PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Potri.013G157500.1
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: 874aa    MW: 96292.8 Da    PI: 6.6184
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.013G157500.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B360.33.3e-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.013G157500.1 330 FEKILSASDAGRIGRLVLPKACAEAYfpAISQSEGIPLRIQDIKGREWTFQFRFwpNNNSRMYVLE-GVTPCIHSMQLKAGDTITFSRID- 418
                         99**************************777778899***************9989999999***9.********************887. PP

                         SEE..EEEEE- CS
                  B3  88 sefelvvkvfr 98 
                          +++lv+++++
  Potri.013G157500.1 419 PGGKLVMGFRK 429
                         77777777765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.8E-29326434IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.41E-21327432IPR015300DNA-binding pseudobarrel domain
CDDcd100175.49E-24328429No hitNo description
PfamPF023621.9E-16330429IPR003340B3 DNA binding domain
PROSITE profilePS5086311.166330431IPR003340B3 DNA binding domain
SMARTSM010195.6E-22330430IPR003340B3 DNA binding domain
PROSITE profilePS5105014.433578628IPR011124Zinc finger, CW-type
PfamPF074964.9E-10583625IPR011124Zinc 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: 874 aa     Download sequence    Send to blast
MGTKICMNAS CQTATTHEWK RGWPLRSGGH ALLCYNCGSA YEDSLFCDTF HSEEPGWREC  60
NICSKHLHCG CIASKFLLEL LDYGGVGCAS CARSSRLHLM QSDEIPNGFS FLARNNAGDS  120
ESIPAENTVA GNSNDEGGLA QLCRLLEANE PSLLHPSKRA NTNGGLGQFR QEEIMHAIGD  180
IGTGFSNVTQ PSIGSPKFSK PNNTSSLLDL RDMHSSLSQP SLSMALGAPS GTTNFVTFPD  240
GAVEGKEQRK TPSSFQQGQR SRPILPKPSK PGLSVSSENN IGAASELRIA RPPAEGRGKN  300
QLLPRYWPRI TDQELQQLSG DLNSNIVPLF EKILSASDAG RIGRLVLPKA CAEAYFPAIS  360
QSEGIPLRIQ DIKGREWTFQ FRFWPNNNSR MYVLEGVTPC IHSMQLKAGD TITFSRIDPG  420
GKLVMGFRKS TNNDEDTQAS GLLDGTASGE TSFSGTVETL LTDPYQNALS KRLKLADGDI  480
GWNNSENHRG RINGDLLQQT TAPTEKKRTQ NIGPKSKRLF MHSEDAMELR LTWEEAQDLL  540
RPPPSVKPTI VTIEDHEFEE YDEPPVFGKR TIFTSRSSGG QEQWAQCDDC SKWRNLPVDA  600
LLPPKWTCSE NAWDSSRCTC SAPEEMTSKD LDNVLGVSKD FKKRRNLRSQ KRFQERESSG  660
LDALATVAVL GDNLDDSGDP SVGATTKHPR HRLGCTCIVC IQPPSGKGKH KPTCTCNVCM  720
TVKRRFKTLM LRKKKRQSER EAEISQKDNM DHKEESEMNG TMSHEVLHIN NPDTEGNQSQ  780
RQIEKPETSA GQIDLNCHPN SEDTSLEIPG LSTMNLVDTA NSPLDNYIKQ NGLSSFVWDQ  840
QGGPAQKSGE SLRRLSDEAF LASIGWTHES IRD*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A2e-703084322126B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1722733KRRFKTLMLRKK
2722735KRRFKTLMLRKKKR
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.013G157500.1
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_024439146.10.0B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A2K1Y6750.0A0A2K1Y675_POPTR; Uncharacterized protein
STRINGPOPTR_0013s15330.10.0(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]