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.006G270100.1

Common Name

B456_006G270100, LOC105800814

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: 1614aa MW: 182180 Da PI: 9.2444

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.006G270100.1	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	1515	1537	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Gorai.006G270100.1 1515 CPvkGCGKKFFSHKYLVQHRRVH 1537 9999*****************99 PP
2	zf-C2H2	11.6	0.00084	1573	1599	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Gorai.006G270100.1 1573 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1599 89********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	4.9E-13	23	64	IPR003349	JmjN domain
PROSITE profile	PS51183	13.314	24	65	IPR003349	JmjN domain
Pfam	PF02375	1.7E-13	25	58	IPR003349	JmjN domain
SMART	SM00558	1.2E-48	199	368	IPR003347	JmjC domain
PROSITE profile	PS51184	33.68	199	368	IPR003347	JmjC domain
SuperFamily	SSF51197	3.84E-25	213	382	No hit	No description
Pfam	PF02373	2.9E-35	232	351	IPR003347	JmjC domain
SMART	SM00355	26	1490	1512	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1513	1537	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.445	1513	1542	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.4E-5	1514	1541	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1515	1537	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.74E-9	1529	1571	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.8E-8	1542	1567	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1543	1567	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1543	1572	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1545	1567	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	5.45E-8	1561	1595	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.3E-9	1568	1596	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.85	1573	1599	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.803	1573	1604	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1575	1599	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009741	Biological Process	response to brassinosteroid
GO:0009826	Biological Process	unidimensional cell growth
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0033169	Biological Process	histone H3-K9 demethylation
GO:0035067	Biological Process	negative regulation of histone acetylation
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 1614 aa Download sequence Send to blast
MAASSLSPEP SQEVFPWLKS LPFAPEYRPT LVEFQDPIAY IFKIEKEASQ YGICKIIPPV 60 PPASKKAAIG NLNRSLLERA VANASSDSKP APTFTTRQQQ IGFCPRKQRP VLKSVWQSGE 120 YYTFQEFEAK AKIFERNYLK KYSKKASLSA LEIETLFWKA TVDQPFDIEY ANDMPGSAFA 180 ALGSKKSSGG GRETGEGVTV AETPWNMRAV SRAKGSLLRF MKEEIPGVTS PMVYIAMLFS 240 WFAWHVEDHD LHSLNYLHMG AGKTWYGVPR DAAVAFEEVV RVDGYAGEFN PLVTFSTLGE 300 KTTVMSPEVF VHAGIPCCRL VQNAGEFVVT FPRAYHSGFS HGFNLGEAAN IATPEWLRVA 360 RDASIRRASI NYPPMVSHFQ LLYDLALDLC SRVPTNIGAK PKSSRLKDKK KCEGETLVKE 420 LFVQDLIQNN DLLHILGKGS SVVLLPKSST DISLSSESRI ASRLRINPKM SLGLCRYKEA 480 MKPSQVLAFD EIMQCKNEEI KGIKGFYSVK GKTVSTYEVD RDSSFTGADY LCKVPSQTLN 540 ANIERESSVQ GDTLSDQRLF TCVTCGILCF ACIAVLQPTE QAARYLMSAD CSFFNDWTFG 600 SGVTRDRFTT THGDGITSEQ NPSTRGMNKT APNALYDVPV QSVECKFQTK NQSKEVPEDT 660 KERRNTSALG LLASTYGNSS DSEDDNVEPK ATASGDETNS TNTIPGRKLQ HNDFKEEAPV 720 HVIDCDPEPG SKRSPPTINQ ELVSNGLGDK CSDPAIESYG AEKMRFSKAF ARMENADSPF 780 APNSDEDSSR MHVFCLEHAI EVEQQLRQIG GVHIFLLCHP EYPRIEAEAK LVAEELGIDY 840 LWNNILFGDA TKDDEVRIRS ALDSEDAIPG NGDWAVKLGI NLFYSSNLSH STLYSKQMPF 900 NFVIYSAFGR NSPASSPTKL NSYGRRSRKQ KKVVAGKWCG KVWMSNQVHP FLTQRDPKEQ 960 EQEKSFHAWA TSDENLESKP ENIRKAETSK VAKRFTRKSK TRAGATPSKK AKCIEPESVV 1020 SDDSLDGNSL RQQQRFFRGK KPKLIEKEKE ISYDSLEDDS LLHHRDLSRR KGAKFIEREA 1080 SESEDVEEDS DDQQFLKNLG GKQGKYIVEN DVVSGDSLDK ISAKQYRRIP RSSRDKFMKR 1140 EGSVSADEQE EISYQFHKRI PRGRQIKLFE RRLAVSDDLR ADNSLKQYRR KPKGKRAKFF 1200 EREEAMSDDA SDNDGSQTQH RRIPSGKQMK CTEREDEFSD DSLEGNPQQQ HGRIAQRKVS 1260 KFSDQEDIVS FDSLKGNSHR QHRRIPRSQL TQFIEREDAG SSDSPDDSSL QQLRRILRSK 1320 HAKILEKEDA VSDDSDDTSP QQLRKTPRSR QGKSIESEDV VSYDSSDENY GQPNSSLRSR 1380 KKKAPTPRQT KQEAPKNVKQ GKRRTTKQVI SQQSKQDTPR NRNTKIEQSA RQDNSYDEDE 1440 IEGGPSTRLR KRARKPSKEL ETKPKVKKQA LKNKAKSASN AKVRDEEAEY QCDMEGCTMS 1500 FGLKQELVLH KKNICPVKGC GKKFFSHKYL VQHRRVHMDD RPLKCPWKGC KMTFKWAWAR 1560 TEHIRVHTGA RPYVCAEEGC GQTFRFVSDF SRHKRKTGHS VKKGKIKHES RKL*

