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 KFK22946.1
Organism
Arabis alpina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Arabideae; Arabis
Family B3
Protein Properties Length: 808aa    MW: 88917.7 Da    PI: 7.5471
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KFK22946.1genomeMPIPBRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.91.9e-18303402198
                 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 ++
  KFK22946.1 303 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRVD-PSGKLILG 399
                 99**************************666678889***************9989999999***9.********************776.88888888 PP

                 EE- CS
          B3  96 vfr 98 
                 +++
  KFK22946.1 400 ARK 402
                 775 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.88E-19300398IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.5E-28300403IPR015300DNA-binding pseudobarrel domain
CDDcd100173.48E-23301402No hitNo description
PfamPF023625.6E-16303402IPR003340B3 DNA binding domain
SMARTSM010191.2E-22303404IPR003340B3 DNA binding domain
PROSITE profilePS5086310.701303404IPR003340B3 DNA binding domain
PROSITE profilePS5105013.476559609IPR011124Zinc finger, CW-type
PfamPF074965.8E-9565606IPR011124Zinc 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
MVLKMCMNAS CGSTSTVEWK KGWPLRSGLL ADLCFRCGSA YESCLFCETF HMDQSGWREC  60
FLCSKRLHCG CIASKLMVEL MDYGGVGCAT CANCHQLNLH KRDENPAVFG RLPMKTLADR  120
QHINGESGMN IDGVRNEADL FSQPQRCDSQ PLGLGGDKRE EFMPHRGFGQ LLKPENTTTG  180
YRLDAGEMNG PSPSPSQPSL NMALAVIPYS PSFSTEGIDG KKHIGASQSH MMQCSAPGLL  240
QKPSKSVLTT PAGTSKSAQP RIGRPPVEGR GKGHLLPRYW PKYTDKEVQQ ISGNLNLNIV  300
PLFEKTLSAS DAGRIGRLVL PKACAEAYFP PISQSEGIPL KIQDVRGKEW TFQFRFWPNN  360
NSRMYVLEGV TPCIQSMMLQ AGDTVTFSRV DPSGKLILGA RKAVNAGDMQ VGVSTNWGLK  420
GCGLTNGTST EDTSSSGVTE NPPSINASSC PSQIPKETNG LPQNLTTPHG EINGGRMCDD  480
PPRVKEKKRT RTIGTKNKRL LLHSEESMEL RVTWEETQDL LRPAPSSKPS IVVIEEHEFE  540
EFDEPPVFGK RTIVTSRPSG EQERWASCDD CSKWRRLPVD ALLPFKWTCV DNVWDENRCS  600
CSAPEESLKE LENALKIGKE YKKRRIGESQ GAKNEQEPSG LDALASAAVL GDTLGEPEVA  660
TTTRHPRHRV GCSCIVCIQP PSGKGRHKPN CGCNVCSTVK RRFKTLMMRR KKKQLERDET  720
AAAAEQENKE AKQAETDKNK GDKEGRIDLN SDPYNREDTE AVAVEKEESR RREVGQCSGV  780
APEGGDVVGV TELEGEAEKI HEEPKSSS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A6e-842814102131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1699711KRRFKTLMMRRKK
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
PlantRegMapKFK22946.1
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_006293696.10.0B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A087FZ940.0A0A087FZ94_ARAAL; Uncharacterized protein
STRINGA0A087FZ940.0(Arabis alpina)
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]