PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

MDP0000232659

Organism

Malus domestica

Taxonomic ID

3750

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Malus

Family

GRAS

Protein Properties

Length: 1007aa MW: 113606 Da PI: 7.3264

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MDP0000232659	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	134.2	1.4e-41	2	183	187	374
GRAS 187 edleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseer 282 ed++ + ++vk +Ea++V l l ++ ++s +le+ ++++v++l P v+vv+e ea+hns+sF++rf++al yysa+fd+le+ + +++++r MDP0000232659 2 EDVKDQLFDVKDDEAVVVYAPLILRTMISRSSCLEN----LMRVVRNLTPCVIVVIEVEANHNSPSFVNRFIDALFYYSAFFDCLETCV-KQEKNR 92 67778889******************99999999....*******************************************97.667888 PP GRAS 283 ikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 + +E+ l++ i+n+v +eg+er+ r t+e Wr+ + ++ + +++ls+ a qa l+ +k++s +++ + ++l+ gWk+ p+ s+SaW+ MDP0000232659 93 VLMEEL-LHEGIRNIVVAEGSERVVRSVTMEVWRAFFARFRMVEINLSNAALYQAXLVAKKFGSPPCTLDRNGKCLIVGWKGTPIHSLSAWK 183 888887.****************************************************999***********************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	18.711	1	163	IPR005202	Transcription factor GRAS
Pfam	PF03514	5.0E-39	2	183	IPR005202	Transcription factor GRAS
PROSITE profile	PS51576	253.045	93	1006	IPR025778	Histone-lysine N-methyltransferase, EZ
PROSITE profile	PS51633	16.829	752	843	IPR026489	CXC domain
Gene3D	G3DSA:2.170.270.10	4.3E-50	761	979	No hit	No description
SuperFamily	SSF82199	1.74E-47	762	974	No hit	No description
SMART	SM01114	1.8E-7	792	829	IPR033467	Tesmin/TSO1-like CXC domain
PROSITE profile	PS50280	13.167	857	973	IPR001214	SET domain
SMART	SM00317	3.9E-31	857	979	IPR001214	SET domain
Pfam	PF00856	2.5E-10	868	972	IPR001214	SET domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0031519	Cellular Component	PcG protein complex
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 1007 aa Download sequence Send to blast
MEDVKDQLFD VKDDEAVVVY APLILRTMIS RSSCLENLMR VVRNLTPCVI VVIEVEANHN 60 SPSFVNRFID ALFYYSAFFD CLETCVKQEK NRVLMEELLH EGIRNIVVAE GSERVVRSVT 120 MEVWRAFFAR FRMVEINLSN AALYQAXLVA KKFGSPPCTL DRNGKCLIVG WKGTPIHSLS 180 AWKYTAEMSR TGTMLSQASN SATELTKFHG EDPSDGIGSL EQKMHQLKLQ IQAERVISVK 240 EKVKKNREKV EGYVSKXISE TSRANLNASS SEQNGSFKLF SSRIEQPLCK ISGFAQGYGE 300 KNWIENQEVL FSSSTKLPLV DKIPPYTTWI FLDRNQRMAE DQSVVGRRRI YYDEDGSEAL 360 VYSGSDDEAE EPEKVKHEFS AGEDRILLMA FQEHGLGEEV VEVVREFIGV PILEILVAGI 420 NDRYNTIKER NREKREPDGC ISLDKSLSAA LDSFDNLFCR RCLVFDCRLH GCSQPLIYPS 480 EKSQWSGHDE NQEPCSDQCY LRLSIVTSER ESAPGSSISA ERPSSXGYTD LTHNERSIPG 540 DAETTTSETI QCSHILKMHN ENTGKRKVMK HTDKVAKDLT IVPDDFHGSS KKQKRLDALD 600 LVTATSEPIP VRVHISRGEP RDVAEVPELR QTSNSTRGQV EGMCSXSEWK PVEKDLYMKG 660 LQIFGRNSCL IARNLLSGLR TCKEVSSYMH NSGSSXPNRS VVEPSSFMED NVKADLDQTE 720 QEMSSKPRLL RRRGKARRLK YSWKSAGHPT MWKRIADGKN DSLKLYTPCE CQSMCGKECS 780 CMSNGTCCEK YCGFRGCHCA KSQCRSRQCP CFAAGRECDP DVCRHCWISC GDGSLGEPPK 840 QGDSQCGNMR LLLRQQQRIL LGKSDVAGWG AFLKNPVNKN DYLGEYTGEI ISHQEADKRG 900 KIYDRDIALH WHYACLLQYV LDAYRKGDKL KFANHSSNPN CHAKVMLVAG DHRVGIFAKE 960 HIDAGEELFY DYCYLSEAAP VWAQKPEGSK RDDSSVSRGR AKKHQAL

