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

KHN31932.1

Organism

Glycine soja

Taxonomic ID

3848

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1309aa MW: 149112 Da PI: 8.6115

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KHN31932.1	genome	TCUHK	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.7	0.00038	1193	1218	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L++H r+ + KHN31932.1 1193 YRCDidGCTMSFGSKQELMHHKRNiC 1218 99********************9877 PP
2	zf-C2H2	13	0.00031	1218	1240	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H KHN31932.1 1218 CPvkGCGKKFFSHKYLVQHRRVH 1240 9999*****************99 PP
3	zf-C2H2	13.7	0.00018	1276	1302	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C dCg++F+ s++ rH r+ H KHN31932.1 1276 YVCAepDCGQTFRFVSDFSRHKRKtgH 1302 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51184	15.809	1	64	IPR003347	JmjC domain
Pfam	PF02373	8.7E-14	1	47	IPR003347	JmjC domain
SuperFamily	SSF51197	8.79E-9	9	82	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.6E-4	1182	1215	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	7.7	1193	1215	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1216	1240	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.944	1216	1245	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.4E-6	1217	1244	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1218	1240	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.79E-9	1232	1274	No hit	No description
Gene3D	G3DSA:3.30.160.60	9.7E-9	1245	1270	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1246	1270	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1246	1275	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1248	1270	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	5.76E-8	1264	1298	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.2E-9	1271	1299	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	1.1	1276	1302	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.697	1276	1307	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1278	1302	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0032259	Biological Process	methylation
GO:0055114	Biological Process	oxidation-reduction process
GO:0003676	Molecular Function	nucleic acid binding
GO:0008168	Molecular Function	methyltransferase activity
GO:0016491	Molecular Function	oxidoreductase activity
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 1309 aa Download sequence Send to blast
MSPEVLISAG VPCCRLVQNA GEFVVTFPRA YHTGFSHGFN CGEAANIATP EWLRFAKDAA 60 IRRASLNYPP MVSHFQLLYD LALALCSRIP VSISAEPRSS RLKDKKGEGE TVTKELFVQD 120 VLQNNDLLHI LGKGSDVVLL PRSSVDISVC SKLRVGSQQS INVRNSEGMH SSKGFVSDDL 180 VFNRSPGIKQ EKSFYFVKDK FTTLCERNRI STFNVNGNIS TASSNPLQRD NDRETSQGDG 240 LSDQRLFSCV TCGILCFSCV AIVQPREPAA RYLMSADCSF FNDWVVGSGV SSNKLTIAHE 300 DATITEPNMY TGRKHVYLFG WMKNNVQDGK HDVTVQSSRE ALNTESENGN TALALLASAY 360 GNSSDSEEDH ITDDSHESNV INSASECLLS HTQNSHASPM TALDRDDNIP STSATCENFM 420 HRRFECNLNH QSVDHSLKKP DYHITSEVKF ENTKMVPNFT SNCSQHTHDA DRSLSNKSMV 480 PFDNKNTSMV LQSDEDSSRM HVFCLEHAAE AEQQLRPIGG AHMLLLCHPD YPKIESEAKM 540 VAEDLGIDYM WKNIAYRHAS TEDEERIQSA LDNEEAIPGN GDWAVKLGIN LFYSANLSRS 600 PLYSKQMPYN SVIYYSFGCS SLASSPIEPK VYQRRVNRQK KVVAGKWCGK VWMSNQVHPL 660 LAKRDSEDVE DEKLILGWIL PDEKFEKSGS TPKRETTSRK SGKKRKMTAE NGRPRKGSYA 720 KKNLVADNST EDKHNSQPRR ILRNKKARFV ERDHAALKGD YSPSYHRKPI SKQANCSESD 780 AVSDDSLDDD DHMQQSRNVK VEKAKFMDND VVSNDTMDYD SDCQQREEHS SKQVEDMERD 840 ANSEDFLDVG SLQLQRKTSR AMHAKSINEE DIISDDQMES PFRKRQKRIP KNRQGKYLTG 900 KDIISDNQLE LKMKKQQRMN PKSRQAKYLN EEDIASDDQL EDHYRRYQRN PKGRQATCVA 960 GEDEMSDDQL ENHCQKQQTN FSRKRQNKGN VREVKNEMCD DQLEDHFLKQ HRRFPKSRQN 1020 KHTEKEVMND LAENNSHLLH RTPKRKQAKC MEEDMNSDDE MEDDQPLRRA LRSKQAKPKT 1080 LLKQANSFQA KKQASRPIKQ GSRLLVKSKA PQQIKQPAHL WNKQSNNTQE FSLYMEEEED 1140 GGPSTRLRKR ATKAQESEGK LKDKQTKRKK VKNAAAAKVS VGHAKMKDGE AEYRCDIDGC 1200 TMSFGSKQEL MHHKRNICPV KGCGKKFFSH KYLVQHRRVH EDERPLKCPW KGCKMTFKWA 1260 WARTEHIRVH TGARPYVCAE PDCGQTFRFV SDFSRHKRKT GHSAKKNCQ

