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.04G191900.1.p

Common Name

GLYMA_04G191900, LOC100775271

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: 1592aa MW: 179776 Da PI: 8.5534

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.04G191900.1.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	12.7	0.00039	1475	1500	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L++H r+ + Glyma.04G191900.1.p 1475 YQCDidGCTMSFGSKQELMHHKRNiC 1500 99********************9877 PP
2	zf-C2H2	12.8	0.00036	1500	1522	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Glyma.04G191900.1.p 1500 CPvkGCGKKFFSHKYLVQHRRVH 1522 9999*****************99 PP
3	zf-C2H2	14.7	9e-05	1558	1584	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C dCg++F+ s+++rH r+ H Glyma.04G191900.1.p 1558 YVCAepDCGQTFRFVSDFRRHKRKtgH 1584 899999*****************9666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	3.2E-15	20	61	IPR003349	JmjN domain
PROSITE profile	PS51183	13.744	21	62	IPR003349	JmjN domain
Pfam	PF02375	1.0E-13	22	55	IPR003349	JmjN domain
SuperFamily	SSF51197	4.39E-27	107	123	No hit	No description
PROSITE profile	PS51184	33.902	175	351	IPR003347	JmjC domain
SuperFamily	SSF51197	4.39E-27	179	370	No hit	No description
SMART	SM00558	4.4E-51	182	351	IPR003347	JmjC domain
Pfam	PF02373	6.7E-36	215	334	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	6.2E-4	1467	1497	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	7.3	1475	1497	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1498	1522	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.944	1498	1527	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.47E-6	1498	1534	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.8E-6	1499	1526	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1500	1522	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.2E-8	1527	1552	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1528	1552	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1528	1557	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1530	1552	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.7E-9	1538	1582	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.1E-9	1553	1581	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.822	1558	1589	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.35	1558	1584	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1560	1584	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: 1592 aa Download sequence Send to blast
MVGVCEGNGE VLSWLKSMPV APEYRPSAAE FQDPIGYIFK IEKEASKYGI CKIIPPFPPS 60 SRKTAIANLN RSLAEAGSTF TTRQQQIGFC PRRPRPVQRP VWQSGDRYTF SEFESKAKSF 120 EKTYLKRHSK KGSGSGSGLG PLETETLFWK ATLDKPFSVE YANDMPGSAF SPKCRHAGDP 180 SSLADTPWNM RAVSRAKGSL LQFMKEEIPG VTSPMVYVAM LFSWFAWHVE DHDLHSLNYL 240 HMGAGKTWYG VPRDAAVAFE EVVRVHGYGG EINPLVTFAT LGEKTTVMSP EVFISAGVPC 300 CRLVQNAGEF VVTFPRAYHS GFSHGFNCGE AANIATPEWL RFAKDAAIRR ASLNYPPMVS 360 HFQLLYDLAL ALCSSIPASI SAEPRSSRLK DKKKGEGETV IKELFVQDVL QNNDLLHILG 420 KGSDVVLLPH SSVDIFVCPK LRVGFQQSIN VRNSEGMHSS KGFVSDDVVF SRSQGIKQEK 480 SFYSVKDNFT TLFERNRISS FDVNGNIRAS SSNPLQRDND RETGQGDSLS DQRLFSCVTC 540 GILCFSCVAI VQPREPAARY LMSADCSFFN DWVVGSGVSS NKFTIALEEA TIAEPNMYTG 600 WMKKNVQDGI HDVSVQSSRE ALNTESENGN TALALLASAY GNSSDSEEDQ IADESHESNV 660 INSASECLLS HTQDSYASPM TALDKGDDFP STSASCEDVH RRFECNLSHQ SLDHSLKKQD 720 YNITSGVTFE NTRTVPNSTS NCSQQAHNAD RSLSNKSMVA FDNKNTSMVL QADEDSSRMH 780 VFCLEHAAEA EQQLRPIGGA HILLLCHPDY PKIEAEAKMV AEDLGIDYMW KKIAYRHAST 840 EDEERIQSAL DNEEAIPGNG DWAVKLGINL FYSANLSRSP LYSKQMPYNS VIYYSFGCSS 900 PASSPVEPKV YQRRVNRQKK VVAGKWCGKV WMSNQVHPLL AKRDSEDVED EKLLLGWILP 960 DEKLERSEIT LKSETTSRKS GKKRKMTAEN GRPKKGSYAK KNVVADNSTE GKHNSQPRRI 1020 LRNKKARCVE RDHAALKGDY CPPYHRKSIS KQANCSESDA VSDDSLDDDD HMHHRRNAIV 1080 EKDKFIDNDV SNDTVDCDSD WQQREELSSK KVEDTERDAI SEDSLDVGSL QLLRKNSRAK 1140 HAKNISQEDI ISDDQMESPL QKRQRRIPKS RQGKYLTGKD IISDDQLEHK KKKQQRKNPK 1200 SRQAKYLNEE DIASDDQLEG HYRRYQRKNS RGRHAKCVAG EDGMPDDQLE DRCQKQQTSF 1260 SRKRQNKGID REVKNEISDD HLEDHFLKQQ RRFPKSRQNK HTDKEVMDDL AENNSHLLHR 1320 TPKRKQAKCM EEDDMNSDDE MEDNQPLRRT LRSKQAKPKT LQQMKQANSF QAKKQASRPI 1380 KQGSRMLVKS KAPQQIKQPS HLRNKQSNNT QEFSLDMEEE EEGGPSTRLR KRATKAQESE 1440 GKLKDKQTKR MKVKNAAAAK VSVGDARMQD GEAEYQCDID GCTMSFGSKQ ELMHHKRNIC 1500 PVKGCGKKFF SHKYLVQHRR VHEDERPLKC PWKGCKMTFK WAWARTEHIR VHTGARPYVC 1560 AEPDCGQTFR FVSDFRRHKR KTGHSAKKNC Q*

