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 MDP0000229344
Organism
Malus domestica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Malus
Family B3
Protein Properties Length: 937aa    MW: 103305 Da    PI: 6.1781
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
MDP0000229344genomeGDRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B359.65.6e-19368468199
                    EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
             B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                    f+kvl+ sd+++ grlvlpk +ae++   +++ e+  ++++d +g++W++++++  +++s++yvl+ G     ++ +L++gD+v+F++++  +++l
  MDP0000229344 368 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGLPIRIQDVKGNEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMELQAGDTVTFSRID-PGGRL 461
                    99**************************555556677***************9989999999***9.********************987.89999 PP

                    EEEEE-S CS
             B3  93 vvkvfrk 99 
                    v++++++
  MDP0000229344 462 VIGFRKA 468
                    9999876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.9E-29364468IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019369.81E-21365467IPR015300DNA-binding pseudobarrel domain
CDDcd100171.19E-24366467No hitNo description
PfamPF023621.8E-16368468IPR003340B3 DNA binding domain
SMARTSM010191.8E-23368469IPR003340B3 DNA binding domain
PROSITE profilePS5086311.209368469IPR003340B3 DNA binding domain
PROSITE profilePS5105014.191629679IPR011124Zinc finger, CW-type
PfamPF074962.6E-9634676IPR011124Zinc 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: 937 aa     Download sequence    Send to blast
MHVFSPGLTH TDPQKPHSPL ITFVNAHCIE LAAAASAVAG FGELEFGAME SKICMNPSCR  60
MANTHEWKTG WPLRSGGFAH LCYKCGVEYE NSVYCNTFHS GETGWRDCNL CHKPLHCGCI  120
VSETLYECLD FGGIGCIGCA SQPHVIQDGD VLNGFGGLKI SDFGDHQSTV PQNGALSDTA  180
NEGELLQLCQ VMEANESNLS SQSQRGEINV SPVQTKREEV TYPRGEVGPG FSSITRPSFG  240
SLTFAKPDNG RIMIEVKDMN KXSSEPSLSM TLGGPSATPN FAQPFTGGIL ERRDQSKMSS  300
SFQQGQKIRP IFPRPLRPPP PIHNVRVARP PAEGRGKSQL LPRYWPRITD QELQKLAGDL  360
NSTIVPLFEK VLSASDAGRI GRLVLPKACA EAYFPPISQS EGLPIRIQDV KGNEWTFQFR  420
FWPNNNSRMY VLEGVTPCIQ SMELQAGDTV TFSRIDPGGR LVIGFRKASR CLDVQESQTS  480
FLPNGTPGET SCPSVVENLV TGSGHSSIYQ MSTGSKDLNA LSGHLHLADG DTSLHSNENH  540
SHFTSEDLQQ KPVSNSDKKR ARNIGPKSKR LLLHSEDVLE LRLTWEEAQD LLRPPLSVKP  600
SIVTIEDHEF EEYDEPPVFG KRSLFIAESE RQEQWARCDD CSKWRRLPVD VLLPPKWTCX  660
ENSWDINRCS CSAPEEVSQE ELDNLLRPSK DLKKRRIVVN HNEAQEHEPS GLDALASASA  720
AILGDSVDYA DEQSVGATTR HPRHRPGCTC IVCIQPPSGK GKHKPTCTCN VCMTVKRRFK  780
TLMMNKRKRK SEREMENAHX DNNDHKDESE MNGMSTEIEL HMNHSSENGS SCEKRIQADV  840
AESSCAGQID LNCEPKHNYV QVSGLTLLRL ADAVAQQPVK NSTKESGLTN RMCEPQAGLG  900
SSLRAQDTAE TDKLLCNEGS LSSVAAAWDL EGRGDED
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A3e-693464752131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1775789KRRFKTLMMNKRKRK
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}.
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_008384662.20.0B3 domain-containing transcription repressor VAL1-like
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A498IPB00.0A0A498IPB0_MALDO; Uncharacterized protein
STRINGXP_008384662.10.0(Malus domestica)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF103233039
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]