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 Sme2.5_03023.1_g00006.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
Family GRAS
Protein Properties Length: 1502aa    MW: 168051 Da    PI: 7.472
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sme2.5_03023.1_g00006.1genomeEGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS280.55.1e-862215722356
                     GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetsekn...sseelaalklf 84 
                               + Ll++Ae vs+++  +a+++L++ +  as++g+p+qR+++yf++AL +r+ r++ +l+ ++ +++++ +n    s+  a++ ++
  Sme2.5_03023.1_g00006.1 221 AQILLAAAEKVSDQQYDRARKFLSQCQLAASNTGNPVQRAVFYFAQALGERIDRETGKLMPKICAETDELNNfciASRFHASYVAL 306
                              689***************************************************8888888887777777778855555555566* PP

                     GRAS  85 sevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRp.egppslRiTgvgspesgskeeleetgerLakfA 169
                              ++  P+ ++ h+t  qaIle+ve++++vHiiD+ i  G+QW++L+qa a+R+ ++  +++iT+++s   ++ke++ +tg+ L++fA
  Sme2.5_03023.1_g00006.1 307 HQEVPFTQVVHFTGIQAILESVETKTKVHIIDLLIRTGVQWASLIQAAAERKhNPIEHMKITAIES---VNKESVLATGKSLESFA 389
                              ***************************************************956666*********...7899************* PP

                     GRAS 170 eelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFle 255
                              +++++pf+fn++   + ++l+ +++++kp+E ++++  + l ++ +e+ +le      +++vk+l+P ++vv+e ea++ns+ F++
  Sme2.5_03023.1_g00006.1 390 KSVNIPFSFNIVFLPDRSQLSEDHFDIKPDEGVVIHAEFCLRSMINEPNCLET----AMRVVKRLQPSLMVVSEVEANLNSPLFVN 471
                              ***********9999******************************99999999....***************************** PP

                     GRAS 256 rflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklll 341
                              rf+++l yysalfd+le  + r++++r+++E+   g  i+n+v  eg+er++r  +l  Wr+ l+++G+++v+ls++   qa+l++
  Sme2.5_03023.1_g00006.1 472 RFIDSLFYYSALFDCLEDIMKRDDQHRMTLEES-YGGGIRNIVRDEGKERVARSVNLDVWRSFLRRFGMEEVKLSDTCLYQANLII 556
                              *********************************.899************************************************* PP

                     GRAS 342 rkvk.sdgyrveeesg 356
                              ++++  +  +v++++g
  Sme2.5_03023.1_g00006.1 557 QQFAcRNSCSVKKSDG 572
                              ****888899998877 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098544.269194569IPR005202Transcription factor GRAS
PfamPF035141.8E-83221572IPR005202Transcription factor GRAS
PROSITE profilePS51576200.5834991502IPR025778Histone-lysine N-methyltransferase, EZ
SuperFamilySSF821992.22E-3412681297No hitNo description
Gene3DG3DSA:2.170.270.102.2E-3712731297No hitNo description
PROSITE profilePS5028011.82413501470IPR001214SET domain
SMARTSM003171.3E-2613501476IPR001214SET domain
SuperFamilySSF821992.22E-3413551473No hitNo description
Gene3DG3DSA:2.170.270.102.2E-3713551476No hitNo description
PfamPF008563.6E-913901469IPR001214SET domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0031519Cellular ComponentPcG protein complex
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 1502 aa     Download sequence    Send to blast
