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

Glyma.06G173800.1.p

Organism

Glycine max

Taxonomic ID

3847

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: 1574aa MW: 178363 Da PI: 8.695

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.06G173800.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.9	0.00033	1482	1504	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Glyma.06G173800.1.p 1482 CPvkGCGKKFFSHKYLVQHRRVH 1504 9999*****************99 PP
2	zf-C2H2	13.4	0.00023	1540	1566	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C dCg++F+ s++ rH r+ H Glyma.06G173800.1.p 1540 YVCAepDCGQTFRFVSDFSRHKRKtgH 1566 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	2.0E-15	20	61	IPR003349	JmjN domain
PROSITE profile	PS51183	13.813	21	62	IPR003349	JmjN domain
Pfam	PF02375	1.4E-13	22	55	IPR003349	JmjN domain
SuperFamily	SSF51197	3.84E-26	176	367	No hit	No description
SMART	SM00558	2.4E-50	180	349	IPR003347	JmjC domain
PROSITE profile	PS51184	33.791	180	349	IPR003347	JmjC domain
Pfam	PF02373	3.9E-36	213	332	IPR003347	JmjC domain
SuperFamily	SSF57667	6.1E-5	1453	1509	No hit	No description
SMART	SM00355	10	1457	1479	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1480	1504	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.944	1480	1509	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.8E-6	1481	1503	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1482	1504	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	4.18E-9	1496	1538	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.7E-10	1504	1532	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1510	1534	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1510	1539	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1512	1534	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	6.92E-8	1528	1562	No hit	No description
Gene3D	G3DSA:3.30.160.60	8.6E-9	1533	1563	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	1.1	1540	1566	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.697	1540	1571	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1542	1566	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: 1574 aa Download sequence Send to blast
MGVVSEGNGD VLPWLKSMPV APEYRPSAAE FQDPISYIFK IEKEASKYGI CKIIPPFPPS 60 SRKTAIANLN RSLAETGSTF TTRQQQIGFC PRRPRPVQRP VWQSGDRYTF TEFESKAKSF 120 EKTYLKRHAK KASGLGPGPL ETETLFWKAT LDKPFSVEYA NDMPGSAFSP KCRRVGDPSS 180 LADTQWNMRA VSRAKGSLLQ FMKEEIPGVT SPMVYVAMLF SWFAWHVEDH DLHSLNYLHM 240 GAGKTWYGVP RDAAVAFEEV VRVHGYGGEI NPLVTFATLG EKTTVMSPEV LISAGVPCCR 300 LVQNAGEFVV TFPRAYHTGF SHGFNCGEAA NIATPEWLRF AKDAAIRRAS LNYPPMVSHF 360 QLLYDLALAL CSRIPVSISA EPRSSRLKDK KGEGETVTKE LFVQDVLQNN DLLHILGKGS 420 DVVLLPRSSV DISVCSKLRV GSQQSINVRN SEGMHSSKGF VSDDLVFNRS PGIKQEKSFY 480 FVKDKFTTLC ERNRISTFNV NGNISTASSN PLQRDNDRET SQGDGLSDQR LFSCVTCGIL 540 CFSCVAIVQP REPAARYLMS ADCSFFNDWV VGSGVSSNKL TIAHEDATIT KPNMYTGWMK 600 NNVQDGKHDV TVQSSREALN TESENGNTAL ALLASAYGNS SDSEEDHITD DSHESNVINS 660 ASECLLSHTQ NSHASPMTAL DRDDNIPSTS ATCENFMHRR FECNLNHQSV DHSLKKQDYN 720 ITSEVKFENT KMVPNFTSNC SQHTHDADRS LSNKSMVPFD NKNTSMVLQS DEDSSRMHVF 780 CLEHAAEAEQ QLRPIGGAHM LLLCHPDYPK IESEAKMVAE DLGIDYMWKN IAYRHASTED 840 EERIQSALDN EEAIPGNGDW AVKLGINLFY SANLSRSPLY SKQMPYNSVI YYSFGCSSLA 900 SSPIEPKVYQ RRVNRQKKVV AGKCYAKRDS EDVEDEKLIL GWILPDEKFE KSGSTPKRET 960 TSRKSGKKRK MTAENGRPRK GSYAKKNLVA DNSTEDKHNS QPRRILRNKK ARCVERDHAA 1020 LKGDYSPSYH RKPISKQANC SESDAVSDDS LDDDDHMQQS RNVKVEKAKF MDNDVVSNDT 1080 MDYDSDCQQR EEHSSKQVED MERDANSEDF LDVGSLQLQR KTSRAMHAKS INEEDIISDD 1140 QMESPFRKRQ KRIPKNRQGK YLTGKDIISD NQLELKMKKQ QRMNPKSRQA KYLNEEDIAS 1200 DDQLEDHYRR YQRNPKGRQA TCVAGEDEMS DDQLENHCQK QQTNFSRKRQ NKGNVREVKN 1260 EMCDDQLEDH FLKQHRRFPK SRQNKHTEKE VMNDLAENNS HLLHRTPKRK QAKCMEDDMN 1320 SDDEMEDDQP LRRALRSKQA KPKTLLKQAN SFQAKKQASR PIKQGSRLLV KSKAPQQIKQ 1380 PAHLWNKQSN NTQEFSLYME EEEDGGPSTR LRKRATKAQE SEGKLKDKQT KRKKVKNAAA 1440 AKVSVGHAKM KDGEAEYRCD IDGCAMSFGS KQELMHHKKN ICPVKGCGKK FFSHKYLVQH 1500 RRVHEDERPL KCPWKGCKMT FKWAWARTEH IRVHTGARPY VCAEPDCGQT FRFVSDFSRH 1560 KRKTGHSAKK NCQ*

