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

CCG027995.1

Organism

Populus euphratica

Taxonomic ID

75702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus

Family

C2H2

Protein Properties

Length: 1685aa MW: 190905 Da PI: 9.1304

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
CCG027995.1	genome	LZU	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	1594	1616	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H CCG027995.1 1594 CPvkGCGKKFFSHKYLVQHRRVH 1616 9999*****************99 PP
2	zf-C2H2	11.6	0.00088	1652	1678	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H CCG027995.1 1652 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1678 89********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	4.8E-14	29	68	IPR003349	JmjN domain
PROSITE profile	PS51183	13.495	30	71	IPR003349	JmjN domain
Pfam	PF02375	3.9E-14	31	64	IPR003349	JmjN domain
SuperFamily	SSF51197	3.3E-28	116	177	No hit	No description
SMART	SM00558	3.6E-52	196	365	IPR003347	JmjC domain
PROSITE profile	PS51184	35.234	196	365	IPR003347	JmjC domain
SuperFamily	SSF51197	3.3E-28	214	383	No hit	No description
Pfam	PF02373	1.3E-36	229	348	IPR003347	JmjC domain
SMART	SM00355	12	1569	1591	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1592	1616	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.383	1592	1621	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.3E-5	1593	1620	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1594	1616	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.52E-9	1608	1650	No hit	No description
Gene3D	G3DSA:3.30.160.60	4.0E-8	1621	1646	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1622	1646	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1622	1651	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1624	1646	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	6.38E-8	1640	1674	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.9E-9	1647	1674	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.85	1652	1678	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.679	1652	1683	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1654	1678	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: 1685 aa Download sequence Send to blast
MAAPSGLSPE PPQPPTSTEV CQWLKNLPLA PEYRPTLSEF QDPIAYIFKI EKEASQYGIC 60 KIIPPVLPSA KKSTLSNLNR SLSARNGDSS APTFTTRQQQ IGFCPRKPRP VQKPVWQSGE 120 TYTFQEFETK AKSFEKNYLK KFSKKGGLSP LEIENLYWKA TLDKPFAVEY ANDMPGSAFS 180 PRKKEGQGVV VGEGMYVGET EWNMRSVSRA KGSLLRFMKE EIPGVTSPMV YIGMIFSWFA 240 WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VAFEEVVRVH GYGGENNPLV TFAVLGEKTT 300 VMSPEVFISA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLTVAKDA 360 AIRRASINYP PMVSHFQLLY DLALEFCTRI PVNISAKPRS SRLKDKQKGE GEMLVKEQFV 420 KNMIQNNDLL HILGKGSSVV LLPRSSSDIS VCSNLRVGSQ LRDNPTLGLS SQKDFMKSSK 480 SSGSDDILMD ENQEINQVKG FFSVKAKFAS LCERNRFSTI NGNECTQSMN MSTERGSPIH 540 GDKLSDQRLF SCVTCGILSF DCLAIIQPKE AASRYLMSAD CSFFNDWVVG SGVTRDVFTV 600 AGGIANIPEQ NSSMRWVRKN TVAGLYDVPV QSHNYQIQMA DQSVEVASSS AKQMESSALG 660 LLALNYGNSS DSEDDQVEAG LSCHDETNFT NCSLESKYQG QSSVFPSYKQ KYYDTETGGH 720 PLSPSKHDRQ GDVPFKSIDM YPEHGGRPDN FKDRSDDTLG CSFGFPANNP ACIESNGLDG 780 RYRDPVSIPH MSLNCSPIVH DTEKTKFNRP TVPIENPDMP FTQRSDRDSS CLHVFCLEHA 840 VEIEQQLRQM GGVHIFLLCH PEYPRIEAEA KSVSEELGID HLWNDITFRD AAKEDEERIQ 900 SALDSEEAIP GSGDWAVKLG INLFYSANLS RSPLYSKQMP YNSVIYNAFG RASPVSSPQK 960 FKVYGRRSGK PKKVVAGKWC GKVWMSNQVH PFLVKRDFVY QNQEQEQERS FHALATPDEK 1020 LEKKPQTIHK NETSRKSGKK RKIIAGSGTA KKVKCLEAEE ADSEDSVGDY SHRQHMRIHN 1080 RKNTEDIERE ISYDLVEDSN QQHGSYRRKW AKSVESDDAV SDDPLAEHVR QQYRRMRRSK 1140 QAKSIKRENT VSYASVENKF RKQLRRVHRS DQAKCSERRC VASDDSLDDN SDQWHGRAPR 1200 STLAKYTERE DANSDDSPEE SSRWQHGRVS RSKLSRYIKK ESAISDDSLE NGFKQHNKRI 1260 SRGKRAQVIR RDNVVSDDSL DESAFQQLPR FSRSKLAKLI EREDAFSDGS LEENIHQQHG 1320 RILRSKQSKF VEREDAISDD SLEDNTHWQR RRIPRSKMAK FVESEDAASD DLQEDDGHQH 1380 CRRIPKRKKA TSIESEDVVS DDQWENNIHG HLRKTSRSKQ PNIAEREGAV SDDLLENSSD 1440 QQDRIILRSK QKKSSMKQGI PRQLKQSARK MIKKETPQLM KQERRIKPET PQLRFGKSHM 1500 NAGQFDSHAE EERGGPSMRL RKRLSKAPKQ SVTRLKEKQN IKKKVKDATA VKAPAGRKNV 1560 KMKDEEAEYQ CDIDGCTMSF LSKQELALHK RNICPVKGCG KKFFSHKYLV QHRRVHIDDR 1620 PLKCPWKGCK MTFKWAWART EHIRVHTGAR PYVCAEEGCG QTFRFVSDFS RHKRKTGHLA 1680 KKGRG