MLGVIPKPSW YYMGNVSECE RLTGRMAEAG DTKRDKAENY SIEHLMDNMA GAEQVSSRPI  60
DSQLHRVDTA KSCNHLSVME NSTYIKNLCT NYGFYQEDAV NQQFQEINQQ EEEMKVHAAH  120
STGQLSRAKI NKVPFLSLAP FELLRNNLRS CKNTGGEKVG DVNGGANVHQ KLSALVIMRL  180
AGERFIQFSS NKFININNLL HPYGSALSNL SPEDNQDVEL AQILLAAAEK VSDQQYDRAR  240
KFLSQCQLAA SNTGNPVQRA VFYFAQALGE RIDRETGKLM PKICAETDEL NNFCIASRFH  300
ASYVALHQEV PFTQVVHFTG IQAILESVET KTKVHIIDLL IRTGVQWASL IQAAAERKHN  360
PIEHMKITAI ESVNKESVLA TGKSLESFAK SVNIPFSFNI VFLPDRSQLS EDHFDIKPDE  420
GVVIHAEFCL RSMINEPNCL ETAMRVVKRL QPSLMVVSEV EANLNSPLFV NRFIDSLFYY  480
SALFDCLEDI MKRDDQHRMT LEESYGGGIR NIVRDEGKER VARSVNLDVW RSFLRRFGME  540
EVKLSDTCLY QANLIIQQFA CRNSCSVKKS DGENEGNSLA SLKYRINQLK RQIQADRVLS  600
VRDKLEENKR KLENHVSELE NHVSELLLLA TSRSDTMKNS GTGKMLSSRI SSPPCKVGGF  660
LQSSGDRDYA NGEEVVSSTT ARLPFIENIP SYTTWIFLDR NQRMTDDQSV VGRRRIYYDQ  720
HGSEALICSD SEEDIAEPEG EKRHFSEGED KILRMASQEF GLKEEVLDIL TQYVGGTTSE  780
ILEHCTVLSE KHQDTDGKSL KDSGESGFGG SMFLDKSLTA ALDSFDNLFC RRCLVFDCHL  840
HGCSQILIDA IEKQSYSSDS EDDRKPCSDQ CYLKVKGAAN QTKYSTVDPV EGPEKHTSEV  900
GSTMVIKRTG DPDEHTDSKM KQGVPDSINT SLEKSDMVLD DQQDPNSCKR RKLSLPTAVS  960
VAEEDGSESN GMSIIANDYV SHSQAPDRSG YNHGTSLHKT GDDVRNEAAD TKKEIVKHAS  1020
CSKNLPEWKP LEKELYSKGV EIFGRNRAES ERLGGKIKGV FLSLHNSLGT FGCTQVRLKG  1080
SPVDYAPAMC RAGKGTALCL IYVALPCICA RGQDEGRKTE IVGACKEVVC GCVRKEVQRL  1140
AITEVRRGRD RSKKNQKRSY SNLLPPRLVV LLKLMNCLIA RNLLPGLKTC MEVSSYMDNR  1200
AVAQRGGSTS LFSEDNGKAD MDSMEPDIPT KSRFLRRRGR TRKLKYSSKS SGHPSIWRRM  1260
ADGKNQSCIQ YNPCGCQPMC GKHCPCLQNA AQKAVRIVSV DATVQRVNAE VDSVRVLRLD  1320
VNVILMSAAI VGLAVVMAHW VSLLGKEKVN VILLSRSDVA GWGAFLKVSR IPNPVYKNDY  1380
LGEYTGELIS HREADKRGKI YDRANSSFLF DLNDQYVLDA YRKGDKLKFA NHSSNPNCYA  1440
KVMLVAGDHR VGIFAKERIE ASEELFYDYR YGPDQAPIWA RKPEGTKNDD SPAPQGRPKK  1500
HQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4mi5_A1e-461352147197211Histone-lysine N-methyltransferase EZH2
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
111471155GRDRSKKNQ
212341240LRRRGRT
Functional Description ? help Back to Top
Source Description
UniProtPolycomb group (PcG) protein. Catalytic subunit of some PcG multiprotein complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target genes. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. PcG proteins are not required to initiate repression, but to maintain it during later stages of development (By similarity). {ECO:0000250}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU0576880.0EU057688.1 Solanum lycopersicum EZ1 (EZ1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
SwissprotQ9ZSM81e-113EZA1_ARATH; Histone-lysine N-methyltransferase EZA1
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA139101114
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G03450.13e-48RGA-like 2
Publications ? help Back to Top
  1. Luo M,Bilodeau P,Dennis ES,Peacock WJ,Chaudhury A
    Expression and parent-of-origin effects for FIS2, MEA, and FIE in the endosperm and embryo of developing Arabidopsis seeds.
    Proc. Natl. Acad. Sci. U.S.A., 2000. 97(19): p. 10637-42
    [PMID:10962025]
  2. Springer NM, et al.
    Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots.