Sequence ? help Back to Top

Protein Sequence Length: 1007 aa Download sequence Send to blast

MEDVKDQLFD VKDDEAVVVY APLILRTMIS RSSCLENLMR VVRNLTPCVI VVIEVEANHN  60
SPSFVNRFID ALFYYSAFFD CLETCVKQEK NRVLMEELLH EGIRNIVVAE GSERVVRSVT  120
MEVWRAFFAR FRMVEINLSN AALYQAXLVA KKFGSPPCTL DRNGKCLIVG WKGTPIHSLS  180
AWKYTAEMSR TGTMLSQASN SATELTKFHG EDPSDGIGSL EQKMHQLKLQ IQAERVISVK  240
EKVKKNREKV EGYVSKXISE TSRANLNASS SEQNGSFKLF SSRIEQPLCK ISGFAQGYGE  300
KNWIENQEVL FSSSTKLPLV DKIPPYTTWI FLDRNQRMAE DQSVVGRRRI YYDEDGSEAL  360
VYSGSDDEAE EPEKVKHEFS AGEDRILLMA FQEHGLGEEV VEVVREFIGV PILEILVAGI  420
NDRYNTIKER NREKREPDGC ISLDKSLSAA LDSFDNLFCR RCLVFDCRLH GCSQPLIYPS  480
EKSQWSGHDE NQEPCSDQCY LRLSIVTSER ESAPGSSISA ERPSSXGYTD LTHNERSIPG  540
DAETTTSETI QCSHILKMHN ENTGKRKVMK HTDKVAKDLT IVPDDFHGSS KKQKRLDALD  600
LVTATSEPIP VRVHISRGEP RDVAEVPELR QTSNSTRGQV EGMCSXSEWK PVEKDLYMKG  660
LQIFGRNSCL IARNLLSGLR TCKEVSSYMH NSGSSXPNRS VVEPSSFMED NVKADLDQTE  720
QEMSSKPRLL RRRGKARRLK YSWKSAGHPT MWKRIADGKN DSLKLYTPCE CQSMCGKECS  780
CMSNGTCCEK YCGFRGCHCA KSQCRSRQCP CFAAGRECDP DVCRHCWISC GDGSLGEPPK  840
QGDSQCGNMR LLLRQQQRIL LGKSDVAGWG AFLKNPVNKN DYLGEYTGEI ISHQEADKRG  900
KIYDRDIALH WHYACLLQYV LDAYRKGDKL KFANHSSNPN CHAKVMLVAG DHRVGIFAKE  960
HIDAGEELFY DYCYLSEAAP VWAQKPEGSK RDDSSVSRGR AKKHQAL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5hyn_A	3e-64	450	974	277	728	Histone-lysine N-methyltransferase EZH2
5hyn_F	3e-64	450	974	277	728	Histone-lysine N-methyltransferase EZH2
5hyn_K	3e-64	450	974	277	728	Histone-lysine N-methyltransferase EZH2
5hyn_Q	3e-64	450	974	277	728	Histone-lysine N-methyltransferase EZH2
6c23_C	3e-64	450	974	277	728	Histone-lysine N-methyltransferase EZH2
6c23_K	3e-64	450	974	277	728	Histone-lysine N-methyltransferase EZH2
6c24_C	3e-64	450	974	277	728	Histone-lysine N-methyltransferase EZH2
6c24_K	3e-64	450	974	277	728	Histone-lysine N-methyltransferase EZH2
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mdo.15865	1e-177	root\| stem

Functional Description ? help Back to Top
Source	Description
UniProt	Polycomb 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
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_028956279.1	0.0	histone-lysine N-methyltransferase EZA1
Swissprot	Q9ZSM8	0.0	EZA1_ARATH; Histone-lysine N-methyltransferase EZA1
TrEMBL	A0A498KAI7	0.0	A0A498KAI7_MALDO; Histone-lysine N-methyltransferase
STRING	XP_009378725.1	0.0	(Pyrus x bretschneideri)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF972	3	3

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G03450.1	2e-28	RGA-like 2

Link Out ? help Back to Top
Phytozome	MDP0000232659

Publications ? help Back to Top
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] 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] Chanvivattana Y, et al. Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development, 2004. 131(21): p. 5263-76 [PMID:15456723] 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] Spillane C, et al. Positive darwinian selection at the imprinted MEDEA locus in plants. Nature, 2007. 448(7151): p. 349-52 [PMID:17637669] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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]