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 PGSC0003DMP400043392
Organism
Solanum tuberosum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
Family B3
Protein Properties Length: 145aa    MW: 16147.5 Da    PI: 9.0763
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400043392genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B341.13.2e-1352134179
                           EEEE-..-HH.HHTT-EE--HHH.HTT....---..--SEEEEEETTS-EEEEEE..EEETTE..EEE-TTHHHHHHHHT--TT-E CS
                    B3   1 ffkvltpsdv.lksgrlvlpkkfaeeh....ggkkeesktltledesgrsWevkliyrkksgr..yvltkGWkeFvkangLkegDf 79 
                           f+k l+ sd+ l+++rlv+pkk+ae++    +g+++  + + + d++g++W++ ++++ +s++  yvl+ G +++  +++ ++gD+
  PGSC0003DMP400043392  52 FQKSLSASDAdLALSRLVIPKKCAEAYfpplSGPHK--IPINILDTDGKEWNFHFRFWPNSRSkmYVLE-GLRDYMVSKKWQAGDV 134
                           78899888862566***************8766654..569999*************777777758888.**************97 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-2149134IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.49E-1649134IPR015300DNA-binding pseudobarrel domain
CDDcd100178.05E-1850134No hitNo description
SMARTSM010192.4E-452144IPR003340B3 DNA binding domain
PfamPF023623.2E-1052134IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0048366Biological Processleaf development
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 145 aa     Download sequence    Send to blast
MASPSSSTTT FCFQCEDSSN SVTFRNGWRL RSGKFAQLCH RCACGRVVTP LFQKSLSASD  60
ADLALSRLVI PKKCAEAYFP PLSGPHKIPI NILDTDGKEW NFHFRFWPNS RSKMYVLEGL  120
RDYMVSKKWQ AGDVDAIASV YASP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6fas_A4e-3048140596B3 domain-containing transcription repressor VAL1
6fas_B4e-3048140596B3 domain-containing transcription repressor VAL1
6j9a_A7e-304814020111B3 domain-containing transcription repressor VAL1
Search in ModeBase
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 VAL1/HSI2. {ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPGSC0003DMP400043392
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1937812e-79AC193781.1 Solanum lycopersicum chromosome 10 clone C10SLe0045H11, complete sequence.
GenBankHG9755222e-79HG975522.1 Solanum lycopersicum chromosome ch10, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006362940.14e-63PREDICTED: B3 domain-containing transcription repressor VAL1-like isoform X4
SwissprotQ5CCK41e-27VAL2_ARATH; B3 domain-containing transcription repressor VAL2
SwissprotQ6Z3U31e-27Y7797_ORYSJ; B3 domain-containing protein Os07g0679700
TrEMBLM1CC791e-104M1CC79_SOLTU; Uncharacterized protein
STRINGVIT_19s0014g03560.t019e-34(Vitis vinifera)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G32010.12e-25HSI2-like 1
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]
  3. 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]
  4. 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]
  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. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]