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

C.cajan_31616

Common Name

KK1_031773

Organism

Cajanus cajan

Taxonomic ID

3821

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Cajanus

Family

C2H2

Protein Properties

Length: 1308aa MW: 146769 Da PI: 8.3797

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
C.cajan_31616	genome	IIPG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12	0.00065	1192	1217	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L +H r+ + C.cajan_31616 1192 YQCDidGCTMSFGSKQELLHHKRNiC 1217 99********************9877 PP
2	zf-C2H2	13.1	0.00029	1217	1239	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H C.cajan_31616 1217 CPvkGCGKKFFSHKYLVQHRRVH 1239 9999*****************99 PP
3	zf-C2H2	12	0.00063	1275	1301	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H C.cajan_31616 1275 YVCAepGCGQTFRFVSDFSRHKRKtgH 1301 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	4.4E-16	17	58	IPR003349	JmjN domain
PROSITE profile	PS51183	14.534	18	59	IPR003349	JmjN domain
Pfam	PF02375	4.3E-14	19	52	IPR003349	JmjN domain
PROSITE profile	PS51184	33.68	181	357	IPR003347	JmjC domain
SuperFamily	SSF51197	1.48E-26	185	374	No hit	No description
SMART	SM00558	8.5E-49	188	357	IPR003347	JmjC domain
Pfam	PF02373	1.8E-35	221	340	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	6.7E-4	1181	1214	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	6.9	1192	1214	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1215	1239	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.944	1215	1244	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.4E-6	1216	1243	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.47E-6	1216	1248	No hit	No description
PROSITE pattern	PS00028	0	1217	1239	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	7.2E-10	1244	1269	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1245	1269	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.614	1245	1274	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1247	1269	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.02E-10	1255	1299	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.7E-10	1270	1298	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.62	1275	1301	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.468	1275	1306	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1277	1301	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:0040010	Biological Process	positive regulation of growth rate
GO:0045815	Biological Process	positive regulation of gene expression, epigenetic
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
GO:0071558	Molecular Function	histone demethylase activity (H3-K27 specific)

Sequence ? help Back to Top
Protein Sequence Length: 1308 aa Download sequence Send to blast
MGGASEDVLP WLKSLPVAPE YRPTVAEFQD PIAYIFKIEK EASKYGICKI IPPFPPSPKK 60 TAIANLNHSL AAVAGSTFTT RQQQIGFCPR RPRPVQRPVW QSGDHYTFHQ FESKAKSFEK 120 TYLKRHAKKG SGSASASASG SGLGLSPLET ETLFWKATLD KPFSVEYAND MPGSAFSPKC 180 RDAGDPSSLA DTPWNMRAVS RANGSLLRFM KEEIPGVTSP MVYVAMLFSW FAWHVEDHDL 240 HSLNYLHMGA GKTWYGVPRD AAVAFEEVVR VHGYGGEINP LVTFAILGEK TTVMSPEVFI 300 SAGVPCCRLV QNAGEFVVTF PRAYHTGFSH GFNCGEAANI ATPEWLRVAK DAAIRRASLN 360 YPPMVSHFQL LYDLALALCS RIPAGISAEP RSSRLKDKKK GEGETVIKEL FVQDVLQNND 420 LLHILGKGSP VVFLPRSSVD ISVCSKLRVG SQQSINVSNS EGMHSSKDNS KPIQRDNERE 480 TSQGEGLSDQ RLFSCVTCGI LSFSCVAIVQ PREPAARYLM SADCSFFNDW VVGSGVSSNK 540 FTIAHDRATI PEPNMYTGRM DEKDVPVQSS REALNTKSEN GNTALALLAS AYGNSSDSEE 600 DQIAIDDHSL KKQDYNITSG VTFENSRTVP NSTSNCSQDA HDAERSLSNK PMIPFDNKNA 660 SMVLQSDEDS SRMHVFCLEH AIEAEQQLRP IGGAHILLLC HPVMSVYVAK YKEIIFSSLM 720 ERLSNFDKNY PKIEAEAKLV AEDLGIDYMW KDTAYRHASK EDEETIQSAL DSEEAIPGNG 780 DWAVKLGINL FYSANLCRSP LYSKQMPYNS VIYYAFGCSS PASSPVEPKV YQRRVNKQKK 840 VVAGKWCGKV WMSNQVHPLL AKRDSEDVED EKLILGWILS DEKIERSEST PKSETTSRKS 900 GDYSPPYHHR KPISKRTNCT ESDAVSDDSL DDDDDYMQHR RNVNVEKAKF IDNDVVSNDS 960 VDCDSDWQQR AELSSKQVED TERDDISEDS LDVVSLQLQR KTSKGKHAKY ISEEDIISDD 1020 QMESHFQKRQ RRIPKSRQGR YITGKDITSD DQLELKVQKQ QRRNPKSRQA KYLNGEDIAS 1080 DDQLEGHFLK NQASRPLKRG SRILMKSKTP QQTKQSSHLR NKQSSNSQEF SLHMEEEEEG 1140 GPSTRLRKRA TKGQESEGKL KGKQTKRKKV KNATAAKVSV GHAKMKDGEP EYQCDIDGCT 1200 MSFGSKQELL HHKRNICPVK GCGKKFFSHK YLVQHRRVHE DERPLKCPWK GCKMTFKWAW 1260 ARTEHIRVHT GERPYVCAEP GCGQTFRFVS DFSRHKRKTG HSAKKSRQ

