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

GSMUA_Achr10P03980_001

Organism

Musa acuminata

Taxonomic ID

4641

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Zingiberales; Musaceae; Musa

Family

C2H2

Protein Properties

Length: 1497aa MW: 166667 Da PI: 9.0028

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSMUA_Achr10P03980_001	genome	CIRAD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	13.2	0.00027	1008	1031	1	22
EEET..TTTEEESSHHHHHHHHHH CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt 22 y+C C++sFs+k +L H r GSMUA_Achr10P03980_001 1008 YTCDieGCSMSFSTKQDLALHKRD 1031 99*******************985 PP
2	zf-C2H2	12.4	0.00047	1033	1055	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H ++H GSMUA_Achr10P03980_001 1033 CPvkGCGKKFFSHKYLVQHRKVH 1055 9999*****************99 PP
3	zf-C2H2	11	0.0013	1091	1117	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H GSMUA_Achr10P03980_001 1091 YVCWesGCGQTFRFVSDFSRHKRKtgH 1117 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	1.7E-16	31	72	IPR003349	JmjN domain
PROSITE profile	PS51183	14.659	32	73	IPR003349	JmjN domain
Pfam	PF02375	2.2E-15	33	66	IPR003349	JmjN domain
SMART	SM00558	2.1E-42	183	353	IPR003347	JmjC domain
PROSITE profile	PS51184	32.42	183	353	IPR003347	JmjC domain
SuperFamily	SSF51197	2.03E-22	197	347	No hit	No description
Pfam	PF02373	1.8E-32	216	336	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	4.0E-4	1003	1030	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	7.3	1008	1030	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.49	1031	1055	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.967	1031	1060	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.52E-5	1032	1067	No hit	No description
PROSITE pattern	PS00028	0	1033	1055	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.1E-4	1033	1059	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Gene3D	G3DSA:3.30.160.60	4.9E-8	1060	1084	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0026	1061	1085	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.72	1061	1090	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1063	1085	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.18E-9	1071	1115	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.4E-9	1085	1114	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	1	1091	1117	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1091	1122	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1093	1117	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.710.10	1.6E-9	1171	1237	No hit	No description
PROSITE profile	PS50097	9.889	1171	1232	IPR000210	BTB/POZ domain
SuperFamily	SSF54695	2.35E-9	1171	1237	IPR011333	SKP1/BTB/POZ domain
