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

Achn375731

Organism

Actinidia chinensis

Taxonomic ID

3625

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; Ericales; Actinidiaceae; Actinidia

Family

C2H2

Protein Properties

Length: 1425aa MW: 159007 Da PI: 8.2031

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Achn375731	genome	IKGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.8	0.00073	1308	1333	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L+ H r+ + Achn375731 1308 YPCDveGCTMSFVSKQELVLHKRNiC 1333 899999****************9877 PP
2	zf-C2H2	13.1	0.0003	1333	1355	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Achn375731 1333 CPvkGCGKKFFSHKYLVQHRRVH 1355 9999*****************99 PP
3	zf-C2H2	11.8	0.00073	1391	1417	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Achn375731 1391 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1417 89********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	1.2E-13	26	67	IPR003349	JmjN domain
PROSITE profile	PS51183	14.548	27	68	IPR003349	JmjN domain
Pfam	PF02375	4.5E-13	28	61	IPR003349	JmjN domain
PROSITE profile	PS51184	23.635	196	351	IPR003347	JmjC domain
SMART	SM00558	9.3E-32	196	351	IPR003347	JmjC domain
SuperFamily	SSF51197	5.49E-17	210	354	No hit	No description
Pfam	PF02373	9.1E-20	229	333	IPR003347	JmjC domain
SMART	SM00355	13	1308	1330	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1331	1355	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.445	1331	1360	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1333	1355	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.2E-5	1333	1359	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.23E-9	1347	1389	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.3E-8	1360	1385	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.824	1361	1390	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0036	1361	1385	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1363	1385	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	4.98E-8	1379	1413	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.4E-9	1386	1414	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.85	1391	1417	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.032	1391	1422	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1393	1417	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: 1425 aa Download sequence Send to blast
MASSSAPVAA EQLTTEVFPW LKTLPLAPEY NPTLAEFEDP IAYIFKIETE ASKYGICKIV 60 PPVAAPPKKT SIANLNRSLS ARSTTANPKS PPTFTTRQQQ IGFCPRKHRP VQKPVWQSGE 120 NYTFPQFEAK AKSFERNYLK KFPKKGLSAL EVETLYWKAF GDKPFSVEYA NDMPGSAFAP 180 VSARKKDRET GEAVTNVGET AWNMRGVSRA KGSLLRFMKE EIPGVTSPMV YLAMMFSWFA 240 WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VALEEVIRVH GYGGEINPLV TFAILGEKTT 300 VMSPEVLISA GIPCCRAYHS GFSHGFNCGE AANIATPGWL RVAKDAAIRR AAINCPPMVS 360 HFQLLYDLAL SLCSRIPKSI DSEPRSSRLK HKRRGEGETL IKKLFVEDVM KNNDLLHILA 420 EGSSIVLLPQ NSLDDSVYSN SCIASRFKGN SSFPLGLCNP EEEFKASESL GSENLMLDRK 480 GGIKQLAGFY AVKGEFSSAC DGNRSSLLHG SDDSSSLASQ IHKPNTERER TIHGHKLSDQ 540 GLFSCVTCGI LSFACVAIVQ PKDSAAHYLM SADCGIFNDG DVGPRVTSDA NFSGLDSCSG 600 WVGKRTPDGL FDVPIQSADH IQTVDQSPEV LSDPEIQKGP SALGLLALAY SSSDSEDEEV 660 ETDIPVYDSE TISRDCSPES RLQCDDDTRL PSVKIRNEAT GCHIHDFGDD VPLQVIDSWR 720 DNHPPRSNFR YSNQVFDCSA ELETDNIVST ESDSVGGRLT HQMKLSAAAS NGSPVAQAVT 780 SRSNTYVPSE NTSMSFAPKS GDDSYRPHVF CLQHAAEVEQ QLRPIGGSHI LLLCHPDYPE 840 LEAEAKLVAE ELAIDYFWND IAFREATKED EERIQTALES EEGTHGNGDW AVKLGINLFY 900 SANLGRSPLY SKQMPYNSII YKAFGRNSLT NSPTKPKFHG KGSGRQKKIV VAGKWCGKVW 960 MSNQVHPLLV ERDAEEGEED NTSFRGWAKP EVKRERLSES ARPAETNFEI RKIGKKRKNT 1020 CQKEGGPIKK SKCMKVDDSV KPSDASPEGN QQYSRNFRNL RNKQLKLESP QPQRSSDRNK 1080 SRFDSFIEDA LEGGPSTRLR KRTSKLPVED KLELKKHTGG KKAKKYPTGK MRDEEEGEYP 1140 NDMEPVLKRY TASKKAKKGP TGKMRDEEEG EYASDVEPVW KRHTASKRTK KGPIGKMRDE 1200 EEGEYPSDEE PVWKRHTASK RTKKGPIVKM RDEEEGGYPS DEELVWKRHT ASKRAKKGPT 1260 VKMRAEEEGE YPSDEEPVLK KHTPIKKTKK GPTVKMRDEE EVGEEGEYPC DVEGCTMSFV 1320 SKQELVLHKR NICPVKGCGK KFFSHKYLVQ HRRVHMDDRP LKCPWKGCKM AFKWAWARTE 1380 HIRVHTGARP YVCAEEGCGQ TFRFVSDFSR HKRKTGHSTK KGRG*

