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

Gh_A07G2281

Organism

Gossypium hirsutum

Taxonomic ID

3635

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

C2H2

Protein Properties

Length: 1402aa MW: 159763 Da PI: 9.4529

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_A07G2281	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	13	0.00031	1312	1334	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Gh_A07G2281 1312 CPvkGCGKKFFSHKYLVQHRRVH 1334 9999*****************99 PP
2	zf-C2H2	12.5	0.00043	1370	1396	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ Cg++F+ s++ rH r+ H Gh_A07G2281 1370 YVCGeeGCGQTFRFVSDFSRHKRKtgH 1396 99********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	5.3E-15	24	65	IPR003349	JmjN domain
PROSITE profile	PS51183	13.536	25	66	IPR003349	JmjN domain
Pfam	PF02375	3.1E-14	26	59	IPR003349	JmjN domain
SMART	SM00558	8.1E-48	200	369	IPR003347	JmjC domain
PROSITE profile	PS51184	33.284	200	369	IPR003347	JmjC domain
SuperFamily	SSF51197	4.39E-26	214	386	No hit	No description
Pfam	PF02373	5.5E-35	233	352	IPR003347	JmjC domain
SMART	SM00355	8.4	1287	1309	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1310	1334	IPR015880	Zinc finger, C2H2-like
SuperFamily	SSF57667	4.1E-6	1310	1347	No hit	No description
PROSITE profile	PS50157	12.362	1310	1339	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.3E-5	1312	1338	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1312	1334	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	3.2E-8	1339	1364	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1340	1364	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1340	1369	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1342	1364	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.63E-9	1350	1394	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.0E-9	1365	1393	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.76	1370	1396	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.884	1370	1401	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1372	1396	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: 1402 aa Download sequence Send to blast
MACSSHHSLE QSQEAFSWLK SMPLAPEYRP TLAEFQDPIA YIFKIEKEAS QYGICKIIPP 60 VPPASKKTAI GNLNRSLLAR AEANASSDLK PTPTFTTRQQ QIGFCPRKPR PVQKPVWQSG 120 EYYTFQEFEA KAKSFERNYL KKYSKKGTLS ALEVETLFWK ATVDKPAMVE YANDMPGSAF 180 VPLNPKKSSG GGREAGEGVT VGETPWNMRA VSRAKGSLLR FMKEEIPGVT SPMVYIAMLF 240 SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP RDAAVAFEEV VRLDGYGGEF NPLVTFSTLG 300 EKTTVMSPEV FLHAGIPCCR LVQNAGEFVV TFPRAYHSGF SHGFNFGEAA NIATPEWLRV 360 ARDAAIRRAS INYPPMVSHF QLLYDLALEL CSRIPMSISA KPKSSRLKDK RKNEGENLVK 420 ELFVQNLIQN NNLLHILGKG SSVVLLPKSS SDISLCSDLR CQSRINPRMS LSLYKDIIKS 480 SKDVGSDETV IGGNEEIKGI KGFYSVKGNF ASMYEERKIQ YTDSGFSPSE VNTSRNPSLS 540 RLNSEEESPF DIKNGSPETF DPDLEFKTDN LILRRSNGLE DKFRDPMTSS HVNPNYSRAA 600 HGIEKMRFSM AVLPMENVDI PCVQRTDEDS SRMHVFCLEH AVEVEQQLRQ IGGVQVFLLC 660 HPEYPRIEAE AKLVAEELGI DYPWNDILFG DATKDDKERI QSALDSEDSI PGNGDWAVKL 720 GINLFYSANL SRSTLYSKQM PYNWIIYSAF GRNSSDSSPK KLNVYGRRSG KPRKVVAGKW 780 CGKVWMSNQV HPFLAQRDPE EQEQERSFHA RAISDENVER KPENVLKAET MKVVNRKRKS 840 RAEITLNKKV KRVESEGAVL DDSLDGSSLR QQQIVFRGKK PRLVEKEETV SCDLLEDDSL 900 LRHWNLSRNR RAKFIERENA ESEDAEEDFT HQQQRSNLRG RHNKYIEEDD EVSGDLLNES 960 SLKQYRRTPR SLQAKFSDGE NGVSDDEQEE ISHKLHRRIP RGKQIKSSKR NTAVSDDSLK 1020 QYRRMRKGKQ TKVFERDDAM SDYASDDDSQ YQIRRIPRGK QMKCMERDDA FSDDSVEDNS 1080 QQQHQRILSS KAAKFTERRR VHRSQLTEFI EMEDAVSSDS PDDNSSLRQP RRIPRSKQPE 1140 ILEREDAISD DSLDGSHQSN RSLRNRKKKG PTLCQMKQET AQNVKQVKHR STEQVISQQV 1200 KQETPQNWNT KIKQTARHCS SSSDEDEIEE GGPSTRLRKR TRKPPKRPET KPKEKKQAGK 1260 KKVKNALNSK TLSGQNSAKV RDEEVEYQCD MEGCSMSFGS KQALLLHKRN ICPVKGCGKK 1320 FFSHKYLVQH RRVHLDDRPL KCPWKGCKMT FKWAWARTEH IRVHTGARPY VCGEEGCGQT 1380 FRFVSDFSRH KRKTGHSGKK GS

