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

Lj4g3v1389260.1

Organism

Lotus japonicus

Taxonomic ID

34305

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1569aa MW: 177321 Da PI: 8.4317

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj4g3v1389260.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.3	5.8e-05	1454	1479	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L++H r+ + Lj4g3v1389260.1 1454 YQCDieGCTMSFETKQELTSHKRNiC 1479 99********************9877 PP
2	zf-C2H2	12.8	0.00035	1479	1501	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Lj4g3v1389260.1 1479 CPvkGCGKKFFSHKYLVQHRRVH 1501 9999*****************99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	2.5E-17	18	59	IPR003349	JmjN domain
PROSITE profile	PS51183	14.88	19	60	IPR003349	JmjN domain
Pfam	PF02375	6.4E-14	20	53	IPR003349	JmjN domain
SMART	SM00558	1.1E-48	175	344	IPR003347	JmjC domain
PROSITE profile	PS51184	32.531	178	344	IPR003347	JmjC domain
SuperFamily	SSF51197	5.49E-25	193	350	No hit	No description
Pfam	PF02373	2.7E-36	208	327	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	7.4E-5	1446	1476	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	6.6	1454	1476	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1477	1501	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.508	1477	1506	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1479	1501	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.4E-5	1479	1505	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.71E-9	1493	1535	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.7E-8	1506	1531	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1507	1531	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1507	1536	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1509	1531	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.65E-7	1525	1559	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.9E-8	1532	1559	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	4.7	1537	1563	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	9.307	1537	1568	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1539	1563	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 1569 aa Download sequence Send to blast
MAACSSEEVF PWLKSLPVAP EYRPTAAEFH DPIGYIFKIE KEASKYGICK IIPPVSPSPK 60 KTAISNLNRC QPQFTTRQQQ IGFCPRRQQP VRRPVWHSGN QYSFREFESK AKTFEKSFLK 120 KGKKSTPLSP LEVETLYWKA TVDKPFSVEY ANDMPGSAFC PMKENVYGGG DGYVTVGETA 180 WNMRGVSRAN GSLLRFMKEE IPGVTSPMVY LAMMFSWFAW HVEDHDLHSL NYLHMGAPKT 240 WYGVPKDAAV AFEDVVRVHG YGGEINPLVT FSILGEKTTV MSPEVFIRAG VPCCRLVQNA 300 GEFVVTFPRA YHTGFSHGFN CGEAANIATP EWLTFAKDAA IRRASINYPP MVSHFQLLYD 360 LGLALCSRIP GRIAEPRSSR LKDKRKGAGE TVVKELFVQD VLQNNDLLHI LGSGSSIVLL 420 PHSSSDFSVC SKLRVGSQQL KVKSEPFLNV CNSEGMGSSK GFISGDLVSN KNHGVKNVKG 480 FYSVKEKFAS LCERNRGEVC PSSSKTLQRD SEKETSQGDG LSDQRLFSCV TCGILSFSCV 540 AIVQPKEPAA RYLMSADCSF FNDWIEGSGV TSNKFTVENE DANVPKPTTY TGWTKQNARY 600 DLYDVPVQSV EQLTQIVDQN HKQVLNTESK KGNTALALLA SAYGNSSDSE EDQDGLDIAV 660 EGDELNVMEH PAASRSQEEI SCLPSHLQDC HASPMVRLDR GDDNPLKSID DYEYSMHKKI 720 EHIMSPLDHS VKSEDYNITS EVAFKNNRDI THSAGICSRD TRGGTSLSGK AVIPVNNNNN 780 VPLVPPSDED SSRMHVFCLE HAAEADKQLR PIGGAHIFLF CHPDYPKIEA EAKVVVEELG 840 IGYTWKNTVY RHANREDEKR IQSALDSEEA NPGNGDWAVK LGINLFYSAN LSRSPLYSKQ 900 MPYNSVIYNA FGCSSPTSSP TEPKVYKRRA NKQKKVVAGK WCGKVWMSNQ VHPLLAKRDL 960 EDVEDEKSLH GRPLSDEKFE SDSTLKRNTM VRKSGRKRKM TVESGGTREG SFAERDWPSD 1020 SSLEDKSNQS QRRIPRSKQT RHIERDDTAS EGDYSPLQHH KKPISKHTKF MQSDAVSDDS 1080 LDDNTLQQWR KGTVKEAKFI DSDVVSDDTM DHDSDWPHRA ELSNKQDAIS EDSLGVGSLQ 1140 LQSNTPKSKY DQYIAEEDVI SDDQTEVYFQ KQKGRITISS QSKYLSENYT MISDDHMQHH 1200 MQKNQRRNPK SRKGKYLDQE DVISDDEVED HSRKYQRRIP KDRQAKCFGE EDSMSDDQLD 1260 DNFQKTQTNV RSRRQSKSSG REVMDDSTEN NSQLLRGTPK RKQVKCMDED YVSSDDQMEE 1320 DSHQQHRRTL RSKQSKSQTL QQMKQANPRA TRKTSRPVKR GALVLMKSKA PRKTKQQPRV 1380 LNSQSGTSRD EDSQIEQEEE GGPSTRLRKR VPKTEKEPEG ESKEKETKRK RVKNTAASKV 1440 SRGKARVKDE EGEYQCDIEG CTMSFETKQE LTSHKRNICP VKGCGKKFFS HKYLVQHRRV 1500 HEDDRPLKCP WKGCKMTFKW AWARTEHIRV HTGARPYVCA EPGCAQTFRF VSDFSRHKRK 1560 TGHVAKSRE