    Plant Physiol., 2003. 132(2): p. 907-25
    [PMID:12805620]
  3. Chanvivattana Y, et al.
    Interaction of Polycomb-group proteins controlling flowering in Arabidopsis.
    Development, 2004. 131(21): p. 5263-76
    [PMID:15456723]
  4. Wang D,Tyson MD,Jackson SS,Yadegari R
    Partially redundant functions of two SET-domain polycomb-group proteins in controlling initiation of seed development in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2006. 103(35): p. 13244-9
    [PMID:16924116]
  5. Spillane C, et al.
    Positive darwinian selection at the imprinted MEDEA locus in plants.
    Nature, 2007. 448(7151): p. 349-52
    [PMID:17637669]
  6. Johnston AJ,Matveeva E,Kirioukhova O,Grossniklaus U,Gruissem W
    A dynamic reciprocal RBR-PRC2 regulatory circuit controls Arabidopsis gametophyte development.
    Curr. Biol., 2008. 18(21): p. 1680-6
    [PMID:18976913]
  7. Aichinger E, et al.
    CHD3 proteins and polycomb group proteins antagonistically determine cell identity in Arabidopsis.
    PLoS Genet., 2009. 5(8): p. e1000605
    [PMID:19680533]
  8. Almada R, et al.
    Epigenetic repressor-like genes are differentially regulated during grapevine (Vitis vinifera L.) development.
    Plant Cell Rep., 2011. 30(10): p. 1959-68
    [PMID:21681473]
  9. He C,Chen X,Huang H,Xu L
    Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues.
    PLoS Genet., 2012. 8(8): p. e1002911
    [PMID:22927830]
  10. Lindner M, et al.
    TAF13 interacts with PRC2 members and is essential for Arabidopsis seed development.
    Dev. Biol., 2013. 379(1): p. 28-37
    [PMID:23506837]
  11. Footitt S,Müller K,Kermode AR,Finch-Savage WE
    Seed dormancy cycling in Arabidopsis: chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals.
    Plant J., 2015. 81(3): p. 413-25
    [PMID:25439058]
  12. Liang SC, et al.
    Kicking against the PRCs - A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2.
    PLoS Genet., 2015. 11(12): p. e1005660
    [PMID:26642436]
  13. Xu M,Hu T,Smith MR,Poethig RS
    Epigenetic Regulation of Vegetative Phase Change in Arabidopsis.
    Plant Cell, 2016. 28(1): p. 28-41
    [PMID:26704382]
  14. Wang H, et al.
    Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements.
    PLoS Genet., 2016. 12(1): p. e1005771
    [PMID:26760036]
  15. de Lucas M, et al.
    Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation.
    Plant Cell, 2016. 28(10): p. 2616-2631
    [PMID:27650334]
  16. Xu Y, et al.
    Regulation of Vegetative Phase Change by SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA.
    Plant Physiol., 2016. 172(4): p. 2416-2428
    [PMID:27803189]
  17. Oliva M, et al.
    FIE, a nuclear PRC2 protein, forms cytoplasmic complexes in Arabidopsis thaliana.
    J. Exp. Bot., 2016. 67(21): p. 6111-6123
    [PMID:27811080]
  18. Wang H, et al.
    Correction: Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements.
    PLoS Genet., 2017. 13(1): p. e1006574
    [PMID:28122004]
  19. Zhou Y,Romero-Campero FJ,Gómez-Zambrano Á,Turck F,Calonje M
    H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity.
    Genome Biol., 2017. 18(1): p. 69
    [PMID:28403905]
  20. Zhou Y, et al.
    Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3 levels in dividing cells in Arabidopsis thaliana.
    Proc. Natl. Acad. Sci. U.S.A., 2017. 114(18): p. 4833-4838
    [PMID:28428341]
  21. Qiu Y,Liu SL,Adams KL
    Concerted Divergence after Gene Duplication in Polycomb Repressive Complexes.
    Plant Physiol., 2017. 174(2): p. 1192-1204
    [PMID:28455403]
  22. Kim DH,Xi Y,Sung S
    Modular function of long noncoding RNA, COLDAIR, in the vernalization response.
    PLoS Genet., 2017. 13(7): p. e1006939
    [PMID:28759577]