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 Thecc1EG028873t4
Common NameTCM_028873
Organism
Theobroma cacao
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma
Family HB-other
Protein Properties Length: 261aa    MW: 30303.7 Da    PI: 7.2729
Description HB-other family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG028873t4genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox19.12.3e-0647105753
                       --HHHHHHHHHHHHH..SSS--HHHHHHHHHHC..........TS-HHHHHHHHHHHHH CS
          Homeobox   7 ftkeqleeLeelFek..nrypsaeereeLAkkl..........gLterqVkvWFqNrRa 53 
                       ft  ++ e+e+ +++  ++++++e  +eLA++            +t +qV++WFq + +
  Thecc1EG028873t4  47 FTLAEILEMENIYKEigEKTLNKEFCQELATNFscssnrmgksAVTWQQVQIWFQEKQM 105
                       88899*********888**************************************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466892.77E-547112IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.603.0E-447113IPR009057Homeodomain-like
PfamPF167194.5E-21148226IPR032001SAWADEE 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: 261 aa     Download sequence    Send to blast
MTLFTLLKPP KTKSIVTFKG NSACIGKDFR FWSVMDDKDS WDSVSEFTLA EILEMENIYK  60
EIGEKTLNKE FCQELATNFS CSSNRMGKSA VTWQQVQIWF QEKQMETQSK QRPSPMALEL  120
FVDLSSANSS KPPGSLRRHK GKVEDLKELS FEARSSKDYA WYDVDSFLTY RVLSTGELEV  180
RVRFSGFAKT EDEWVNVEKA VRERSIPLEP SECNIVKIGD LVLCYQSCLW FRYLNRTTVK  240
SWCFAFWIYI HELPIKITQH *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4iup_A9e-37148226381SAWADEE HOMEODOMAIN HOMOLOG 1
4iup_B9e-37148226381SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_A1e-36148226381SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_B1e-36148226381SAWADEE HOMEODOMAIN HOMOLOG 1
4iur_A1e-36148226381SHH1 SAWADEE
4iur_B1e-36148226381SHH1 SAWADEE
4iut_A1e-36148226381SAWADEE HOMEODOMAIN HOMOLOG 1
4iut_B1e-36148226381SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_A1e-36148226381SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_B1e-36148226381SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_A1e-36148226381SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_B1e-36148226381SAWADEE 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}.
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_021294598.11e-153LOW QUALITY PROTEIN: protein SAWADEE HOMEODOMAIN HOMOLOG 1-like
SwissprotQ9XI473e-74SHH1_ARATH; Protein SAWADEE HOMEODOMAIN HOMOLOG 1
TrEMBLA0A061GAK20.0A0A061GAK2_THECC; F9L1.16, putative isoform 2
STRINGEOY269091e-164(Theobroma cacao)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18380.13e-35sequence-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. Motamayor JC, et al.
    The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
    Genome Biol., 2013. 14(6): p. r53
    [PMID:23731509]
  4. 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]
  5. 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]