PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Neem_4176_f_1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family B3
Protein Properties Length: 873aa    MW: 96276.2 Da    PI: 6.8219
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_4176_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B356.93.9e-18324423198
                    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++ l+++d +g++W +++++  +++s++yvl+ G     ++ +L++gD+++F++++  +++l
  Neem_4176_f_1 324 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGVPLRIQDVKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLRAGDTITFSRID-PGGKL 417
                    99**************************666778999***************9989999999***9.********************887.77777 PP

                    EEEEE- CS
             B3  93 vvkvfr 98 
                     +++++
  Neem_4176_f_1 418 IMGFRK 423
                    777776 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.4E-29320430IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.89E-20321423IPR015300DNA-binding pseudobarrel domain
CDDcd100172.79E-23322423No hitNo description
PROSITE profilePS5086311.039324425IPR003340B3 DNA binding domain
SMARTSM010193.1E-21324425IPR003340B3 DNA binding domain
PfamPF023622.1E-15324423IPR003340B3 DNA binding domain
PROSITE profilePS5105014.422593643IPR011124Zinc finger, CW-type
PfamPF074961.5E-10598640IPR011124Zinc 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: 873 aa     Download sequence    Send to blast
MYARSAYENF VFCDTFHLDE PGWRECYLCC KRLHCGCIAS KPLLELLDYG GVGCHSCAIS  60
SRLHLSRKNG LSDGHLWDCC YSICLIQRDE IRNGFGAPTV NDSHNIRSTA IESRATAIES  120
RVVGDGGAEG KLTHLCRIME ANESNLLAPS HRGDTNVSLG KEKREDIVHS FGEVGAGFSS  180
ATQPSAGSSK FTKPDSDRSM LDIRDMHESV VQRSLSMSLA VASGNSKFVI PFSNGAADVR  240
EQSKAPPSFQ QGQRSRPILP KPPKTGLTIT SETSKSTGSQ LRIARPPAEG RGKNHLLPRY  300
WPRITDQELQ QLSGDLNSTI VPLFEKVLSA SDAGRIGRLV LPKACAEAYF PPISQSEGVP  360
LRIQDVKGKE WVFQFRFWPN NNSRMYVLEG VTPCIQSMQL RAGDTITFSR IDPGGKLIMG  420
FRKASNAEDT QDAQTSAVPN GTQSGDISLS GVTENLPTVS GYSGLFQTLK GSKEPHVNAL  480
SEHSTLAEGA INWHKSENHV GKTNGDSPQQ SAPSMEKKRT RNIGSKNKRL LMHSEEALEL  540
RLTWEEAQDL LRPPPSAKPS IVTIEDHEFE EYDEPPVFGK RTIFTSRPSG TWFRGQEQWA  600
QCDDCSKWRK LPMDVLLPPK WTCSDNVWDS IRCSCSAPEE MSQKDLENLL KVGRDCKKRK  660
IAEGHKLDEE HEPSGLDALA SAAVLGDDAG DSGEPSVGAT TKHPRHRPGC TCIVCIQPPS  720
GKGKHKPTCT CNVCMTVKRR FKTLMLRKKR RQSEREAEAA EVAQKNNDNK ESKADVPEAE  780
TSSGQIDLDL NCHPNREEMQ TEEPGMNIMT LEQRTNVPLE NYMQQQQQPN GLGSLSSCVL  840
QQAAANGEND KLMSDEGFLA SVGWGRDQEP NLD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A7e-733024312131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1737748KRRFKTLMLRKK
2737749KRRFKTLMLRKKR
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}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4415347e-51AM441534.1 Vitis vinifera contig VV78X035471.3, whole genome shotgun sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006432020.10.0B3 domain-containing transcription repressor VAL1
RefseqXP_006491930.10.0B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLV4T1N20.0V4T1N2_9ROSI; Uncharacterized protein
STRINGXP_006491930.10.0(Citrus sinensis)
STRINGXP_006432020.10.0(Citrus clementina)
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. Q├╝esta 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]