Sequence ? help Back to Top

Protein Sequence Length: 1308 aa Download sequence Send to blast

MGGASEDVLP WLKSLPVAPE YRPTVAEFQD PIAYIFKIEK EASKYGICKI IPPFPPSPKK  60
TAIANLNHSL AAVAGSTFTT RQQQIGFCPR RPRPVQRPVW QSGDHYTFHQ FESKAKSFEK  120
TYLKRHAKKG SGSASASASG SGLGLSPLET ETLFWKATLD KPFSVEYAND MPGSAFSPKC  180
RDAGDPSSLA DTPWNMRAVS RANGSLLRFM KEEIPGVTSP MVYVAMLFSW FAWHVEDHDL  240
HSLNYLHMGA GKTWYGVPRD AAVAFEEVVR VHGYGGEINP LVTFAILGEK TTVMSPEVFI  300
SAGVPCCRLV QNAGEFVVTF PRAYHTGFSH GFNCGEAANI ATPEWLRVAK DAAIRRASLN  360
YPPMVSHFQL LYDLALALCS RIPAGISAEP RSSRLKDKKK GEGETVIKEL FVQDVLQNND  420
LLHILGKGSP VVFLPRSSVD ISVCSKLRVG SQQSINVSNS EGMHSSKDNS KPIQRDNERE  480
TSQGEGLSDQ RLFSCVTCGI LSFSCVAIVQ PREPAARYLM SADCSFFNDW VVGSGVSSNK  540
FTIAHDRATI PEPNMYTGRM DEKDVPVQSS REALNTKSEN GNTALALLAS AYGNSSDSEE  600
DQIAIDDHSL KKQDYNITSG VTFENSRTVP NSTSNCSQDA HDAERSLSNK PMIPFDNKNA  660
SMVLQSDEDS SRMHVFCLEH AIEAEQQLRP IGGAHILLLC HPVMSVYVAK YKEIIFSSLM  720
ERLSNFDKNY PKIEAEAKLV AEDLGIDYMW KDTAYRHASK EDEETIQSAL DSEEAIPGNG  780
DWAVKLGINL FYSANLCRSP LYSKQMPYNS VIYYAFGCSS PASSPVEPKV YQRRVNKQKK  840
VVAGKWCGKV WMSNQVHPLL AKRDSEDVED EKLILGWILS DEKIERSEST PKSETTSRKS  900
GDYSPPYHHR KPISKRTNCT ESDAVSDDSL DDDDDYMQHR RNVNVEKAKF IDNDVVSNDS  960
VDCDSDWQQR AELSSKQVED TERDDISEDS LDVVSLQLQR KTSKGKHAKY ISEEDIISDD  1020
QMESHFQKRQ RRIPKSRQGR YITGKDITSD DQLELKVQKQ QRRNPKSRQA KYLNGEDIAS  1080
DDQLEGHFLK NQASRPLKRG SRILMKSKTP QQTKQSSHLR NKQSSNSQEF SLHMEEEEEG  1140
GPSTRLRKRA TKGQESEGKL KGKQTKRKKV KNATAAKVSV GHAKMKDGEP EYQCDIDGCT  1200
MSFGSKQELL HHKRNICPVK GCGKKFFSHK YLVQHRRVHE DERPLKCPWK GCKMTFKWAW  1260
ARTEHIRVHT GERPYVCAEP GCGQTFRFVS DFSRHKRKTG HSAKKSRQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	2e-79	7	378	4	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	2e-79	7	378	4	353	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1146	1168	RKRATKGQESEGKLKGKQTKRKK

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	C.cajan_31616

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC235340	0.0	AC235340.1 Glycine max strain Williams 82 clone GM_WBb0086A04, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_007137965.1	0.0	hypothetical protein PHAVU_009G169700g
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A151RVM6	0.0	A0A151RVM6_CAJCA; Jumonji/ARID domain-containing protein 2
STRING	XP_007137965.1	0.0	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF5648	32	50

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]