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 Thecc1EG006969t1
Common NameTCM_006969
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 B3
Protein Properties Length: 150aa    MW: 17232.7 Da    PI: 6.7788
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG006969t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B360.13.9e-19601381698
                       EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS
                B3  16 lvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98 
                         +p+ fa++h +g+  +  t+tl+ ++g++W v++iy   +g+  + kGW eFv +n+L+egD++vF+l +++e  l+v++fr
  Thecc1EG006969t1  60 HHIPRWFARKHlNGV--N-GTITLQVSEGKKWPVRCIYV--DGHLKFCKGWAEFVLDNNLDEGDVCVFELLNTEEIVLKVTIFR 138
                       37*********8666..2.38***************664..44466889********************999999999999998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.3E-6138IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.94E-6142IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS508637.951140IPR003340B3 DNA binding domain
SuperFamilySSF1019363.14E-2443138IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086313.54945140IPR003340B3 DNA binding domain
SMARTSM010191.0E-1446140IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.103.9E-2354138IPR015300DNA-binding pseudobarrel domain
PfamPF023625.3E-1860138IPR003340B3 DNA binding domain
CDDcd100171.43E-1962138No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 150 aa     Download sequence    Send to blast
MWFDSGWNVF VEHYSICVGY SLVLRYEGNS HSNVHVHNLA ICVMYFLVFR YNGNSHCNVH  60
HIPRWFARKH LNGVNGTITL QVSEGKKWPV RCIYVDGHLK FCKGWAEFVL DNNLDEGDVC  120
VFELLNTEEI VLKVTIFRVL EDAGSVNQL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A6e-295914163144B3 domain-containing transcription factor VRN1
4i1k_B6e-295914163144B3 domain-containing transcription factor VRN1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtInvolved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner. {ECO:0000269|PubMed:12114624}.
UniProtInvolved in the regulation of vernalization (By similarity). Binds to DNA in vitro in a non-sequence-specific manner. XLG2 promotes the DNA binding activity of RTV1 specifically to promoter regions of FT and SOC1 in vivo and thus leads to the activation of floral integrator genes. {ECO:0000250, ECO:0000269|PubMed:22232549}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By cold. {ECO:0000269|PubMed:22232549}.
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_017970119.12e-55PREDICTED: B3 domain-containing transcription factor VRN1 isoform X2
SwissprotQ8L3W11e-26VRN1_ARATH; B3 domain-containing transcription factor VRN1
SwissprotQ9XIB53e-27REM19_ARATH; B3 domain-containing protein REM19
TrEMBLA0A061E7A51e-105A0A061E7A5_THECC; Uncharacterized protein
STRINGEOX981381e-106(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM112428103
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G49480.11e-29related to vernalization1 1
Publications ? help Back to Top
  1. Conte MG,Gaillard S,Droc G,Perin C
    Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants.
    BMC Genomics, 2008. 9: p. 183
    [PMID:18426584]
  2. 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]
  3. Mantegazza O, et al.
    Analysis of the arabidopsis REM gene family predicts functions during flower development.
    Ann. Bot., 2014. 114(7): p. 1507-15
    [PMID:25002525]
  4. Kumar A,Singh A,Panigrahy M,Sahoo PK,Panigrahi KCS
    Carbon nanoparticles influence photomorphogenesis and flowering time in Arabidopsis thaliana.
    Plant Cell Rep., 2018. 37(6): p. 901-912
    [PMID:29541883]