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 Thecc1EG042290t1
Common NameTCM_042290
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: 906aa    MW: 99424.5 Da    PI: 6.8201
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG042290t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B360.13.7e-19333432198
                       EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                       f+kvl+ sd+++ grlvlpk +ae++   +++ e+  l+++d +g++W++++++  +++s++yvl+ G     ++ +L++gD+v+F++++  +
  Thecc1EG042290t1 333 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGLPLRIQDVKGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLRAGDTVTFSRID-PG 423
                       99**************************555556677***************9989999999***9.********************887.78 PP

                       E..EEEEE- CS
                B3  90 felvvkvfr 98 
                       ++lv+++++
  Thecc1EG042290t1 424 GKLVMGFRK 432
                       878888776 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.16E-20330433IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.0E-30330435IPR015300DNA-binding pseudobarrel domain
CDDcd100179.46E-24331432No hitNo description
PfamPF023622.6E-16333432IPR003340B3 DNA binding domain
PROSITE profilePS5086311.223333434IPR003340B3 DNA binding domain
SMARTSM010199.8E-23333433IPR003340B3 DNA binding domain
PROSITE profilePS5105014.17597647IPR011124Zinc finger, CW-type
PfamPF074968.6E-11602644IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010030Biological Processpositive regulation of seed germination
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:2000034Biological Processregulation of seed maturation
GO:0005634Cellular Componentnucleus
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 906 aa     Download sequence    Send to blast
MGSKICMNSS CGTASTHEWK KGWPLRSGGF AHLCYRCGSA YEDSVYCDTF HLEESGWREC  60
RLCGKRLHCG CIASKYLLEL LDYGGVGCTS CANSSRLHSV RRIQTHGDEI PNGFSAMPMN  120
NAGSSSVESK AVGDHVDERT LAQLCKIMEA NECNLLPQSQ RGDPNASLGQ HRGEEAMCSV  180
GEVGAGFSNS MQPYVRPPNF AQTDNARPAL DIRDIHDSLS QPSLSMTLGG PSGNPNFVLP  240
FSSGLAEGKE QSKMSSSFQQ GQRSRPILPK PSKNGLATSS EVNKSMVPQA RIARPPVEGR  300
GKNHLLPRYW PRITDQELQQ LSGDLKSTIV PLFEKVLSAS DAGRIGRLVL PKACAEAYFP  360
PISQSEGLPL RIQDVKGKEW TFQFRFWPNN NSRMYVLEGV TPCIQSMQLR AGDTVTFSRI  420
DPGGKLVMGF RKATNSDTQE GQTSSLPNGA HSGETSNSGG IENLSTVSAY SGLFQTPKAG  480
KDPLVNSLSE HLSLADGTIS WGRGQNHGDG ANEDPVQQPA VNAEKKRTRN IGSKSKRLLM  540
HSEDALELRL TWEEAQDLLR PPPSVKPSIV TIEDHEFEEY DEPPVFGKRT IFAAQPSGGQ  600
EQWAQCDDCS KWRRLPVDVL LPPKWTCSDN VWDSSRCSCS ASEEISPKEL ENLLRVGRDL  660
KKRKILESPK LATEREPSGL DALASAAVLG DKMGDVGESS IGATTKHPRH RPGCTCIVCI  720
QPPSGKGKHK PTCTCNVCMT VKRRFKTLML RKKKRQSERE AEISQKDNNG HKDESELNDT  780
RLDHSENEGS HSRIQAEVAE TSTGQIDLNC HPNREDLQLE EQGLNMMSLV QAAGMPMENY  840
IKQNGLPSLI SEQQGSLGSH ALSQANKENE RHLSDEEFLA SVGWEHDNRS DEGHKEPSLE  900
RNGLQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A3e-713114412132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1741752KRRFKTLMLRKK
2741754KRRFKTLMLRKKKR
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL2/HSL1. {ECO:0000269|PubMed:15894743, ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
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_007017086.20.0PREDICTED: B3 domain-containing transcription repressor VAL1 isoform X1
RefseqXP_017983611.10.0PREDICTED: B3 domain-containing transcription repressor VAL1 isoform X1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A061GYW30.0A0A061GYW3_THECC; High-level expression of sugar-inducible gene 2, putative isoform 1
STRINGEOY347050.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69232440
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G30470.10.0high-level expression of sugar-inducible gene 2
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. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  3. Schneider A, et al.
    Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos.
    Plant J., 2016. 85(2): p. 305-19
    [PMID:26678037]
  4. Chhun T, et al.
    HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth.
    Plant Cell Physiol., 2016. 57(8): p. 1689-706
    [PMID:27335347]
  5. Qüesta JI,Song J,Geraldo N,An H,Dean C
    Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization.
    Science, 2016. 353(6298): p. 485-8
    [PMID:27471304]
  6. Yuan W, et al.
    A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis.
    Nat. Genet., 2016. 48(12): p. 1527-1534
    [PMID:27819666]
  7. Merini W, et al.
    The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development.
    Plant Physiol., 2017. 173(1): p. 627-641
    [PMID:27837089]
  8. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]
  9. Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD
    HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis.
    Plant Cell, 2018. 30(3): p. 600-619
    [PMID:29475938]
  10. Sasnauskas G,Kauneckaite K,Siksnys V
    Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
    Nucleic Acids Res., 2018. 46(8): p. 4316-4324
    [PMID:29660015]
  11. Wu B, et al.
    Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.
    Biochem. Biophys. Res. Commun., 2018. 501(2): p. 415-422
    [PMID:29733847]