Sequence ? help Back to Top

Protein Sequence Length: 1592 aa Download sequence Send to blast

MVGVCEGNGE VLSWLKSMPV APEYRPSAAE FQDPIGYIFK IEKEASKYGI CKIIPPFPPS  60
SRKTAIANLN RSLAEAGSTF TTRQQQIGFC PRRPRPVQRP VWQSGDRYTF SEFESKAKSF  120
EKTYLKRHSK KGSGSGSGLG PLETETLFWK ATLDKPFSVE YANDMPGSAF SPKCRHAGDP  180
SSLADTPWNM RAVSRAKGSL LQFMKEEIPG VTSPMVYVAM LFSWFAWHVE DHDLHSLNYL  240
HMGAGKTWYG VPRDAAVAFE EVVRVHGYGG EINPLVTFAT LGEKTTVMSP EVFISAGVPC  300
CRLVQNAGEF VVTFPRAYHS GFSHGFNCGE AANIATPEWL RFAKDAAIRR ASLNYPPMVS  360
HFQLLYDLAL ALCSSIPASI SAEPRSSRLK DKKKGEGETV IKELFVQDVL QNNDLLHILG  420
KGSDVVLLPH SSVDIFVCPK LRVGFQQSIN VRNSEGMHSS KGFVSDDVVF SRSQGIKQEK  480
SFYSVKDNFT TLFERNRISS FDVNGNIRAS SSNPLQRDND RETGQGDSLS DQRLFSCVTC  540
GILCFSCVAI VQPREPAARY LMSADCSFFN DWVVGSGVSS NKFTIALEEA TIAEPNMYTG  600
WMKKNVQDGI HDVSVQSSRE ALNTESENGN TALALLASAY GNSSDSEEDQ IADESHESNV  660
INSASECLLS HTQDSYASPM TALDKGDDFP STSASCEDVH RRFECNLSHQ SLDHSLKKQD  720
YNITSGVTFE NTRTVPNSTS NCSQQAHNAD RSLSNKSMVA FDNKNTSMVL QADEDSSRMH  780
VFCLEHAAEA EQQLRPIGGA HILLLCHPDY PKIEAEAKMV AEDLGIDYMW KKIAYRHAST  840
EDEERIQSAL DNEEAIPGNG DWAVKLGINL FYSANLSRSP LYSKQMPYNS VIYYSFGCSS  900
PASSPVEPKV YQRRVNRQKK VVAGKWCGKV WMSNQVHPLL AKRDSEDVED EKLLLGWILP  960
DEKLERSEIT LKSETTSRKS GKKRKMTAEN GRPKKGSYAK KNVVADNSTE GKHNSQPRRI  1020
LRNKKARCVE RDHAALKGDY CPPYHRKSIS KQANCSESDA VSDDSLDDDD HMHHRRNAIV  1080
EKDKFIDNDV SNDTVDCDSD WQQREELSSK KVEDTERDAI SEDSLDVGSL QLLRKNSRAK  1140
HAKNISQEDI ISDDQMESPL QKRQRRIPKS RQGKYLTGKD IISDDQLEHK KKKQQRKNPK  1200
SRQAKYLNEE DIASDDQLEG HYRRYQRKNS RGRHAKCVAG EDGMPDDQLE DRCQKQQTSF  1260
SRKRQNKGID REVKNEISDD HLEDHFLKQQ RRFPKSRQNK HTDKEVMDDL AENNSHLLHR  1320
TPKRKQAKCM EEDDMNSDDE MEDNQPLRRT LRSKQAKPKT LQQMKQANSF QAKKQASRPI  1380
KQGSRMLVKS KAPQQIKQPS HLRNKQSNNT QEFSLDMEEE EEGGPSTRLR KRATKAQESE  1440
GKLKDKQTKR MKVKNAAAAK VSVGDARMQD GEAEYQCDID GCTMSFGSKQ ELMHHKRNIC  1500
PVKGCGKKFF SHKYLVQHRR VHEDERPLKC PWKGCKMTFK WAWARTEHIR VHTGARPYVC  1560
AEPDCGQTFR FVSDFRRHKR KTGHSAKKNC Q*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	3e-80	12	375	6	356	Transcription factor jumonji (Jmj) family protein
6ip4_A	3e-80	12	375	6	356	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1429	1451	RKRATKAQESEGKLKDKQTKRMK

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.04G191900.1.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_006578679.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	I1JXF4	0.0	I1JXF4_SOYBN; Uncharacterized protein
STRING	GLYMA04G36620.1	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.04G191900.1.p
Entrez Gene	100775271

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]