Sequence ? help Back to Top

Protein Sequence Length: 1309 aa Download sequence Send to blast

MSPEVLISAG VPCCRLVQNA GEFVVTFPRA YHTGFSHGFN CGEAANIATP EWLRFAKDAA  60
IRRASLNYPP MVSHFQLLYD LALALCSRIP VSISAEPRSS RLKDKKGEGE TVTKELFVQD  120
VLQNNDLLHI LGKGSDVVLL PRSSVDISVC SKLRVGSQQS INVRNSEGMH SSKGFVSDDL  180
VFNRSPGIKQ EKSFYFVKDK FTTLCERNRI STFNVNGNIS TASSNPLQRD NDRETSQGDG  240
LSDQRLFSCV TCGILCFSCV AIVQPREPAA RYLMSADCSF FNDWVVGSGV SSNKLTIAHE  300
DATITEPNMY TGRKHVYLFG WMKNNVQDGK HDVTVQSSRE ALNTESENGN TALALLASAY  360
GNSSDSEEDH ITDDSHESNV INSASECLLS HTQNSHASPM TALDRDDNIP STSATCENFM  420
HRRFECNLNH QSVDHSLKKP DYHITSEVKF ENTKMVPNFT SNCSQHTHDA DRSLSNKSMV  480
PFDNKNTSMV LQSDEDSSRM HVFCLEHAAE AEQQLRPIGG AHMLLLCHPD YPKIESEAKM  540
VAEDLGIDYM WKNIAYRHAS TEDEERIQSA LDNEEAIPGN GDWAVKLGIN LFYSANLSRS  600
PLYSKQMPYN SVIYYSFGCS SLASSPIEPK VYQRRVNRQK KVVAGKWCGK VWMSNQVHPL  660
LAKRDSEDVE DEKLILGWIL PDEKFEKSGS TPKRETTSRK SGKKRKMTAE NGRPRKGSYA  720
KKNLVADNST EDKHNSQPRR ILRNKKARFV ERDHAALKGD YSPSYHRKPI SKQANCSESD  780
AVSDDSLDDD DHMQQSRNVK VEKAKFMDND VVSNDTMDYD SDCQQREEHS SKQVEDMERD  840
ANSEDFLDVG SLQLQRKTSR AMHAKSINEE DIISDDQMES PFRKRQKRIP KNRQGKYLTG  900
KDIISDNQLE LKMKKQQRMN PKSRQAKYLN EEDIASDDQL EDHYRRYQRN PKGRQATCVA  960
GEDEMSDDQL ENHCQKQQTN FSRKRQNKGN VREVKNEMCD DQLEDHFLKQ HRRFPKSRQN  1020
KHTEKEVMND LAENNSHLLH RTPKRKQAKC MEEDMNSDDE MEDDQPLRRA LRSKQAKPKT  1080
LLKQANSFQA KKQASRPIKQ GSRLLVKSKA PQQIKQPAHL WNKQSNNTQE FSLYMEEEED  1140
GGPSTRLRKR ATKAQESEGK LKDKQTKRKK VKNAAAAKVS VGHAKMKDGE AEYRCDIDGC  1200
TMSFGSKQEL MHHKRNICPV KGCGKKFFSH KYLVQHRRVH EDERPLKCPW KGCKMTFKWA  1260
WARTEHIRVH TGARPYVCAE PDCGQTFRFV SDFSRHKRKT GHSAKKNCQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	3e-69	1191	1307	21	137	Lysine-specific demethylase REF6
6a58_A	3e-69	1191	1307	21	137	Lysine-specific demethylase REF6
6a59_A	3e-69	1191	1307	21	137	Lysine-specific demethylase REF6
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1147	1169	RKRATKAQESEGKLKDKQTKRKK

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	KHN31932.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC235340	0.0	AC235340.1 Glycine max strain Williams 82 clone GM_WBb0086A04, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_028236974.1	0.0	lysine-specific demethylase REF6-like
Swissprot	Q9STM3	1e-110	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A0B2RJC7	0.0	A0A0B2RJC7_GLYSO; Lysine-specific demethylase REF6
STRING	GLYMA06G18290.2	0.0	(Glycine max)

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	1e-112	relative of early flowering 6

Publications ? help Back to Top
Qi X, et al. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun, 2014. 5: p. 4340 [PMID:25004933] 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]