l+++d +g++W++++++  +++s++yvl+ G     ++  L++gD+v+F++++  +++l ++
  Tp4g13000 306 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRVD-PGGKLILG 402
                99**************************666678889***************9989999999***9.********************765.67766665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.3E-28303415IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.49E-19303402IPR015300DNA-binding pseudobarrel domain
CDDcd100175.13E-23304401No hitNo description
PROSITE profilePS5086310.588306407IPR003340B3 DNA binding domain
SMARTSM010193.2E-22306406IPR003340B3 DNA binding domain
PfamPF023621.5E-15306402IPR003340B3 DNA binding domain
PROSITE profilePS5105013.844559609IPR011124Zinc finger, CW-type
PfamPF074965.9E-10565606IPR011124Zinc 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: 808 aa     Download sequence    Send to blast
MFQVKMGSRM CMNASCGSTS TVEWKKGWPL RSGALADLCY RCGSAYESSL FCETFHMDQS  60
GWRECYLCSK RLHCGCIASK LMVEFMDYGG VGCTTCSSYY QPNMNKRGEN PGVCSRLPMK  120
TLAERKHTNG ETGMNIEGGR NEADLFSQSQ RCDSQPLVTG GDKREEELMP HRGFGKLMKS  180
GNTTGYRLDA GEMHESSSPS QPSLNMALAV LPYSPSFSTP VDGQKHIGAS QSHIVQCSAS  240
SILQKPSKCV LGTPPGTSKS AQARIGRPPV EGRGKGHLLP RYWPKYTDKE VQQISGNLNL  300
NIVPLFEKTL SASDAGRIGR LVLPKACAEA YFPPISQSEG IPLKIQDVRG KEWTFQFRFW  360
PNNNSRMYVL EGVTPCIQSM MLQAGDTVTF SRVDPGGKLI LGSRKAANTK DMQGCGLING  420
TSNEDTSSSG VTETPSSINA SSCPSQVPEE LKGLPEHLSL PHGGSSLKKS EINGGRICDD  480
PPRVKDKKRT RTIGAKNKRL LLHSEESMEL RVTWEEAQEL LRPSPSAKPT IVVIEEHEFE  540
EFDEPPVFGK RTLITSRSSG EQERWASCDD CSKWRRLPVD ALLPAKWTCS DNVWDGSRCS  600
CSAPEESLKE LDNILRMGKE CKKRRIGVSQ TGKTEQEPSG LDALASAASA AVLGEQEIAT  660
TTRHPRHRVG CSCIVCIQPP SGKGRHKPSC GCNVCSTVKR RFKTLMMRRK KKQLERDGAA  720
AADEENKEVK QAEPDKNKAE KEGKTGRIDL NSDPYNREDV EAVAVEKDGS KSREVGQCSG  780
VAQDGDVLGV MELEAEAEEI REEAKGSS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A1e-852844142132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1698710KRRFKTLMMRRKK
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
PlantRegMapTp4g13000
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_006410148.10.0B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLV4NXH20.0V4NXH2_EUTSA; Uncharacterized protein
STRINGXP_006410148.10.0(Eutrema salsugineum)
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]