Sequence ? help Back to Top

Protein Sequence Length: 1402 aa Download sequence Send to blast

MACSSHHSLE QSQEAFSWLK SMPLAPEYRP TLAEFQDPIA YIFKIEKEAS QYGICKIIPP  60
VPPASKKTAI GNLNRSLLAR AEANASSDLK PTPTFTTRQQ QIGFCPRKPR PVQKPVWQSG  120
EYYTFQEFEA KAKSFERNYL KKYSKKGTLS ALEVETLFWK ATVDKPAMVE YANDMPGSAF  180
VPLNPKKSSG GGREAGEGVT VGETPWNMRA VSRAKGSLLR FMKEEIPGVT SPMVYIAMLF  240
SWFAWHVEDH DLHSLNYLHM GAGKTWYGVP RDAAVAFEEV VRLDGYGGEF NPLVTFSTLG  300
EKTTVMSPEV FLHAGIPCCR LVQNAGEFVV TFPRAYHSGF SHGFNFGEAA NIATPEWLRV  360
ARDAAIRRAS INYPPMVSHF QLLYDLALEL CSRIPMSISA KPKSSRLKDK RKNEGENLVK  420
ELFVQNLIQN NNLLHILGKG SSVVLLPKSS SDISLCSDLR CQSRINPRMS LSLYKDIIKS  480
SKDVGSDETV IGGNEEIKGI KGFYSVKGNF ASMYEERKIQ YTDSGFSPSE VNTSRNPSLS  540
RLNSEEESPF DIKNGSPETF DPDLEFKTDN LILRRSNGLE DKFRDPMTSS HVNPNYSRAA  600
HGIEKMRFSM AVLPMENVDI PCVQRTDEDS SRMHVFCLEH AVEVEQQLRQ IGGVQVFLLC  660
HPEYPRIEAE AKLVAEELGI DYPWNDILFG DATKDDKERI QSALDSEDSI PGNGDWAVKL  720
GINLFYSANL SRSTLYSKQM PYNWIIYSAF GRNSSDSSPK KLNVYGRRSG KPRKVVAGKW  780
CGKVWMSNQV HPFLAQRDPE EQEQERSFHA RAISDENVER KPENVLKAET MKVVNRKRKS  840
RAEITLNKKV KRVESEGAVL DDSLDGSSLR QQQIVFRGKK PRLVEKEETV SCDLLEDDSL  900
LRHWNLSRNR RAKFIERENA ESEDAEEDFT HQQQRSNLRG RHNKYIEEDD EVSGDLLNES  960
SLKQYRRTPR SLQAKFSDGE NGVSDDEQEE ISHKLHRRIP RGKQIKSSKR NTAVSDDSLK  1020
QYRRMRKGKQ TKVFERDDAM SDYASDDDSQ YQIRRIPRGK QMKCMERDDA FSDDSVEDNS  1080
QQQHQRILSS KAAKFTERRR VHRSQLTEFI EMEDAVSSDS PDDNSSLRQP RRIPRSKQPE  1140
ILEREDAISD DSLDGSHQSN RSLRNRKKKG PTLCQMKQET AQNVKQVKHR STEQVISQQV  1200
KQETPQNWNT KIKQTARHCS SSSDEDEIEE GGPSTRLRKR TRKPPKRPET KPKEKKQAGK  1260
KKVKNALNSK TLSGQNSAKV RDEEVEYQCD MEGCSMSFGS KQALLLHKRN ICPVKGCGKK  1320
FFSHKYLVQH RRVHLDDRPL KCPWKGCKMT FKWAWARTEH IRVHTGARPY VCGEEGCGQT  1380
FRFVSDFSRH KRKTGHSGKK GS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	9e-75	18	390	8	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	9e-75	18	390	8	353	Arabidopsis JMJ13
Search in ModeBase

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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017605239.1	0.0	PREDICTED: lysine-specific demethylase JMJ705-like
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2P5VTK8	0.0	A0A2P5VTK8_GOSBA; Uncharacterized protein
STRING	Gorai.001G061900.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5259	28	43

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]