SMART	SM00225	6.1E-10	1171	1276	IPR000210	BTB/POZ domain
Pfam	PF00651	2.1E-7	1171	1272	IPR000210	BTB/POZ domain
Gene3D	G3DSA:3.30.710.10	1.6E-9	1276	1303	No hit	No description
SuperFamily	SSF54695	2.35E-9	1276	1306	IPR011333	SKP1/BTB/POZ domain
CDD	cd14734	3.55E-14	1276	1335	No hit	No description
SuperFamily	SSF57933	5.1E-15	1351	1459	IPR000197	Zinc finger, TAZ-type
Gene3D	G3DSA:1.20.1020.10	5.1E-17	1351	1460	IPR000197	Zinc finger, TAZ-type
SMART	SM00551	1.7E-8	1352	1451	IPR000197	Zinc finger, TAZ-type
Pfam	PF02135	5.0E-11	1359	1450	IPR000197	Zinc finger, TAZ-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
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:0003712	Molecular Function	transcription cofactor activity
GO:0004402	Molecular Function	histone acetyltransferase activity
GO:0005515	Molecular Function	protein binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 1497 aa Download sequence Send to blast
MASAVSSSAQ GVVASEPPPM EVPPWLKSLP LAPEFHPTLQ EFQDPIAYIL KIEKEAADYG 60 ICKIVPPLPS APKKTAQQIG FCPRRPRPVQ KPVWQSGERY TLQQFEAKAR QFERSYLRRT 120 AGGGGRKAAT APALSPLEME TLFWRASADK PFSVEYANDM PGSGFAPLAA AAGRRCREEV 180 PANLGESAWN MRGVSRAKGS LLRFMKEEIP GVTSPMVYVA MLFSWFAWHV EDHELHSLNY 240 LHMGAGKTWY GVPRDAGLAF EEVVGVHGYG GDGNPLMTFA ILGEKTTVMS PEVFVGAGIP 300 CCSRLVQNAG DFVVTFPGSY HLGFSHGFNC GEAANIATPE WLKFAKGAAV RRASIDCPPL 360 VSHFQLLYAL ALSLCTRMPM CEGSEPRSSR LKDKIKGEGE EMVKNAFVQS VIQNNYLLSV 420 LLDSGNSCVV LPQNAPESPL CSTSLVRSQV KVKPRKSLGI CNFNGLFSFK GNFTSTGNDK 480 TVSLGTDNKF VNADHYSTSF ACVAVVQPRE TTAKYLMSAD CSFLDDHVSG SGEASGISRD 540 TNQRTNNNSL VADIVYCTAY PVQVSDQSVE MISDVTCPSG ASALDLLASI YEDSSDVEDE 600 DPENGKLVSA SYLEDNRTVA NSGTTTKFVG EPRGAQCREL DGQNAEDHYS NLKMGNLTSV 660 FKDLPVNLMQ GSDKDSSRLH VFCLEHAAEI EKQLQPIGGV HMMVLCHPDY PKIESEAKLL 720 AKEQGIGYIW KNVKFREANE EDQERIRAAI EDEQVMPMNS DWTVKLGINL CYTANLSKSP 780 LYSKQMPYNP VIYKAFGRDS TGNSPMKPKA TRRCPGRQKK IVAAGRWCGK VWMSNQVHPY 840 LAHKKETQEQ EQTEGLYSFD TDQNPLIEID IGHSSGLSSK RNSSGSNLAA NNSGKKRKRP 900 SKMAKSKKPL YSSTMADRNS KTDYVSAIPA SPLGRTLRSS HLRHNDSSSQ GKSSLKNESG 960 GPGTHLKKRS SKSEELKNKL ASKKQSTKRK AKNTQTASLA VKGKEEEYTC DIEGCSMSFS 1020 TKQDLALHKR DICPVKGCGK KFFSHKYLVQ HRKVHMDDRP LVCPWKGCKM TFKWPWARTE 1080 HIRVHTGDRP YVCWESGCGQ TFRFVSDFSR HKRKTGHSAK KGRRRSGLDR WVVEAQNIRR 1140 WLGNMTEEEK KRGEAEIQRW LEVGSVEIPP ADVRIVTSGG RRIPVHSTVL ASASPVLESI 1200 LGGPHKGRSR GREIPILGVP CDAVHAFVHS LYFARCVSAT EEEMIGEHGM HLLALSHAYR 1260 VGWLKRAAER ALSLRLTAEG VVDVLVLSQR CDAPRLHLRC MQLLSKDFAA VEQTEAWRFL 1320 QDHDPWLELH ILQFLHHAHL RRRRQARRKA EQRLYAELHE AMDCLRHICA DGCGEVGPSG 1380 RLLPADARPP CPNAVSCRGL RQLIRHFAAC DRQKRQQHGC RRCKRLWQLL RLHASICDEV 1440 DDASCKVPLC IQFKQRMQEK EGELEEDEDE RWRLLVKKVA SARVMSHLAK RQSQVLV

