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 29976.m000497
Common NameRCOM_1163180
Organism
Ricinus communis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
Family B3
Protein Properties Length: 861aa    MW: 94578.2 Da    PI: 6.8525
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
29976.m000497genomeJCVIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B362.85.5e-20327427199
                    EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
             B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                    f+kvl+ sd+++ grlvlpk +ae++   +++ e+  l+++d +gr+W++++++  +++s++yvl+ G     +a +L++gD+++F++++  +++l
  29976.m000497 327 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGLPLRIQDVKGREWTFQFRFwpNNNSRMYVLE-GVTPCIQAMKLRAGDTITFSRID-PGGKL 420
                    99**************************555556677***************9989999999***9.********************987.99999 PP

                    EEEEE-S CS
             B3  93 vvkvfrk 99 
                    vv+++++
  29976.m000497 421 VVGFRKA 427
                    **99976 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-29323428IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019367.46E-21324427IPR015300DNA-binding pseudobarrel domain
CDDcd100172.18E-25325426No hitNo description
SMARTSM010191.8E-24327428IPR003340B3 DNA binding domain
PROSITE profilePS5086311.519327428IPR003340B3 DNA binding domain
PfamPF023624.2E-17327427IPR003340B3 DNA binding domain
PROSITE profilePS5105013.907561611IPR011124Zinc finger, CW-type
PfamPF074965.9E-10566608IPR011124Zinc 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: 861 aa     Download sequence    Send to blast
MGSKICMNAS CGVTKTHEWR RGWTLRSGGY ALLCYTCGSA YENSVYCDTF HLEEPGWREC  60
YNCNKRLHCG CIASKSLFEL LDYGGVECTG CVKSSQLHSI HGDEIPKGFG SLTLNNAGDP  120
DSIPLENRAT NGALDDGRLA QLCRLMEANE PQLLCQSEGA DTNAGLGQFR QEEVMHPIGE  180
AGTSFSIASQ SSVVPSKFPN GGRSILDMRD MHGSHAQPSL NMALGAPSGT TSFIQYACGA  240
VDGREQGKTP PFLQGQRSRP ILPKPSKTGF SGSSDTNKTA VTELRIARPP AEGRGKNQLL  300
PRYWPRITDQ ELQQLSGDLN SNIVPLFEKV LSASDAGRIG RLVLPKACAE AYFPPISQSE  360
GLPLRIQDVK GREWTFQFRF WPNNNSRMYV LEGVTPCIQA MKLRAGDTIT FSRIDPGGKL  420
VVGFRKATNN SLDTQDAQTS ALPNGAASAE TSFSGTVTVS ADGDTGGNKS ENYGGRINGD  480
AVQQSTAEKK RTRNIGPKSK RLLMHSEDAL ELRLTWEEAQ DLLRPPPSVK PSIVTIEDHE  540
FEEYDEPPVF GKRTIFADRP SGGQEQWAQC DDCSKWRKLP EDALLPPKWT CLDNVWDSSR  600
CTCSAPEEMN PKDLDTLLRG SKDFKRRRMA DRHKPSSECE PSGLDALASA AVLGDNIGDL  660
GEPSVGATTK HPRHRPGCTC IVCIQPPSGK GKHKPTCTCN VCMTVKRRFK TLMLRKKKRQ  720
SEREAEISQK DDNDRKDEFA MIGRLSHAVL NLNNSENEGN YNRKQTEIPE TSSGQIDLNS  780
HPNREDMQLD IQGLSMMNLA NAANLPFDNY VKQNGLADFL CERQASMGSC LHSQNNGESL  840
IRLSDEAFLA SVGWNHESKG D
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A4e-713054292126B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1705716KRRFKTLMLRKK
2705718KRRFKTLMLRKKKR
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMap29976.m000497
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_015577721.10.0B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLB9SD760.0B9SD76_RICCO; Transcription factor, putative
STRINGXP_002523945.10.0(Ricinus communis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF103233039
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. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]
  8. 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]
  9. 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]
  10. 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]