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

Tp57577_TGAC_v2_mRNA39997

Organism

Trifolium pratense

Taxonomic ID

57577

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium

Family

C2H2

Protein Properties

Length: 1500aa MW: 168459 Da PI: 8.2087

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp57577_TGAC_v2_mRNA39997	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.2	0.0011	1383	1408	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 ++C C++sF +k +L +H r+ + Tp57577_TGAC_v2_mRNA39997 1383 HQCDieGCTMSFESKQELLHHKRNvC 1408 789999****************9877 PP
2	zf-C2H2	13.4	0.00022	1407	1430	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 +Cp Cgk F ++ +L++H r+H Tp57577_TGAC_v2_mRNA39997 1407 VCPvkGCGKKFFSHKYLVQHRRVH 1430 69999*****************99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	2.6E-15	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	14.589	20	61	IPR003349	JmjN domain
Pfam	PF02375	2.3E-13	21	54	IPR003349	JmjN domain
PROSITE profile	PS51184	33.006	179	348	IPR003347	JmjC domain
SMART	SM00558	1.4E-48	179	348	IPR003347	JmjC domain
SuperFamily	SSF51197	5.22E-25	193	362	No hit	No description
Pfam	PF02373	1.7E-35	212	331	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	8.3E-4	1375	1405	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	10	1383	1405	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0037	1406	1430	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.612	1406	1435	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	8.7E-6	1407	1434	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1408	1430	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.32E-9	1422	1464	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.6E-8	1435	1460	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.554	1436	1465	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0016	1436	1460	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1438	1460	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	5.03E-8	1454	1488	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.0E-9	1461	1488	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	1.2	1466	1492	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.762	1466	1497	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1468	1492	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009741	Biological Process	response to brassinosteroid
GO:0009826	Biological Process	unidimensional cell growth
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0033169	Biological Process	histone H3-K9 demethylation
GO:0035067	Biological Process	negative regulation of histone acetylation
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 1500 aa Download sequence Send to blast
MALSESNADV FPWLKSMPVA PEYRPTPAEF EDPIGYIFKI EKEASKYGIC KIIPPFPPSP 60 KKTAIANLNR SLPNSTFTTR QQQIGFCPRK SRPVKRPVWQ SGDHYTFTEF EAKAKWFEKS 120 YLKKHSKKKG NGGGALEMET LFWKATVDKP FSVEYANDMP GSAFSMSSSK FRHSGESASV 180 AHSAWNMRGV SRAKGSLLRF MKEEIPGVTS PMVYLAMLFS WFAWHVEDHD LHSLNYLHMG 240 ASKTWYGVPR DAAVAFEDVV RVHGYGGEIN PLVTFSILGE KTTVMSPEVF ISAGVPCCRL 300 VQNAGEFVVT FPRAYHTGFS HGFNCGEAAN IATPEWLRVA KDAAIRRASI NYPPMVSHFQ 360 LLYDLALALC SRVPGGISAG PRSSRLKDKK KGEGDSVVKE LFVQDVLRNN DLLHVLGKES 420 SVVLLPRSSV DISICSKLRV GCRQQKVNPG FSINVCNSEG MNSSKGFVSD DLVFNRNCGI 480 VQEKNSHSVK GEFNLLSEGK GISPFDANSN TSPSSSKQLH RGKESETSQG DGLSDQRLFS 540 CVTCGLLNFS CVAIVRPSEP AARYLMSANC SFFNDWVVGS GVPSNKFTVA GEDENIPEPN 600 IHTEWTEKNA QVEALNTEGG NANTALALLA SAYGNSSDSE EDAVDNHESN TIHSTSESLP 660 SNVQVSHDNP MTRHDKDDIL SESTSYKAHG FEGNLSQPCD QSLEDQDYKT TSGVALENTR 720 QMPYSTTYSS QDANNAEKSL SVEAMVAVNH KNALLVPQCD EDSSRMHVFC LEHAVDAEQQ 780 LRPIGGAHIL LLCHPDYPKI EAEAKLVAED LGIDYMWKNI AYRHGTKEDE ERIQLAVDSE 840 EAIPGNGDWA VKLGINLFYS ANLSRSPLYS KQMPYNSVIY YAFGRSTQAS SPIEPKVYQR 900 RSDKHKKVVA GKWCGKVWMS NQVHPLLAKR DSEDVEDEKS LHGLVLPNVK IEASGNNSAE 960 DKPNPRPRRI VKQARGVEKD GAAESDLVSD DSLDDDYRMR RMSFNVKKAK FIDNDAVSDD 1020 AMDLDSDCHQ MGELRSKQVE YTERDSISED SLDVGSLQHR KTSRNKHANC IIEDAISDDQ 1080 MENGCQMQQN RIPKKRQGKS LAEKDSVISD DQLELNMQKQ WRSNSRSRKA KYLTEEDSVS 1140 DNQANVYCRK YQRRTVKVRQ ARCVVGEDLM SDDQLKDPFL NQKPSISRRK NKVIDREVKN 1200 EMSDDQLDDH FQKQQKKIPK GRRHTKQTDE EVIDDSAEDD MSLNNEMEDD SLQQYKRTHP 1260 TKQSKPKTLR QMKQSKSLQI KNQTPKPVKR GVGLRMKSKA AQQVKQPSRL RSKQSGSSRE 1320 PSLDMEEEEE GGPSTRLRKR VQKAQESEVK STEKQTKRKS AKDVTATKVS ARDPKTEDEE 1380 AEHQCDIEGC TMSFESKQEL LHHKRNVCPV KGCGKKFFSH KYLVQHRRVH EDDRPLKCPW 1440 KGCKMSFKWA WARTEHIRVH TGVRPYACAE PGCGQTFRFV SDFSRHKRKT GHLAKKIRQ*

