PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cc01_g15330
Common NameGSCOC_T00016576001
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
Family B3
Protein Properties Length: 842aa    MW: 92081.3 Da    PI: 6.7962
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cc01_g15330genomeCGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B360.62.7e-19314413198
                  EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 
                  f+kvl+ sd+++ grlvlpk +ae++   +++ e+  ++++d +g++W++++++  +++s++yvl+ G     +  +L++gD+v+F++++  +++lv+
  Cc01_g15330 314 FEKVLSASDAGRIGRLVLPKACAEAYfpPINQSEGLPIRIQDVKGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQNMQLQAGDTVTFSRID-PGGQLVM 409
                  99**************************666667778***************9989999999***9.********************887.6666666 PP

                  EEE- CS
           B3  95 kvfr 98 
                  ++++
  Cc01_g15330 410 GFRK 413
                  6655 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.1E-29310417IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.4E-21312416IPR015300DNA-binding pseudobarrel domain
CDDcd100174.76E-24312413No hitNo description
SMARTSM010192.0E-22314414IPR003340B3 DNA binding domain
PfamPF023621.2E-16314413IPR003340B3 DNA binding domain
PROSITE profilePS5086311.335314415IPR003340B3 DNA binding domain
PROSITE profilePS5105013.518544593IPR011124Zinc finger, CW-type
PfamPF074969.3E-10549590IPR011124Zinc 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: 842 aa     Download sequence    Send to blast
MGSKICMNEV CRLTTSPEWK QGWGLKSGGF ATLCSSCGTA YENLVFCEKF HLDEDGWREC  60
KICRKRIHCG CVASKMLHEF LDFGGVGCIT CVKQMDTPSL RTVKILGDEI PNGTIGHRSF  120
DSLLQLCNNV DVNGSKKMFK PHKVGTNASL GQKKGEGTAL PFEQVNTSSP NFTPQSVGSS  180
MFVKPEISRQ NQGFKDMAES LAQPSVNFSL SNALSASGSA LPISEGIVEG SEQNRVSTAQ  240
QGQRARQILP KPPKPGSSVG SENTKGMGSQ TRIARPPAEG RGRSQLLPRY WPRITDQELQ  300
QISGDLKSTV VPLFEKVLSA SDAGRIGRLV LPKACAEAYF PPINQSEGLP IRIQDVKGKE  360
WTFQFRFWPN NNSRMYVLEG VTPCIQNMQL QAGDTVTFSR IDPGGQLVMG FRKSTTNVET  420
QDPQPSGLPN GGSPGETSYL GASDNMLAIS ENGNNGGQIH EDSSQRNILI PEKKKARNIG  480
LKNKRLLMHS DDAMELRVTW EEAQELLRPP TNSPTIIKIE DCEFEEYDEP PIFGKRTIFT  540
VQPSGQQEQW AQCDNCSKWR RLPMHVLVPA RWTCPDNAWV LNSTCSAPDD INPRELEALN  600
IASKDFKRRR IVETKVAEDY EPSGLDALAT AAVLGDNMGD LTEMSVGATT KHPRHRPGCS  660
CIVCIQPPSG KGKHPPSCKC NVCLTVKRRF KTLMMRKKKR QSDREAELLQ GKDQETPPLD  720
MSEMEGAAEQ ALLLTNHSDA ERSQNGSLME AGESNKGQLD LNCHPSREED MLAEAAAGIN  780
LATLIDAASI PLDVYMRQDG VASLSHHLLP SHAPGDGEGS LPEEGCSASA NMGPEKKGKE  840
E*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A3e-682924212131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1606610KRRRI
2686697KRRFKTLMMRKK
3686699KRRFKTLMMRKKKR
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_027112477.10.0B3 domain-containing transcription repressor VAL1-like isoform X2
RefseqXP_027112486.10.0B3 domain-containing transcription repressor VAL1-like isoform X3
SwissprotQ6Z3U30.0Y7797_ORYSJ; B3 domain-containing protein Os07g0679700
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A068U8U90.0A0A068U8U9_COFCA; Uncharacterized protein
STRINGXP_009772834.10.0(Nicotiana sylvestris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA14912365
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. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  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]