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 Potri.019G130300.1
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family B3
Protein Properties Length: 855aa    MW: 94140.7 Da    PI: 6.4212
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.019G130300.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B361.11.9e-19330429198
                         EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                         f+k+l+ sd+++ grlvlpk +ae++   +++ e++ l+++d +gr+W++++++  +++s++yvl+ G     ++ +Lk+gD+++F++++ 
  Potri.019G130300.1 330 FEKILSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDIKGREWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLKAGDTITFSRID- 418
                         99**************************666678889***************9989999999***9.********************887. PP

                         SEE..EEEEE- CS
                  B3  88 sefelvvkvfr 98 
                          +++lv+++++
  Potri.019G130300.1 419 PGGKLVMGFRK 429
                         77777777765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.104.7E-30326433IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.57E-21327431IPR015300DNA-binding pseudobarrel domain
CDDcd100171.46E-24328429No hitNo description
SMARTSM010197.0E-24330430IPR003340B3 DNA binding domain
PROSITE profilePS5086311.321330431IPR003340B3 DNA binding domain
PfamPF023621.2E-16330429IPR003340B3 DNA binding domain
PROSITE profilePS5105014.412560610IPR011124Zinc finger, CW-type
PfamPF074962.0E-10565607IPR011124Zinc 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: 855 aa     Download sequence    Send to blast
MGTKICMNAS CQTTTTHEWK RGWPLRSGGH ALLCFNCGSA YEDSLFCDTF HSEEPGWREC  60
NICTKRLHCG CIASKFLLEL LDYGGVGCSS CARSSRLHSM QSDEIPNGYG SLTRNNAGDL  120
ESIPVESTVA ANDYDEGGLA QLCRLIEASE PSLLHPSERA NANGCLGQFR QEEIRHAIGD  180
IGTGFSNMTL PSVGSSKFTN PDNMSSLLDM RDMHCSLSEP SLSMALGAPS GTTNFAPFPG  240
GAVEGREQGK TPSSFQQGQR SRPILPKPSK PGLLSSSENN KGSASELRIA RPPAEGRGKN  300
QLLPRYWPRI TDQELQQLSG DLNSNIVPLF EKILSASDAG RIGRLVLPKA CAEAYFPPIS  360
QSEGIPLKIQ DIKGREWTFQ FRFWPNNNSR MYVLEGVTPC IQSMQLKAGD TITFSRIDPG  420
GKLVMGFRKS TNNNEDIQDA QASGLPDGTA SGETSLSADG YIGWNNSENH GGGINGDLLQ  480
QTTAPTEKKR TRNIGPKSKR LLMHSEDAME LRLTWEEAQD LLRPPPSVKP TIVTIEDHEF  540
EEYDEPPVFG KRTIFTSRSP GRQEQWAQCD DCSKWRKLPV DALLPPKWTC SENAWDSSRC  600
TCSVPEEMTP KDLDNLLRVS KDFKKRRILE SQKRFQNCEP SGLDALASAA VLGDNLDDSG  660
EPSVGATTKH PRHRPGCTCI VCIQPPSGKG KHKPTCTCNV CMTVKRRFKT LMLRKKKRQS  720
EREAETSQKD NMDRKESEAN GTMSHEVLPI NNPETEVGQS KTQTEKPETS AGQIDLNCHP  780
NREDMPLDMP GLSTMNLVDL ANTPLDNYIK QNGLSSLVWD QEGGQAQHSG ESLRRLSDEA  840
FLASIGWAHE SRRD*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A2e-723084322126B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1704715KRRFKTLMLRKK
2704717KRRFKTLMLRKKKR
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
PlantRegMapPotri.019G130300.1
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_024447572.10.0B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A2K1WTD30.0A0A2K1WTD3_POPTR; Uncharacterized protein
STRINGPOPTR_0019s15070.10.0(Populus trichocarpa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF103233039
Representative plantOGRP12361446
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]