Sequence ? help Back to Top

Protein Sequence Length: 1500 aa Download sequence Send to blast

MALSESNADV FPWLKSMPVA PEYRPTPAEF EDPIGYIFKI EKEASKYGIC KIIPPFPPSP  60
KKTAIANLNR SLPNSTFTTR QQQIGFCPRK SRPVKRPVWQ SGDHYTFTEF EAKAKWFEKS  120
YLKKHSKKKG NGGGALEMET LFWKATVDKP FSVEYANDMP GSAFSMSSSK FRHSGESASV  180
AHSAWNMRGV SRAKGSLLRF MKEEIPGVTS PMVYLAMLFS WFAWHVEDHD LHSLNYLHMG  240
ASKTWYGVPR DAAVAFEDVV RVHGYGGEIN PLVTFSILGE KTTVMSPEVF ISAGVPCCRL  300
VQNAGEFVVT FPRAYHTGFS HGFNCGEAAN IATPEWLRVA KDAAIRRASI NYPPMVSHFQ  360
LLYDLALALC SRVPGGISAG PRSSRLKDKK KGEGDSVVKE LFVQDVLRNN DLLHVLGKES  420
SVVLLPRSSV DISICSKLRV GCRQQKVNPG FSINVCNSEG MNSSKGFVSD DLVFNRNCGI  480
VQEKNSHSVK GEFNLLSEGK GISPFDANSN TSPSSSKQLH RGKESETSQG DGLSDQRLFS  540
CVTCGLLNFS CVAIVRPSEP AARYLMSANC SFFNDWVVGS GVPSNKFTVA GEDENIPEPN  600
IHTEWTEKNA QVEALNTEGG NANTALALLA SAYGNSSDSE EDAVDNHESN TIHSTSESLP  660
SNVQVSHDNP MTRHDKDDIL SESTSYKAHG FEGNLSQPCD QSLEDQDYKT TSGVALENTR  720
QMPYSTTYSS QDANNAEKSL SVEAMVAVNH KNALLVPQCD EDSSRMHVFC LEHAVDAEQQ  780
LRPIGGAHIL LLCHPDYPKI EAEAKLVAED LGIDYMWKNI AYRHGTKEDE ERIQLAVDSE  840
EAIPGNGDWA VKLGINLFYS ANLSRSPLYS KQMPYNSVIY YAFGRSTQAS SPIEPKVYQR  900
RSDKHKKVVA GKWCGKVWMS NQVHPLLAKR DSEDVEDEKS LHGLVLPNVK IEASGNNSAE  960
DKPNPRPRRI VKQARGVEKD GAAESDLVSD DSLDDDYRMR RMSFNVKKAK FIDNDAVSDD  1020
AMDLDSDCHQ MGELRSKQVE YTERDSISED SLDVGSLQHR KTSRNKHANC IIEDAISDDQ  1080
MENGCQMQQN RIPKKRQGKS LAEKDSVISD DQLELNMQKQ WRSNSRSRKA KYLTEEDSVS  1140
DNQANVYCRK YQRRTVKVRQ ARCVVGEDLM SDDQLKDPFL NQKPSISRRK NKVIDREVKN  1200
EMSDDQLDDH FQKQQKKIPK GRRHTKQTDE EVIDDSAEDD MSLNNEMEDD SLQQYKRTHP  1260
TKQSKPKTLR QMKQSKSLQI KNQTPKPVKR GVGLRMKSKA AQQVKQPSRL RSKQSGSSRE  1320
PSLDMEEEEE GGPSTRLRKR VQKAQESEVK STEKQTKRKS AKDVTATKVS ARDPKTEDEE  1380
AEHQCDIEGC TMSFESKQEL LHHKRNVCPV KGCGKKFFSH KYLVQHRRVH EDDRPLKCPW  1440
KGCKMSFKWA WARTEHIRVH TGVRPYACAE PGCGQTFRFV SDFSRHKRKT GHLAKKIRQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	5e-80	6	369	1	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	5e-80	6	369	1	353	Arabidopsis JMJ13