Sequence ? help Back to Top

Protein Sequence Length: 1685 aa Download sequence Send to blast

MAAPSGLSPE PPQPPTSTEV CQWLKNLPLA PEYRPTLSEF QDPIAYIFKI EKEASQYGIC  60
KIIPPVLPSA KKSTLSNLNR SLSARNGDSS APTFTTRQQQ IGFCPRKPRP VQKPVWQSGE  120
TYTFQEFETK AKSFEKNYLK KFSKKGGLSP LEIENLYWKA TLDKPFAVEY ANDMPGSAFS  180
PRKKEGQGVV VGEGMYVGET EWNMRSVSRA KGSLLRFMKE EIPGVTSPMV YIGMIFSWFA  240
WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VAFEEVVRVH GYGGENNPLV TFAVLGEKTT  300
VMSPEVFISA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLTVAKDA  360
AIRRASINYP PMVSHFQLLY DLALEFCTRI PVNISAKPRS SRLKDKQKGE GEMLVKEQFV  420
KNMIQNNDLL HILGKGSSVV LLPRSSSDIS VCSNLRVGSQ LRDNPTLGLS SQKDFMKSSK  480
SSGSDDILMD ENQEINQVKG FFSVKAKFAS LCERNRFSTI NGNECTQSMN MSTERGSPIH  540
GDKLSDQRLF SCVTCGILSF DCLAIIQPKE AASRYLMSAD CSFFNDWVVG SGVTRDVFTV  600
AGGIANIPEQ NSSMRWVRKN TVAGLYDVPV QSHNYQIQMA DQSVEVASSS AKQMESSALG  660
LLALNYGNSS DSEDDQVEAG LSCHDETNFT NCSLESKYQG QSSVFPSYKQ KYYDTETGGH  720
PLSPSKHDRQ GDVPFKSIDM YPEHGGRPDN FKDRSDDTLG CSFGFPANNP ACIESNGLDG  780
RYRDPVSIPH MSLNCSPIVH DTEKTKFNRP TVPIENPDMP FTQRSDRDSS CLHVFCLEHA  840
VEIEQQLRQM GGVHIFLLCH PEYPRIEAEA KSVSEELGID HLWNDITFRD AAKEDEERIQ  900
SALDSEEAIP GSGDWAVKLG INLFYSANLS RSPLYSKQMP YNSVIYNAFG RASPVSSPQK  960
FKVYGRRSGK PKKVVAGKWC GKVWMSNQVH PFLVKRDFVY QNQEQEQERS FHALATPDEK  1020
LEKKPQTIHK NETSRKSGKK RKIIAGSGTA KKVKCLEAEE ADSEDSVGDY SHRQHMRIHN  1080
RKNTEDIERE ISYDLVEDSN QQHGSYRRKW AKSVESDDAV SDDPLAEHVR QQYRRMRRSK  1140
QAKSIKRENT VSYASVENKF RKQLRRVHRS DQAKCSERRC VASDDSLDDN SDQWHGRAPR  1200
STLAKYTERE DANSDDSPEE SSRWQHGRVS RSKLSRYIKK ESAISDDSLE NGFKQHNKRI  1260
SRGKRAQVIR RDNVVSDDSL DESAFQQLPR FSRSKLAKLI EREDAFSDGS LEENIHQQHG  1320
RILRSKQSKF VEREDAISDD SLEDNTHWQR RRIPRSKMAK FVESEDAASD DLQEDDGHQH  1380
CRRIPKRKKA TSIESEDVVS DDQWENNIHG HLRKTSRSKQ PNIAEREGAV SDDLLENSSD  1440
QQDRIILRSK QKKSSMKQGI PRQLKQSARK MIKKETPQLM KQERRIKPET PQLRFGKSHM  1500
NAGQFDSHAE EERGGPSMRL RKRLSKAPKQ SVTRLKEKQN IKKKVKDATA VKAPAGRKNV  1560
KMKDEEAEYQ CDIDGCTMSF LSKQELALHK RNICPVKGCG KKFFSHKYLV QHRRVHIDDR  1620
PLKCPWKGCK MTFKWAWART EHIRVHTGAR PYVCAEEGCG QTFRFVSDFS RHKRKTGHLA  1680
KKGRG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	9e-79	18	379	3	346	Transcription factor jumonji (Jmj) family protein
6ip4_A	9e-79	18	379	3	346	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1381	1387	RRIPKRK

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}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC235753	6e-76	AC235753.2 Medicago truncatula clone mth2-128c9, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_011040431.1	0.0	PREDICTED: lysine-specific demethylase REF6-like
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2K1YB81	0.0	A0A2K1YB81_POPTR; Uncharacterized protein
STRING	POPTR_0012s09390.1	0.0	(Populus trichocarpa)

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]