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

Gorai.001G061900.1

Common Name

B456_001G061900, LOC105786591

Organism

Gossypium raimondii

Taxonomic ID

29730

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: 1589aa MW: 180137 Da PI: 9.0312

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.001G061900.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.8	0.00035	1498	1520	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Gorai.001G061900.1 1498 CPvkGCGKKFFSHKYLVQHRRVH 1520 9999*****************99 PP
2	zf-C2H2	12.4	0.00049	1556	1582	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ Cg++F+ s++ rH r+ H Gorai.001G061900.1 1556 YVCGeeGCGQTFRFVSDFSRHKRKtgH 1582 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	3.6E-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	5.22E-26	214	386	No hit	No description
Pfam	PF02373	6.4E-35	233	352	IPR003347	JmjC domain
SMART	SM00355	7.9	1473	1495	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.362	1496	1525	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	4.78E-6	1496	1533	No hit	No description
SMART	SM00355	0.0045	1496	1520	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.6E-5	1497	1524	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1498	1520	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	3.7E-8	1525	1550	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1526	1550	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1526	1555	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1528	1550	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.1E-9	1536	1580	No hit	No description
Gene3D	G3DSA:3.30.160.60	7.0E-9	1551	1579	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.76	1556	1582	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.884	1556	1587	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1558	1582	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: 1589 aa Download sequence Send to blast
MACSSHHSLE QSQEAFSWLK SMPLAPEYRP TLAEFQDPIA YIFKIEKEAS QYGICKIIPP 60 VPPASKKTAI GNLNRSLLVR 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 RKSEGENLVK 420 ELFVQNLIQN NNLLHILGKG SSVVLLPKSS SDISLCSHLR CQSRINPRMS LSLYKDIIKS 480 SKDVGSDETV IGGNEEIKGI KGFYSVKGNF ASMYEGNRDS SFRGNDYSCR FPSQTSNTTR 540 ERDSAILDDA LPDQRLFSCV TCGILCFACV AVLQPTDQAA RYLMSADCSF FNDWTVGSGV 600 THDGFNAAHG DAITSEQNPC SRRMNKSAPN SLYDVSVQPV DSKFRMGDQS NQVLEDTEKR 660 GESSALGLLA STYGNSSDSE EDLPEPNATI FHDETNPTNV SPERKIQYND SGFSPSDVNT 720 SRNPSLSRLD SEEESPFDIK NGSPETFDPD LEFKTDNLIS RRSNGLEDKF RDPMTSSHVN 780 PNYSRAAHGI EKMRFSMAVL PMENVDIPFV QRTDEDSSRM HVFCLEHAVE VEQQLRQIGG 840 VQVFLLCHPE YPKIEAEAKL VAEELGIDYP WNDILFGDAT KDDKERIQSA LDSEDAIPGN 900 GDWAVKLGIN LFYSANLSRS TLYSKQMPYN WIIYSAFGRN SSDSSLKKLN VYGRRSGKPR 960 KVVVGKWCGR VWMSNQVHPF LAQRDSEEQE QERSFHAQAI SDENVERKPE NVPKAETMKV 1020 VNRKRKSRAE ITLNKKVKRV ESEGAVSDDS LDGSSLRQQQ IVFRGKKPRL VKKEEAVSCD 1080 LLEDDSLLRH WNLSRNRRAK FIERENAESE DAEEDFTHQQ QRSNLRGRHH KYIEEDDEVS 1140 GDLHNESSLK QYRRTPRSLQ AKFLDGENGV SDDEQEEISH KLHRRIPRGK QIKSSKRNTA 1200 VSDDSLKQYR RMRKGKQTKV FERDDAMSDY ASDDDSQYQI RRIPRGKQMK CMERYDAFSD 1260 DSVEDNSQQQ HRRILSSKAA KFTERRRVHR SQLTEFIETE DAVSSDSPDD NSSLRQPRRI 1320 PRSKQPEILE REDAISDDSL DGSHQSNRSL RNRKKKGPTL CQMKRETAQN VKQVKRRSTE 1380 QVISQRVKQE TPQNRNTKTK QTARHCSSSS DEDEIEGGPS TRLRKRTRKP LKQPETKPKE 1440 KKQAGKKKVK NALNSKTLSG QNSAKVRDEE VEYQCDMEGC SMSFGSKQAL ILHKRNICPV 1500 KGCGKKFFSH KYLVQHRRVH LDDRPLKCPW KGCKMTFKWA WARTEHIRVH TGARPYVCGE 1560 EGCGQTFRFV SDFSRHKRKT GHSGKKGR*