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). {ECO:0000269\|PubMed:15377760, ECO:0000269\|PubMed:18467490, ECO:0000269\|PubMed:20711170, ECO:0000269\|PubMed:21642989, ECO:0000269\|PubMed:25105952, ECO:0000269\|PubMed:27111034, ECO:0000269\|PubMed:27111035}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00608	ChIP-seq	Transfer from AT3G48430	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp57577_TGAC_v2_mRNA39997

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC235753	0.0	AC235753.2 Medicago truncatula clone mth2-128c9, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013460954.1	0.0	lysine-specific demethylase REF6 isoform X2
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2Z6NB75	0.0	A0A2Z6NB75_TRISU; Uncharacterized protein
STRING	XP_004501832.1	0.0	(Cicer arietinum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF5648	32	50

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G48430.1	0.0	relative of early flowering 6

Link Out ? help Back to Top
Phytozome	Tp57577_TGAC_v2_mRNA39997

Publications ? help Back to Top
Li C, et al. Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nat. Genet., 2016. 48(6): p. 687-93 [PMID:27111034] Cui X, et al. REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis. Nat. Genet., 2016. 48(6): p. 694-9 [PMID:27111035] Hyun Y, et al. Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem. Dev. Cell, 2016. 37(3): p. 254-66 [PMID:27134142] Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE Research progress on the autonomous flowering time pathway in Arabidopsis. Physiol Mol Biol Plants, 2017. 23(3): p. 477-485 [PMID:28878488] Li C, et al. Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis. Plant Biotechnol. J., 2018. 16(8): p. 1446-1451 [PMID:29331085] Wang X, et al. The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis. PLoS Genet., 2019. 15(4): p. e1008068 [PMID:30969965] Qiu Q, et al. DNA methylation repels targeting of Arabidopsis REF6. Nat Commun, 2019. 10(1): p. 2063 [PMID:31048693]