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 Thecc1EG028873t3
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: 247aa    MW: 28696.4 Da    PI: 5.1036
Description HB-other family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG028873t3genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox19.22.1e-061371753
                      --HHHHHHHHHHHHH..SSS--HHHHHHHHHHC..........TS-HHHHHHHHHHHHH CS
          Homeobox  7 ftkeqleeLeelFek..nrypsaeereeLAkkl..........gLterqVkvWFqNrRa 53
                      ft  ++ e+e+ +++  ++++++e  +eLA++            +t +qV++WFq + +
  Thecc1EG028873t3 13 FTLAEILEMENIYKEigEKTLNKEFCQELATNFscssnrmgksAVTWQQVQIWFQEKQM 71
                      88899*********888**************************************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466892.54E-51378IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.602.7E-41379IPR009057Homeodomain-like
PfamPF167191.4E-38114241IPR032001SAWADEE 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: 247 aa     Download sequence    Send to blast
MDDKDSWDSV SEFTLAEILE MENIYKEIGE KTLNKEFCQE LATNFSCSSN RMGKSAVTWQ  60
QVQIWFQEKQ METQSKQRPS PMALELFVDL SSANSSKPPG SLRRHKGKVE DLKELSFEAR  120
SSKDYAWYDV DSFLTYRVLS TGELEVRVRF SGFAKTEDEW VNVEKAVRER SIPLEPSECN  180
IVKIGDLVLC YQDREHYQVY YDAHVVDIQR RVHDVRGCSC IFVVCYDHDY SKEKVPLQRL  240
CCRPPQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4iup_A2e-551142463135SAWADEE HOMEODOMAIN HOMOLOG 1
4iup_B2e-551142463135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_A2e-551142463135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_B2e-551142463135SAWADEE HOMEODOMAIN HOMOLOG 1
4iur_A2e-551142463135SHH1 SAWADEE
4iur_B2e-551142463135SHH1 SAWADEE
4iut_A2e-551142463135SAWADEE HOMEODOMAIN HOMOLOG 1
4iut_B2e-551142463135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_A2e-551142463135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_B2e-551142463135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_A2e-551142463135SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_B2e-551142463135SAWADEE 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_007024289.20.0PREDICTED: protein SAWADEE HOMEODOMAIN HOMOLOG 1 isoform X1
SwissprotQ9XI477e-94SHH1_ARATH; Protein SAWADEE HOMEODOMAIN HOMOLOG 1
TrEMBLA0A061GBD90.0A0A061GBD9_THECC; Sequence-specific DNA binding, putative isoform 3
STRINGEOY269091e-175(Theobroma cacao)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18380.13e-59sequence-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]