Sequence ? help Back to Top

Protein Sequence Length: 1569 aa Download sequence Send to blast

MAACSSEEVF PWLKSLPVAP EYRPTAAEFH DPIGYIFKIE KEASKYGICK IIPPVSPSPK  60
KTAISNLNRC QPQFTTRQQQ IGFCPRRQQP VRRPVWHSGN QYSFREFESK AKTFEKSFLK  120
KGKKSTPLSP LEVETLYWKA TVDKPFSVEY ANDMPGSAFC PMKENVYGGG DGYVTVGETA  180
WNMRGVSRAN GSLLRFMKEE IPGVTSPMVY LAMMFSWFAW HVEDHDLHSL NYLHMGAPKT  240
WYGVPKDAAV AFEDVVRVHG YGGEINPLVT FSILGEKTTV MSPEVFIRAG VPCCRLVQNA  300
GEFVVTFPRA YHTGFSHGFN CGEAANIATP EWLTFAKDAA IRRASINYPP MVSHFQLLYD  360
LGLALCSRIP GRIAEPRSSR LKDKRKGAGE TVVKELFVQD VLQNNDLLHI LGSGSSIVLL  420
PHSSSDFSVC SKLRVGSQQL KVKSEPFLNV CNSEGMGSSK GFISGDLVSN KNHGVKNVKG  480
FYSVKEKFAS LCERNRGEVC PSSSKTLQRD SEKETSQGDG LSDQRLFSCV TCGILSFSCV  540
AIVQPKEPAA RYLMSADCSF FNDWIEGSGV TSNKFTVENE DANVPKPTTY TGWTKQNARY  600
DLYDVPVQSV EQLTQIVDQN HKQVLNTESK KGNTALALLA SAYGNSSDSE EDQDGLDIAV  660
EGDELNVMEH PAASRSQEEI SCLPSHLQDC HASPMVRLDR GDDNPLKSID DYEYSMHKKI  720
EHIMSPLDHS VKSEDYNITS EVAFKNNRDI THSAGICSRD TRGGTSLSGK AVIPVNNNNN  780
VPLVPPSDED SSRMHVFCLE HAAEADKQLR PIGGAHIFLF CHPDYPKIEA EAKVVVEELG  840
IGYTWKNTVY RHANREDEKR IQSALDSEEA NPGNGDWAVK LGINLFYSAN LSRSPLYSKQ  900
MPYNSVIYNA FGCSSPTSSP TEPKVYKRRA NKQKKVVAGK WCGKVWMSNQ VHPLLAKRDL  960
EDVEDEKSLH GRPLSDEKFE SDSTLKRNTM VRKSGRKRKM TVESGGTREG SFAERDWPSD  1020
SSLEDKSNQS QRRIPRSKQT RHIERDDTAS EGDYSPLQHH KKPISKHTKF MQSDAVSDDS  1080
LDDNTLQQWR KGTVKEAKFI DSDVVSDDTM DHDSDWPHRA ELSNKQDAIS EDSLGVGSLQ  1140
LQSNTPKSKY DQYIAEEDVI SDDQTEVYFQ KQKGRITISS QSKYLSENYT MISDDHMQHH  1200
MQKNQRRNPK SRKGKYLDQE DVISDDEVED HSRKYQRRIP KDRQAKCFGE EDSMSDDQLD  1260
DNFQKTQTNV RSRRQSKSSG REVMDDSTEN NSQLLRGTPK RKQVKCMDED YVSSDDQMEE  1320
DSHQQHRRTL RSKQSKSQTL QQMKQANPRA TRKTSRPVKR GALVLMKSKA PRKTKQQPRV  1380
LNSQSGTSRD EDSQIEQEEE GGPSTRLRKR VPKTEKEPEG ESKEKETKRK RVKNTAASKV  1440
SRGKARVKDE EGEYQCDIEG CTMSFETKQE LTSHKRNICP VKGCGKKFFS HKYLVQHRRV  1500
HEDDRPLKCP WKGCKMTFKW AWARTEHIRV HTGARPYVCA EPGCAQTFRF VSDFSRHKRK  1560
TGHVAKSRE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	1e-79	12	358	8	346	Transcription factor jumonji (Jmj) family protein
6ip4_A	1e-79	12	358	8	346	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	922	928	PKVYKRR

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269\|PubMed:15377760, ECO:0000269\|PubMed:18713399}.

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lj4g3v1389260.1

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_004515844.1	0.0	lysine-specific demethylase REF6-like
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A1S2Z6B7	0.0	A0A1S2Z6B7_CICAR; lysine-specific demethylase REF6-like
STRING	XP_004515844.1	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

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]