Sequence ? help Back to Top

Protein Sequence Length: 1425 aa Download sequence Send to blast

MASSSAPVAA EQLTTEVFPW LKTLPLAPEY NPTLAEFEDP IAYIFKIETE ASKYGICKIV  60
PPVAAPPKKT SIANLNRSLS ARSTTANPKS PPTFTTRQQQ IGFCPRKHRP VQKPVWQSGE  120
NYTFPQFEAK AKSFERNYLK KFPKKGLSAL EVETLYWKAF GDKPFSVEYA NDMPGSAFAP  180
VSARKKDRET GEAVTNVGET AWNMRGVSRA KGSLLRFMKE EIPGVTSPMV YLAMMFSWFA  240
WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VALEEVIRVH GYGGEINPLV TFAILGEKTT  300
VMSPEVLISA GIPCCRAYHS GFSHGFNCGE AANIATPGWL RVAKDAAIRR AAINCPPMVS  360
HFQLLYDLAL SLCSRIPKSI DSEPRSSRLK HKRRGEGETL IKKLFVEDVM KNNDLLHILA  420
EGSSIVLLPQ NSLDDSVYSN SCIASRFKGN SSFPLGLCNP EEEFKASESL GSENLMLDRK  480
GGIKQLAGFY AVKGEFSSAC DGNRSSLLHG SDDSSSLASQ IHKPNTERER TIHGHKLSDQ  540
GLFSCVTCGI LSFACVAIVQ PKDSAAHYLM SADCGIFNDG DVGPRVTSDA NFSGLDSCSG  600
WVGKRTPDGL FDVPIQSADH IQTVDQSPEV LSDPEIQKGP SALGLLALAY SSSDSEDEEV  660
ETDIPVYDSE TISRDCSPES RLQCDDDTRL PSVKIRNEAT GCHIHDFGDD VPLQVIDSWR  720
DNHPPRSNFR YSNQVFDCSA ELETDNIVST ESDSVGGRLT HQMKLSAAAS NGSPVAQAVT  780
SRSNTYVPSE NTSMSFAPKS GDDSYRPHVF CLQHAAEVEQ QLRPIGGSHI LLLCHPDYPE  840
LEAEAKLVAE ELAIDYFWND IAFREATKED EERIQTALES EEGTHGNGDW AVKLGINLFY  900
SANLGRSPLY SKQMPYNSII YKAFGRNSLT NSPTKPKFHG KGSGRQKKIV VAGKWCGKVW  960
MSNQVHPLLV ERDAEEGEED NTSFRGWAKP EVKRERLSES ARPAETNFEI RKIGKKRKNT  1020
CQKEGGPIKK SKCMKVDDSV KPSDASPEGN QQYSRNFRNL RNKQLKLESP QPQRSSDRNK  1080
SRFDSFIEDA LEGGPSTRLR KRTSKLPVED KLELKKHTGG KKAKKYPTGK MRDEEEGEYP  1140
NDMEPVLKRY TASKKAKKGP TGKMRDEEEG EYASDVEPVW KRHTASKRTK KGPIGKMRDE  1200
EEGEYPSDEE PVWKRHTASK RTKKGPIVKM RDEEEGGYPS DEELVWKRHT ASKRAKKGPT  1260
VKMRAEEEGE YPSDEEPVLK KHTPIKKTKK GPTVKMRDEE EVGEEGEYPC DVEGCTMSFV  1320
SKQELVLHKR NICPVKGCGK KFFSHKYLVQ HRRVHMDDRP LKCPWKGCKM AFKWAWARTE  1380
HIRVHTGARP YVCAEEGCGQ TFRFVSDFSR HKRKTGHSTK KGRG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	5e-66	1308	1421	23	136	Lysine-specific demethylase REF6
6a58_A	5e-66	1308	1421	23	136	Lysine-specific demethylase REF6
6a59_A	5e-66	1308	1421	23	136	Lysine-specific demethylase REF6
6ip0_A	2e-63	15	372	3	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	2e-63	15	372	3	353	Arabidopsis JMJ13
Search in ModeBase

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}.

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_028116352.1	0.0	LOW QUALITY PROTEIN: lysine-specific demethylase REF6-like
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2R6QGG9	0.0	A0A2R6QGG9_ACTCH; Lysine-specific demethylase
STRING	XP_008239384.1	0.0	(Prunus mume)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA4988	23	31

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]