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

Achn113981

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: 1276aa MW: 141675 Da PI: 8.8726

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Achn113981	genome	IKGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.6	0.00089	1159	1184	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L+ H r+ + Achn113981 1159 YTCDmeGCTMSFGSKQELVLHKRNvC 1184 99********************9877 PP
2	zf-C2H2	13.6	0.0002	1183	1206	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 +Cp Cgk F ++ +L++H r+H Achn113981 1183 VCPvkGCGKKFFSHKYLVQHRRVH 1206 69999*****************99 PP
3	zf-C2H2	11.9	0.00071	1242	1268	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ Cg++F+ s++ rH r+ H Achn113981 1242 YVCTeaGCGQTFRFVSDFSRHKRKtgH 1268 99*********************9775 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	9.1E-14	16	57	IPR003349	JmjN domain
PROSITE profile	PS51183	14.825	17	58	IPR003349	JmjN domain
Pfam	PF02375	5.9E-13	18	51	IPR003349	JmjN domain
SMART	SM00558	1.2E-46	180	349	IPR003347	JmjC domain
PROSITE profile	PS51184	32.19	183	349	IPR003347	JmjC domain
SuperFamily	SSF51197	1.02E-24	194	347	No hit	No description
Pfam	PF02373	1.2E-36	213	332	IPR003347	JmjC domain
SMART	SM00355	11	1159	1181	IPR015880	Zinc finger, C2H2-like
SuperFamily	SSF57667	3.13E-6	1182	1219	No hit	No description
PROSITE profile	PS50157	12.632	1182	1211	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0037	1182	1206	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.2E-5	1183	1210	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1184	1206	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.2E-9	1211	1236	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.01E-9	1211	1264	No hit	No description
PROSITE profile	PS50157	11.614	1212	1241	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0014	1212	1236	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1214	1236	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	3.3E-10	1237	1265	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.783	1242	1273	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.19	1242	1268	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1244	1268	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: 1276 aa Download sequence Send to blast
MASEQEVFPW LKALPLAPEY RPTRPEFEDP IAYIFKIEKE ASKYGICKIV PPLAAPPKKR 60 VVADMNRSLL ARPGSSEPTF TTRQQQIGFC PRRHCPVQKP VWQSGESYTL SQFKAKAKGF 120 EKNFLKKSPR KGLSALEIET HFWEASGDKP FSVEYANDIP GSAFAPVGVR SEKEAGEGVT 180 VGETAWNMRG VSRAKGSLLR FMKAEIPGVM SPMVYVAMMF SWFAWHVEDH DLHSLNYLHM 240 GAGKTWYGVP REAAVAFEEV VRVHGYGGEI NPLVTFAVLG EKTTVMSPEV LIGAGVPCCR 300 LVQNVGEFVV TFPRAYHSGF SHGFNCSEAA NIATPEWLRV ANDAAIRRAS IKCPPMVSHF 360 QLLYDLALSL CSRVSKSISN EPKSSRLKNK KKGEGEVLIK ELFVEDVIRN NDLLHILGEG 420 SSVVLLPQNS LDNSVCSDLF VSSQFKGNPR LSFGLSTPKE EIKASDSLVS RQIMVDRMLA 480 VKQLAGFYPV KGRFSSMFDG NRLSMLSGSD DAYTVASRTP KVNPGRERTA QGDRLSDQGL 540 FSCVTCGILC FACVAIVQPR EAAANYLMSA DCSIFNDQDV GPAVNSDGCT VSTVAANSSE 600 LNFYSGVMGK STPDGLFDVP IHSAEGIQIV QQSTEVDTDS ETQKAASALG QLAINYGNSS 660 DSDEEEVEAD IPFYNSGTKS RDCSPVNKLQ FDDRGLTSLK HHSEGSDCHR LGFGRDVPLQ 720 VVDSYEDDGH LISNFRGKYQ TFDRSAKFQT DNIASIESNS VGSRYRHQMK LSTADSSGSQ 780 VTPKAVTSSN VIVPSGNATV PFASRSDEDS SRLHVFCLQH AARVEQQLRP IGGARIMLLC 840 HPDYPEIENE SKLVAEELGI DYCWNNVAFR EACEEDEERI QLAVESDVAV HGNGDWAVKL 900 GIHLYYSANL SRSPLYSKQM PYNSVIYKVF GHSSPVNSVT KLKVNERRSS KQKKIVVAGK 960 WCGKVWMSNQ VHPLLAGRYT AEDVGEEGRT MHALAKREVK HERLPESTLA AEIISAIRKT 1020 GKRRKSTREA GAMMKLKYQK IHDPGKASED SPDEGYEQLY KKIIRSKKVK SETPRSERSC 1080 DRNARRFESC IEDELDGGPS TRLRKRNLNP SKELVLKKLI ESKPVLKKQT SSKKAKKSPA 1140 VKTLVAQGNM NMRDNEGEYT CDMEGCTMSF GSKQELVLHK RNVCPVKGCG KKFFSHKYLV 1200 QHRRVHVDDR PLKCPWKGCK MTFKWAWART EHIRVHTGER PYVCTEAGCG QTFRFVSDFS 1260 RHKRKTGHHA KKGRG*