Sequence ? help Back to Top

Protein Sequence Length: 1497 aa Download sequence Send to blast

MASAVSSSAQ GVVASEPPPM EVPPWLKSLP LAPEFHPTLQ EFQDPIAYIL KIEKEAADYG  60
ICKIVPPLPS APKKTAQQIG FCPRRPRPVQ KPVWQSGERY TLQQFEAKAR QFERSYLRRT  120
AGGGGRKAAT APALSPLEME TLFWRASADK PFSVEYANDM PGSGFAPLAA AAGRRCREEV  180
PANLGESAWN MRGVSRAKGS LLRFMKEEIP GVTSPMVYVA MLFSWFAWHV EDHELHSLNY  240
LHMGAGKTWY GVPRDAGLAF EEVVGVHGYG GDGNPLMTFA ILGEKTTVMS PEVFVGAGIP  300
CCSRLVQNAG DFVVTFPGSY HLGFSHGFNC GEAANIATPE WLKFAKGAAV RRASIDCPPL  360
VSHFQLLYAL ALSLCTRMPM CEGSEPRSSR LKDKIKGEGE EMVKNAFVQS VIQNNYLLSV  420
LLDSGNSCVV LPQNAPESPL CSTSLVRSQV KVKPRKSLGI CNFNGLFSFK GNFTSTGNDK  480
TVSLGTDNKF VNADHYSTSF ACVAVVQPRE TTAKYLMSAD CSFLDDHVSG SGEASGISRD  540
TNQRTNNNSL VADIVYCTAY PVQVSDQSVE MISDVTCPSG ASALDLLASI YEDSSDVEDE  600
DPENGKLVSA SYLEDNRTVA NSGTTTKFVG EPRGAQCREL DGQNAEDHYS NLKMGNLTSV  660
FKDLPVNLMQ GSDKDSSRLH VFCLEHAAEI EKQLQPIGGV HMMVLCHPDY PKIESEAKLL  720
AKEQGIGYIW KNVKFREANE EDQERIRAAI EDEQVMPMNS DWTVKLGINL CYTANLSKSP  780
LYSKQMPYNP VIYKAFGRDS TGNSPMKPKA TRRCPGRQKK IVAAGRWCGK VWMSNQVHPY  840
LAHKKETQEQ EQTEGLYSFD TDQNPLIEID IGHSSGLSSK RNSSGSNLAA NNSGKKRKRP  900
SKMAKSKKPL YSSTMADRNS KTDYVSAIPA SPLGRTLRSS HLRHNDSSSQ GKSSLKNESG  960
GPGTHLKKRS SKSEELKNKL ASKKQSTKRK AKNTQTASLA VKGKEEEYTC DIEGCSMSFS  1020
TKQDLALHKR DICPVKGCGK KFFSHKYLVQ HRKVHMDDRP LVCPWKGCKM TFKWPWARTE  1080
HIRVHTGDRP YVCWESGCGQ TFRFVSDFSR HKRKTGHSAK KGRRRSGLDR WVVEAQNIRR  1140
WLGNMTEEEK KRGEAEIQRW LEVGSVEIPP ADVRIVTSGG RRIPVHSTVL ASASPVLESI  1200
LGGPHKGRSR GREIPILGVP CDAVHAFVHS LYFARCVSAT EEEMIGEHGM HLLALSHAYR  1260
VGWLKRAAER ALSLRLTAEG VVDVLVLSQR CDAPRLHLRC MQLLSKDFAA VEQTEAWRFL  1320
QDHDPWLELH ILQFLHHAHL RRRRQARRKA EQRLYAELHE AMDCLRHICA DGCGEVGPSG  1380
RLLPADARPP CPNAVSCRGL RQLIRHFAAC DRQKRQQHGC RRCKRLWQLL RLHASICDEV  1440
DDASCKVPLC IQFKQRMQEK EGELEEDEDE RWRLLVKKVA SARVMSHLAK RQSQVLV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	3e-71	25	442	8	413	Transcription factor jumonji (Jmj) family protein
6ip4_A	3e-71	25	442	8	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}.

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_020106930.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	M0RF75	0.0	M0RF75_MUSAM; Uncharacterized protein
STRING	GSMUA_Achr10P03980_001	0.0	(Musa acuminata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP5346	32	46

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]