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 Thecc1EG006971t4
Common NameTCM_006971
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: 248aa    MW: 28679.7 Da    PI: 9.8344
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG006971t4genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B363.82.6e-20145235498
                       E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEE CS
                B3   4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvk 95 
                       vl ps+  + ++++lp  fae+h +g++     ++l+ ++g++W v++ yr+++    +++GW eF  +n+L egD++vF+l +++ef l+v+
  Thecc1EG006971t4 145 VLRPSYLYRGCIMYLPSCFAEKHlSGVSG---FIKLQLPDGKQWPVRCLYRGGR--AKFSQGWYEFTLENNLGEGDVCVFELLRSREFVLKVT 232
                       7889*******************866743...5***************666665..5699**********************999******** PP

                       EE- CS
                B3  96 vfr 98 
                       vfr
  Thecc1EG006971t4 233 VFR 235
                       *98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS508639.206146IPR003340B3 DNA binding domain
SuperFamilySSF1019365.3E-7239IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.9E-7239IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.8E-25134235IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.69E-26135235IPR015300DNA-binding pseudobarrel domain
CDDcd100179.29E-24140235No hitNo description
SMARTSM010195.6E-23142237IPR003340B3 DNA binding domain
PROSITE profilePS5086313.465142237IPR003340B3 DNA binding domain
PfamPF023623.0E-18145235IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009909Biological Processregulation of flower development
GO:0010048Biological Processvernalization response
GO:0005654Cellular Componentnucleoplasm
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 248 aa     Download sequence    Send to blast
KKADNKVWFQ EGWQEFVERY YIRVGYFLIF RYEGNSAFSN LFGGTKLNNC INWTGEVNLH  60
TSKGVNNQPI RGAELPKPKK PGRKKRKFDP NEQDSSVGHE DEVEMRFRFY ESASARKRTV  120
TAEERERAIN AAKAFEPTNP FCRVVLRPSY LYRGCIMYLP SCFAEKHLSG VSGFIKLQLP  180
DGKQWPVRCL YRGGRAKFSQ GWYEFTLENN LGEGDVCVFE LLRSREFVLK VTVFRVLEST  240
GLMNRPQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-7810823815144B3 domain-containing transcription factor VRN1
4i1k_B1e-7810823815144B3 domain-containing transcription factor VRN1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
17786PKKPGRKKRK
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}.
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_017971809.10.0PREDICTED: B3 domain-containing transcription factor VRN1 isoform X4
SwissprotQ8L3W11e-106VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLA0A061E7B20.0A0A061E7B2_THECC; DNA binding protein, putative isoform 4 (Fragment)
STRINGEOX981411e-161(Theobroma cacao)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18990.12e-84B3 family protein
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]