Sequence ? help Back to Top

Protein Sequence Length: 1276 aa Download sequence Send to blast

MASEQEVFPW LKALPLAPEY RPTRPEFEDP IAYIFKIEKE ASKYGICKIV PPLAAPPKKR  60
VVADMNRSLL ARPGSSEPTF TTRQQQIGFC PRRHCPVQKP VWQSGESYTL SQFKAKAKGF  120
EKNFLKKSPR KGLSALEIET HFWEASGDKP FSVEYANDIP GSAFAPVGVR SEKEAGEGVT  180
VGETAWNMRG VSRAKGSLLR FMKAEIPGVM SPMVYVAMMF SWFAWHVEDH DLHSLNYLHM  240
GAGKTWYGVP REAAVAFEEV VRVHGYGGEI NPLVTFAVLG EKTTVMSPEV LIGAGVPCCR  300
LVQNVGEFVV TFPRAYHSGF SHGFNCSEAA NIATPEWLRV ANDAAIRRAS IKCPPMVSHF  360
QLLYDLALSL CSRVSKSISN EPKSSRLKNK KKGEGEVLIK ELFVEDVIRN NDLLHILGEG  420
SSVVLLPQNS LDNSVCSDLF VSSQFKGNPR LSFGLSTPKE EIKASDSLVS RQIMVDRMLA  480
VKQLAGFYPV KGRFSSMFDG NRLSMLSGSD DAYTVASRTP KVNPGRERTA QGDRLSDQGL  540
FSCVTCGILC FACVAIVQPR EAAANYLMSA DCSIFNDQDV GPAVNSDGCT VSTVAANSSE  600
LNFYSGVMGK STPDGLFDVP IHSAEGIQIV QQSTEVDTDS ETQKAASALG QLAINYGNSS  660
DSDEEEVEAD IPFYNSGTKS RDCSPVNKLQ FDDRGLTSLK HHSEGSDCHR LGFGRDVPLQ  720
VVDSYEDDGH LISNFRGKYQ TFDRSAKFQT DNIASIESNS VGSRYRHQMK LSTADSSGSQ  780
VTPKAVTSSN VIVPSGNATV PFASRSDEDS SRLHVFCLQH AARVEQQLRP IGGARIMLLC  840
HPDYPEIENE SKLVAEELGI DYCWNNVAFR EACEEDEERI QLAVESDVAV HGNGDWAVKL  900
GIHLYYSANL SRSPLYSKQM PYNSVIYKVF GHSSPVNSVT KLKVNERRSS KQKKIVVAGK  960
WCGKVWMSNQ VHPLLAGRYT AEDVGEEGRT MHALAKREVK HERLPESTLA AEIISAIRKT  1020
GKRRKSTREA GAMMKLKYQK IHDPGKASED SPDEGYEQLY KKIIRSKKVK SETPRSERSC  1080
DRNARRFESC IEDELDGGPS TRLRKRNLNP SKELVLKKLI ESKPVLKKQT SSKKAKKSPA  1140
VKTLVAQGNM NMRDNEGEYT CDMEGCTMSF GSKQELVLHK RNVCPVKGCG KKFFSHKYLV  1200
QHRRVHVDDR PLKCPWKGCK MTFKWAWART EHIRVHTGER PYVCTEAGCG QTFRFVSDFS  1260
RHKRKTGHHA KKGRG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	4e-76	3	437	1	413	Transcription factor jumonji (Jmj) family protein
6ip4_A	4e-76	3	437	1	413	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	A0A2R6PUP2	0.0	A0A2R6PUP2_ACTCH; Lysine-specific demethylase
STRING	VIT_17s0000g09980.t01	0.0	(Vitis vinifera)

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]