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 Lj0g3v0332199.1
Organism
Lotus japonicus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
Family HB-other
Protein Properties Length: 262aa    MW: 29925.4 Da    PI: 4.4479
Description HB-other family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lj0g3v0332199.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox22.91.5e-071465751
                     --HHHHHHHHHHHHH..SSS--HHHHHHHHHHC.....TS-HHHHHHHHHHH CS
         Homeobox  7 ftkeqleeLeelFek..nrypsaeereeLAkkl.....gLterqVkvWFqNr 51
                     ++++q  eLe+ ++   ++  +++  +e+A+ l     +++ +qV+ WFqN+
  Lj0g3v0332199.1 14 LSTDQMLELERIYNDmgENAFDQNLCQEIAATLsaantSISWEQVQQWFQNK 65
                     6899**********666999****************9**************7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000860.001041365No hitNo description
Gene3DG3DSA:1.10.10.602.9E-41465IPR009057Homeodomain-like
PfamPF000464.7E-51465IPR001356Homeobox domain
PfamPF167193.6E-35104231IPR032001SAWADEE domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006306Biological ProcessDNA methylation
GO:0006346Biological Processmethylation-dependent chromatin silencing
GO:0031047Biological Processgene silencing by RNA
GO:0003677Molecular FunctionDNA binding
GO:0003682Molecular Functionchromatin binding
Sequence ? help Back to Top
Protein Sequence    Length: 262 aa     Download sequence    Send to blast
MVELSLIDSP FPKLSTDQML ELERIYNDMG ENAFDQNLCQ EIAATLSAAN TSISWEQVQQ  60
WFQNKLHESQ DRAASLNQLV DISDTPSLRS STVLQGNRGA VVSDLAFEAR STKDLAWHDV  120
SMLLNYRVLS TGELEARVRY AGFGKGEDEW VNVKYGVRDR SIPLEPAECH KGKEGDLVLC  180
FPERDDYALY CDARVLSIQR KQHDETDCKC IYTVRFLHDN SEEAIHWERV CYRPTQEESV  240
VYHNSPEPTI EPSMSAIENL WG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4iuq_A3e-531032362135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_B3e-531032362135SAWADEE HOMEODOMAIN HOMOLOG 1
4iur_A3e-531032362135SHH1 SAWADEE
4iur_B3e-531032362135SHH1 SAWADEE
4iut_A3e-531032362135SAWADEE HOMEODOMAIN HOMOLOG 1
4iut_B3e-531032362135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_A3e-531032362135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_B3e-531032362135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_A3e-531032362135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_B3e-531032362135SAWADEE HOMEODOMAIN HOMOLOG 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Lja.214930.0floral bud
Functional Description ? help Back to Top
Source Description
UniProtInvolved in RNA-directed DNA methylation (RdDM). Required for the silencing of some endogenous RdDM targets and accumulation of 24-nt siRNAs, but not for the production of Pol V-dependent transcripts. Functions in transcriptional silencing through both DNA methylation-dependent and -independent pathways. Required for both maintenance and de-novo DNA methylation. Plays a role in the recruitment of Pol IV to genomic regions associated with K9 methylated histone H3 that are targets for RdDM. {ECO:0000269|PubMed:21811420, ECO:0000269|PubMed:22064704, ECO:0000269|PubMed:23636332, ECO:0000269|PubMed:23637343}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLj0g3v0332199.1
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_020227511.11e-108protein SAWADEE HOMEODOMAIN HOMOLOG 1 isoform X1
RefseqXP_029129365.11e-108protein SAWADEE HOMEODOMAIN HOMOLOG 1 isoform X1
SwissprotQ9XI478e-72SHH1_ARATH; Protein SAWADEE HOMEODOMAIN HOMOLOG 1
TrEMBLA0A151SH361e-107A0A151SH36_CAJCA; Uncharacterized protein
STRINGGLYMA07G01880.31e-106(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF27041415
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18380.14e-43sequence-specific DNA binding transcription factors;sequence-specific DNA binding
Publications ? help Back to Top
  1. Liu J, et al.
    An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing.
    Cell Res., 2011. 21(12): p. 1691-700
    [PMID:22064704]
  2. Law JA, et al.
    Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
    Nature, 2013. 498(7454): p. 385-9
    [PMID:23636332]
  3. Ma L, et al.
    Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway.
    Genome Biol Evol, 2015. 7(9): p. 2648-62
    [PMID:26338185]
  4. Wang F,Axtell MJ
    AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana.
    Plant J., 2017. 90(1): p. 37-47
    [PMID:28002617]