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 XP_010522011.1
Organism
Tarenaya hassleriana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Cleomaceae; Tarenaya
Family B3
Protein Properties Length: 829aa    MW: 91066.8 Da    PI: 8.2376
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_010522011.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B361.71.2e-19328427198
                     EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                     f+k+l+ sd+++ grlvlpk +ae++  ++ + e++ l+++d +g++W++++++  +++s++yvl+ G     ++ +L++gD+v+F++++  +++
  XP_010522011.1 328 FEKTLSASDAGRIGRLVLPKACAEAYfpSIHQSEGIPLKIQDVKGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRID-PGGK 420
                     99**************************667778899***************9989999999***9.********************887.7888 PP

                     .EEEEE- CS
              B3  92 lvvkvfr 98 
                     lv+++++
  XP_010522011.1 421 LVLGFRK 427
                     8888776 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.109.2E-31325433IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.12E-21325431IPR015300DNA-binding pseudobarrel domain
CDDcd100175.61E-24326427No hitNo description
PROSITE profilePS5086310.955328429IPR003340B3 DNA binding domain
PfamPF023627.6E-17328427IPR003340B3 DNA binding domain
SMARTSM010194.3E-23328429IPR003340B3 DNA binding domain
PROSITE profilePS5105013.844581631IPR011124Zinc finger, CW-type
PfamPF074964.2E-10586628IPR011124Zinc 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: 829 aa     Download sequence    Send to blast
MDTKYSNSSL LISRWPKSNM GQKICMNASC ATTNTVEWKK GWPLRAGGVA DLCFRCGSAY  60
ESSLFCDTFH KEQSGWRECF LCHKRLHCGC IASKLMVELL DFGGVGCTNC SSCYSSSLNK  120
RSESQDLLGR LTMMLAERQP PNGESGILGN NIDSGRLSQL CQVVEANEPD RFPQSQRGDP  180
KTLLGGDKRE EFMPQPELGK LFKPESTKSV METRDMQESL SQPSLSMSLA VTPSGPPFPS  240
GVVEGKKQSN VTRSPTVQSS CSVLPKPSKS AVSTPGTSKA ASCPLRSARP PVEGRGRNHL  300
LPRYWPRITD QELQQISGNL NSKIVPLFEK TLSASDAGRI GRLVLPKACA EAYFPSIHQS  360
EGIPLKIQDV KGKEWTFQFR FWPNNNSRMY VLEGVTPCIQ SMQLQAGDTV TFSRIDPGGK  420
LVLGFRKTAC GGEQQGSGLT NGTSAEDTSS SGVTENPSSI NDPAGPLQMP KEMKGLPEHL  480
SSPDGEISLQ KNKNNGVRTG DGSPQIKEKK RTRNIGTKNK RLLLHNEESM ELRLTWEEAQ  540
DLLRPSPSAK PTIVTIEDNE FEEYDEPPVF GKKTVFTSRP SGGQEQWAQC DDCSKWRRLP  600
LDALLPSRWT CSDNVWDLDR CSCSVPEKNL KELESFLGVG RETKKQRSGE KQREGRKEEA  660
SGLEALASAA ALGDSIGDGS RGAAVAVAVA TTTRHPRHRE GCSCIVCIQP PSGKGKHKPT  720
CCCNVCMTVK RRFRTLMLRK KKKQQQLDLR GKEEEEEEEE EAQKAEPDKN KPGKEGSTSG  780
RIDLNSDPYN KEGVGIPLRE KEDEAVESRG NGRGGLLGGV ADQENRSKE
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A8e-743064362132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1729740KRRFRTLMLRKK
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
PlantRegMapXP_010522011.1
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_010522012.10.0PREDICTED: B3 domain-containing transcription repressor VAL1-like isoform X1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLR0HB220.0R0HB22_9BRAS; Uncharacterized protein
STRINGXP_010522011.10.0(Tarenaya hassleriana)
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]