Sequence ? help Back to Top

Protein Sequence Length: 1589 aa Download sequence Send to blast

MACSSHHSLE QSQEAFSWLK SMPLAPEYRP TLAEFQDPIA YIFKIEKEAS QYGICKIIPP  60
VPPASKKTAI GNLNRSLLVR 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 RKSEGENLVK  420
ELFVQNLIQN NNLLHILGKG SSVVLLPKSS SDISLCSHLR CQSRINPRMS LSLYKDIIKS  480
SKDVGSDETV IGGNEEIKGI KGFYSVKGNF ASMYEGNRDS SFRGNDYSCR FPSQTSNTTR  540
ERDSAILDDA LPDQRLFSCV TCGILCFACV AVLQPTDQAA RYLMSADCSF FNDWTVGSGV  600
THDGFNAAHG DAITSEQNPC SRRMNKSAPN SLYDVSVQPV DSKFRMGDQS NQVLEDTEKR  660
GESSALGLLA STYGNSSDSE EDLPEPNATI FHDETNPTNV SPERKIQYND SGFSPSDVNT  720
SRNPSLSRLD SEEESPFDIK NGSPETFDPD LEFKTDNLIS RRSNGLEDKF RDPMTSSHVN  780
PNYSRAAHGI EKMRFSMAVL PMENVDIPFV QRTDEDSSRM HVFCLEHAVE VEQQLRQIGG  840
VQVFLLCHPE YPKIEAEAKL VAEELGIDYP WNDILFGDAT KDDKERIQSA LDSEDAIPGN  900
GDWAVKLGIN LFYSANLSRS TLYSKQMPYN WIIYSAFGRN SSDSSLKKLN VYGRRSGKPR  960
KVVVGKWCGR VWMSNQVHPF LAQRDSEEQE QERSFHAQAI SDENVERKPE NVPKAETMKV  1020
VNRKRKSRAE ITLNKKVKRV ESEGAVSDDS LDGSSLRQQQ IVFRGKKPRL VKKEEAVSCD  1080
LLEDDSLLRH WNLSRNRRAK FIERENAESE DAEEDFTHQQ QRSNLRGRHH KYIEEDDEVS  1140
GDLHNESSLK QYRRTPRSLQ AKFLDGENGV SDDEQEEISH KLHRRIPRGK QIKSSKRNTA  1200
VSDDSLKQYR RMRKGKQTKV FERDDAMSDY ASDDDSQYQI RRIPRGKQMK CMERYDAFSD  1260
DSVEDNSQQQ HRRILSSKAA KFTERRRVHR SQLTEFIETE DAVSSDSPDD NSSLRQPRRI  1320
PRSKQPEILE REDAISDDSL DGSHQSNRSL RNRKKKGPTL CQMKRETAQN VKQVKRRSTE  1380
QVISQRVKQE TPQNRNTKTK QTARHCSSSS DEDEIEGGPS TRLRKRTRKP LKQPETKPKE  1440
KKQAGKKKVK NALNSKTLSG QNSAKVRDEE VEYQCDMEGC SMSFGSKQAL ILHKRNICPV  1500
KGCGKKFFSH KYLVQHRRVH LDDRPLKCPW KGCKMTFKWA WARTEHIRVH TGARPYVCGE  1560
EGCGQTFRFV SDFSRHKRKT GHSGKKGR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	5e-75	18	490	8	452	Transcription factor jumonji (Jmj) family protein
6ip4_A	5e-75	18	490	8	452	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}.

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	JX577634	5e-98	JX577634.1 Gossypium hirsutum clone NBRI_GE9494 microsatellite sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012468557.1	0.0	PREDICTED: lysine-specific demethylase JMJ705-like
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A0D2LVF4	0.0	A0A0D2LVF4_GOSRA; 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

Link Out ? help Back to Top
Phytozome	Gorai.001G061900.1
Entrez Gene	105786591

Publications ? help Back to Top
Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] 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]