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 Potri.001G189200.1
Common NamePOPTR_0001s19000g
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 HB-other
Protein Properties Length: 240aa    MW: 27386.9 Da    PI: 4.8804
Description HB-other family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.001G189200.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox16.21.9e-05561751
                        --HHHHHHHHHHHHH..SSS--HHHHHHHHHHC..........TS-HHHHHHHHHHH CS
            Homeobox  7 ftkeqleeLeelFek..nrypsaeereeLAkkl..........gLterqVkvWFqNr 51
                        ft ++  e+e++F++  +  +  +  e+LA++            +t rqVk WFq r
  Potri.001G189200.1  5 FTLSEMLEMENMFKEleEGPLAPQFCEKLASSFslapsrdgkqAITPRQVKSWFQDR 61
                        7888999*******8735555666689*****999********************88 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS500718.989168IPR001356Homeobox domain
PfamPF167197.1E-40107234IPR032001SAWADEE 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: 240 aa     Download sequence    Send to blast
MDFEFTLSEM LEMENMFKEL EEGPLAPQFC EKLASSFSLA PSRDGKQAIT PRQVKSWFQD  60
RLKKSQPRVA SSNMALKLFA DLSDASASFG ATESSQKLKG NASDLSELIF EALSSKDNAW  120
YDVASFLNYR VVCSGELEVR VRFAGFRNTD DEWVNVRRAV RERSIPLESS ECQRVKVGDL  180
VLCFQEREER AVYCDAHIVE INRKLHDING CRCTFVVRYD HDDFEEEVRL DRLCGRPTP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4iup_A6e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
4iup_B6e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_A7e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_B7e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
4iur_A7e-561062372133SHH1 SAWADEE
4iur_B7e-561062372133SHH1 SAWADEE
4iut_A7e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
4iut_B7e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_A7e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_B7e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_A7e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_B7e-561062372133SAWADEE HOMEODOMAIN HOMOLOG 1
Search in ModeBase
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
PlantRegMapPotri.001G189200.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankCU2314782e-55CU231478.1 Populus EST from mild drought-stressed leaves.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002299736.11e-177protein SAWADEE HOMEODOMAIN HOMOLOG 1 isoform X1
SwissprotQ9XI475e-86SHH1_ARATH; Protein SAWADEE HOMEODOMAIN HOMOLOG 1
TrEMBLB9GGM11e-176B9GGM1_POPTR; Uncharacterized protein
STRINGPOPTR_0001s19000.11e-177(Populus trichocarpa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF27041415
Representative plantOGRP16411419
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18380.12e-57sequence-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]