Sequence ? help Back to Top

Protein Sequence Length: 1574 aa Download sequence Send to blast

MGVVSEGNGD VLPWLKSMPV APEYRPSAAE FQDPISYIFK IEKEASKYGI CKIIPPFPPS  60
SRKTAIANLN RSLAETGSTF TTRQQQIGFC PRRPRPVQRP VWQSGDRYTF TEFESKAKSF  120
EKTYLKRHAK KASGLGPGPL ETETLFWKAT LDKPFSVEYA NDMPGSAFSP KCRRVGDPSS  180
LADTQWNMRA VSRAKGSLLQ FMKEEIPGVT SPMVYVAMLF SWFAWHVEDH DLHSLNYLHM  240
GAGKTWYGVP RDAAVAFEEV VRVHGYGGEI NPLVTFATLG EKTTVMSPEV LISAGVPCCR  300
LVQNAGEFVV TFPRAYHTGF SHGFNCGEAA NIATPEWLRF AKDAAIRRAS LNYPPMVSHF  360
QLLYDLALAL CSRIPVSISA EPRSSRLKDK KGEGETVTKE LFVQDVLQNN DLLHILGKGS  420
DVVLLPRSSV DISVCSKLRV GSQQSINVRN SEGMHSSKGF VSDDLVFNRS PGIKQEKSFY  480
FVKDKFTTLC ERNRISTFNV NGNISTASSN PLQRDNDRET SQGDGLSDQR LFSCVTCGIL  540
CFSCVAIVQP REPAARYLMS ADCSFFNDWV VGSGVSSNKL TIAHEDATIT KPNMYTGWMK  600
NNVQDGKHDV TVQSSREALN TESENGNTAL ALLASAYGNS SDSEEDHITD DSHESNVINS  660
ASECLLSHTQ NSHASPMTAL DRDDNIPSTS ATCENFMHRR FECNLNHQSV DHSLKKQDYN  720
ITSEVKFENT KMVPNFTSNC SQHTHDADRS LSNKSMVPFD NKNTSMVLQS DEDSSRMHVF  780
CLEHAAEAEQ QLRPIGGAHM LLLCHPDYPK IESEAKMVAE DLGIDYMWKN IAYRHASTED  840
EERIQSALDN EEAIPGNGDW AVKLGINLFY SANLSRSPLY SKQMPYNSVI YYSFGCSSLA  900
SSPIEPKVYQ RRVNRQKKVV AGKCYAKRDS EDVEDEKLIL GWILPDEKFE KSGSTPKRET  960
TSRKSGKKRK MTAENGRPRK GSYAKKNLVA DNSTEDKHNS QPRRILRNKK ARCVERDHAA  1020
LKGDYSPSYH RKPISKQANC SESDAVSDDS LDDDDHMQQS RNVKVEKAKF MDNDVVSNDT  1080
MDYDSDCQQR EEHSSKQVED MERDANSEDF LDVGSLQLQR KTSRAMHAKS INEEDIISDD  1140
QMESPFRKRQ KRIPKNRQGK YLTGKDIISD NQLELKMKKQ QRMNPKSRQA KYLNEEDIAS  1200
DDQLEDHYRR YQRNPKGRQA TCVAGEDEMS DDQLENHCQK QQTNFSRKRQ NKGNVREVKN  1260
EMCDDQLEDH FLKQHRRFPK SRQNKHTEKE VMNDLAENNS HLLHRTPKRK QAKCMEDDMN  1320
SDDEMEDDQP LRRALRSKQA KPKTLLKQAN SFQAKKQASR PIKQGSRLLV KSKAPQQIKQ  1380
PAHLWNKQSN NTQEFSLYME EEEDGGPSTR LRKRATKAQE SEGKLKDKQT KRKKVKNAAA  1440
AKVSVGHAKM KDGEAEYRCD IDGCAMSFGS KQELMHHKKN ICPVKGCGKK FFSHKYLVQH  1500
RRVHEDERPL KCPWKGCKMT FKWAWARTEH IRVHTGARPY VCAEPDCGQT FRFVSDFSRH  1560
KRKTGHSAKK NCQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	3e-80	10	370	4	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	3e-80	10	370	4	353	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1411	1433	RKRATKAQESEGKLKDKQTKRKK

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	Glyma.06G173800.1.p

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	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A368UI23	0.0	A0A368UI23_SOYBN; Uncharacterized protein
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
Representative plant	OGRP4401	12	17

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	Glyma.06G173800.1.p

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]