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Plant Transcription
Factor Database
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Transcription Factor Information
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Basic
Information? help
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| TF ID |
Bostr.18473s0107.1.p |
| Organism |
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| Taxonomic ID |
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| Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera
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| Family |
C2H2 |
| Protein Properties |
Length: 151aa MW: 17306.1 Da PI: 9.8283 |
| Description |
C2H2 family protein |
| Gene Model |
| Gene Model ID |
Type |
Source |
Coding Sequence |
| Bostr.18473s0107.1.p | genome | JGI | View CDS |
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| Signature Domain? help Back to Top |
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| No. |
Domain |
Score |
E-value |
Start |
End |
HMM Start |
HMM End |
| 1 | zf-C2H2 | 11.3 | 0.001 | 65 | 88 | 2 | 23 |
EET..TTTEEESSHHHHHHHHHHT CS
zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23
kCp C+++F+ + + Hir+H
Bostr.18473s0107.1.p 65 KCPwkGCKMTFKWAWSRTEHIRVH 88
799*******************99 PP
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| 2 | zf-C2H2 | 13.1 | 0.00029 | 96 | 120 | 3 | 23 |
ET..TTTEEESSHHHHHHHHHH..T CS
zf-C2H2 3 Cp..dCgksFsrksnLkrHirt..H 23
C Cg++F+ s++ rH r+ H
Bostr.18473s0107.1.p 96 CAepGCGQTFRFVSDFSRHKRKtgH 120
66669****************9777 PP
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| Sequence ? help Back to Top |
| Protein Sequence Length: 151 aa
Download sequence Send
to blast |
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPRVHSD 60
DRPLKCPWKG CKMTFKWAWS RTEHIRVHTG ARPYLCAEPG CGQTFRFVSD FSRHKRKTGH 120
SVKKTKKKAL CSQSLNIWNS HCCGQILNLL *
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| 3D Structure ? help Back to Top |
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| PDB ID |
Evalue |
Query Start |
Query End |
Hit Start |
Hit End |
Description |
| 6a57_A | 1e-46 | 56 | 128 | 68 | 140 | Lysine-specific demethylase REF6 |
| 6a58_A | 1e-46 | 56 | 128 | 68 | 140 | Lysine-specific demethylase REF6 |
| 6a59_A | 1e-46 | 56 | 128 | 68 | 140 | Lysine-specific demethylase REF6 |
| Search in ModeBase |
| Functional Description ? help
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| 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 --
Nucleotide ? help
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| Source |
Hit ID |
E-value |
Description |
| GenBank | AL049659 | 6e-92 | AL049659.2 Arabidopsis thaliana DNA chromosome 3, BAC clone T29H11. |
| GenBank | AY664499 | 6e-92 | AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds. |
| GenBank | CP002686 | 6e-92 | CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence. |
| 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]
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