Sequence ? help Back to Top

Protein Sequence Length: 1614 aa Download sequence Send to blast

MAASSLSPEP SQEVFPWLKS LPFAPEYRPT LVEFQDPIAY IFKIEKEASQ YGICKIIPPV  60
PPASKKAAIG NLNRSLLERA VANASSDSKP APTFTTRQQQ IGFCPRKQRP VLKSVWQSGE  120
YYTFQEFEAK AKIFERNYLK KYSKKASLSA LEIETLFWKA TVDQPFDIEY ANDMPGSAFA  180
ALGSKKSSGG GRETGEGVTV AETPWNMRAV SRAKGSLLRF MKEEIPGVTS PMVYIAMLFS  240
WFAWHVEDHD LHSLNYLHMG AGKTWYGVPR DAAVAFEEVV RVDGYAGEFN PLVTFSTLGE  300
KTTVMSPEVF VHAGIPCCRL VQNAGEFVVT FPRAYHSGFS HGFNLGEAAN IATPEWLRVA  360
RDASIRRASI NYPPMVSHFQ LLYDLALDLC SRVPTNIGAK PKSSRLKDKK KCEGETLVKE  420
LFVQDLIQNN DLLHILGKGS SVVLLPKSST DISLSSESRI ASRLRINPKM SLGLCRYKEA  480
MKPSQVLAFD EIMQCKNEEI KGIKGFYSVK GKTVSTYEVD RDSSFTGADY LCKVPSQTLN  540
ANIERESSVQ GDTLSDQRLF TCVTCGILCF ACIAVLQPTE QAARYLMSAD CSFFNDWTFG  600
SGVTRDRFTT THGDGITSEQ NPSTRGMNKT APNALYDVPV QSVECKFQTK NQSKEVPEDT  660
KERRNTSALG LLASTYGNSS DSEDDNVEPK ATASGDETNS TNTIPGRKLQ HNDFKEEAPV  720
HVIDCDPEPG SKRSPPTINQ ELVSNGLGDK CSDPAIESYG AEKMRFSKAF ARMENADSPF  780
APNSDEDSSR MHVFCLEHAI EVEQQLRQIG GVHIFLLCHP EYPRIEAEAK LVAEELGIDY  840
LWNNILFGDA TKDDEVRIRS ALDSEDAIPG NGDWAVKLGI NLFYSSNLSH STLYSKQMPF  900
NFVIYSAFGR NSPASSPTKL NSYGRRSRKQ KKVVAGKWCG KVWMSNQVHP FLTQRDPKEQ  960
EQEKSFHAWA TSDENLESKP ENIRKAETSK VAKRFTRKSK TRAGATPSKK AKCIEPESVV  1020
SDDSLDGNSL RQQQRFFRGK KPKLIEKEKE ISYDSLEDDS LLHHRDLSRR KGAKFIEREA  1080
SESEDVEEDS DDQQFLKNLG GKQGKYIVEN DVVSGDSLDK ISAKQYRRIP RSSRDKFMKR  1140
EGSVSADEQE EISYQFHKRI PRGRQIKLFE RRLAVSDDLR ADNSLKQYRR KPKGKRAKFF  1200
EREEAMSDDA SDNDGSQTQH RRIPSGKQMK CTEREDEFSD DSLEGNPQQQ HGRIAQRKVS  1260
KFSDQEDIVS FDSLKGNSHR QHRRIPRSQL TQFIEREDAG SSDSPDDSSL QQLRRILRSK  1320
HAKILEKEDA VSDDSDDTSP QQLRKTPRSR QGKSIESEDV VSYDSSDENY GQPNSSLRSR  1380
KKKAPTPRQT KQEAPKNVKQ GKRRTTKQVI SQQSKQDTPR NRNTKIEQSA RQDNSYDEDE  1440
IEGGPSTRLR KRARKPSKEL ETKPKVKKQA LKNKAKSASN AKVRDEEAEY QCDMEGCTMS  1500
FGLKQELVLH KKNICPVKGC GKKFFSHKYL VQHRRVHMDD RPLKCPWKGC KMTFKWAWAR  1560
TEHIRVHTGA RPYVCAEEGC GQTFRFVSDF SRHKRKTGHS VKKGKIKHES RKL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	4e-73	17	389	8	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	4e-73	17	389	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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00608	ChIP-seq	Transfer from AT3G48430	Download

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012487613.1	0.0	PREDICTED: lysine-specific demethylase REF6-like
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A0D2S311	0.0	A0A0D2S311_GOSRA; Uncharacterized protein
STRING	Gorai.006G270100.1	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.006G270100.1
Entrez Gene	105800814

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]