TkA08G136830 | RubberDandelionOmics

Gene overview

TkA08G136830

Reference: TK1151 Chr: Chr08 Coordinates: 35539811-35542927 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2571 bp · TkA08G136830|TK1151|cDNA

TCCATGCTGTTTAGCTGGTTTGCTTGGCATGTCGAAGATCATGACTTCCATAGCTTGAATTATATGCATATGGGAGCTAGCAAGACCTGGTATGGCGTACCCAAGGACGCTGCTGTTGCATTTGAAGATGTAGTCAGAGAACATGGTTATGGTGGTGAGATTAATCCACTTGTAACTTTTGCTACCCTTGCACAGAAGACCACAATCATGTCCCCTGAGGTTCTTCTTAAGGCCGGTGTTCCTTGCTGCAGGTTGGTGCA...

CDS

Download CDS FASTA

2376 bp · TkA08G136830|TK1151|CDS

ATGCTGTTTAGCTGGTTTGCTTGGCATGTCGAAGATCATGACTTCCATAGCTTGAATTATATGCATATGGGAGCTAGCAAGACCTGGTATGGCGTACCCAAGGACGCTGCTGTTGCATTTGAAGATGTAGTCAGAGAACATGGTTATGGTGGTGAGATTAATCCACTTGTAACTTTTGCTACCCTTGCACAGAAGACCACAATCATGTCCCCTGAGGTTCTTCTTAAGGCCGGTGTTCCTTGCTGCAGGTTGGTGCAAAA...

Protein

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791 aa · TkA08G136830|TK1151|PROTEIN

MLFSWFAWHVEDHDFHSLNYMHMGASKTWYGVPKDAAVAFEDVVREHGYGGEINPLVTFATLAQKTTIMSPEVLLKAGVPCCRLVQNAGEFVVTFPRAYHSGFSHGFNCAEATNIATPGWLFVAREASIRRVSMRYAPMVSHSQLLYDLALSLFASEPIPEPRSSRLKDKLRGEGDALVKRLFLQDMMQNNELLHVLGKGFPIVVLSEDDLVSWIPSDLSYKTQSSSSTTSSVGLCTENDEGSSFGRCDSPTQKDMVIEE...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`TkA08G136830`
TK1151 ID	TkA08G136830
OH-1004 ID	LXL04_031920
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	99.900
Protein coverage (%)	TK1151 100.000 / OH-1004 71.584 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA08G136830

Location Chr08:35539811-35542927 (+)

Description Similar to REF6: Lysine-specific demethylase REF6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g48430`	Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3, thus acting as a positive regulator of gene expression.	Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time.2004 · DOI: 10.1105/tpc.104.025353 Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis.2008 · DOI: 10.1073/pnas.0802254105 Arabidopsis REF6 is a histone H3 lysine 27 demethylase.2011 · DOI: 10.1038/ng.854 Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis.2014 · DOI: 10.1038/ncomms5601 Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.2016 · DOI: 10.1038/ng.3555 REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.2016 · DOI: 10.1038/ng.3556 An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis.2019 · DOI: 10.1038/s41422-019-0145-8 DNA methylation repels targeting of Arabidopsis REF6.2019 · DOI: 10.1038/s41467-019-10026-1 Epigenetic silencing of a multifunctional plant stress regulator.2019 · DOI: 10.7554/elife.47835 Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms.2020 · DOI: 10.1038/s41421-020-0150-6 Dehydroabietinal promotes flowering time and plant defense in Arabidopsis via the autonomous pathway genes FLOWERING LOCUS D, FVE, and RELATIVE OF EARLY FLOWERING 6.2020 · DOI: 10.1093/jxb/eraa232 The H3K27me3 Demethylase RELATIVE OF EARLY FLOWERING6 Suppresses Seed Dormancy by Inducing Abscisic Acid Catabolism.2020 · DOI: 10.1104/pp.20.01255 A new role for histone demethylases in the maintenance of plant genome integrity.2020 · DOI: 10.7554/elife.58533
`At5g04240`	Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3, thus acting as a positive regulator of gene expression.	Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time.2004 · DOI: 10.1105/tpc.104.025353 Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis.2008 · DOI: 10.1073/pnas.0802254105 Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis.2009 · DOI: 10.1371/journal.pone.0008033 Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state.2014 · DOI: 10.1038/nature13722 A new role for histone demethylases in the maintenance of plant genome integrity.2020 · DOI: 10.7554/elife.58533
`At5g46910`	Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3 with a specific activity for H3K27me3 and involved in the regulation of gene expression.	The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor.2019 · DOI: 10.1038/s41467-019-09310-x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0907400`	Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3 with a specific activity for H3K27me3 and H3K27me2.	Jumonji C domain protein JMJ705-mediated removal of histone H3 lysine 27 trimethylation is involved in defense-related gene activation in rice.2013 · DOI: 10.1105/tpc.113.118802
`Os03g0151300`	Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3.	Se14, encoding a JmjC domain-containing protein, plays key roles in long-day suppression of rice flowering through the demethylation of H3K4me3 of RFT1.2014 · DOI: 10.1371/journal.pone.0096064

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031920 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006952 defense response Biological Process

GO:0009408 response to heat Biological Process

GO:0009612 response to mechanical stimulus Biological Process

GO:0009627 systemic acquired resistance Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009741 response to brassinosteroid Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

KEGG gene cross-reference

ath:AT3G48430

dosa:Os01g0907400

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.925

Rank 1 · TkA08G136830 · TK1151

Cytoplasm0.128

Rank 2 · TkA08G136830 · TK1151

Cell membrane0.032

Rank 3 · TkA08G136830 · TK1151

Mitochondrion0.019

Rank 4 · TkA08G136830 · TK1151

Endoplasmic reticulum0.016

Rank 5 · TkA08G136830 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF02373JmjC1-114 aa

PF30355zf_C2H2-Disco14-20 aa

PF15909zf-C2H2_897-115 aa

PF13465zf-H2C2_2273-280 aa

PF13894zf-C2H2_4564-572 aa

PF11696DUF3292593-665 aa

PF15912VIR_N599-673 aa

PF08070DTHCT626-674 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G136830	`PF02373`	JmjC	1	114	4.6e-36	124.4
TkA08G136830	`PF30355`	zf_C2H2-Disco	14	20	0.045	14.5
TkA08G136830	`PF15909`	zf-C2H2_8	97	115	2.7	9.1
TkA08G136830	`PF13465`	zf-H2C2_2	273	280	0.0017	19.3
TkA08G136830	`PF13894`	zf-C2H2_4	564	572	2.5	9.8
TkA08G136830	`PF11696`	DUF3292	593	665	5.9	5.9
TkA08G136830	`PF15912`	VIR_N	599	673	0.11	12.7
TkA08G136830	`PF08070`	DTHCT	626	674	0.065	14.7
TkA08G136830	`PF26218`	zf_C2H2_ZNF292	673	698	0.27	11.6
TkA08G136830	`PF17017`	zf-C2H2_aberr	676	699	1.8	9.4
TkA08G136830	`PF30355`	zf_C2H2-Disco	678	694	0.045	14.5
TkA08G136830	`PF24446`	DUF7565	678	708	0.47	11.6
TkA08G136830	`PF00096`	zf-C2H2	680	700	2.7e-07	31.4
TkA08G136830	`PF22110`	TFIIIA_zf-C2H2	680	690	0.067	13.9
TkA08G136830	`PF13894`	zf-C2H2_4	680	701	2.5	9.8
TkA08G136830	`PF15909`	zf-C2H2_8	680	705	2.7	9.1

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9STM3`	Arabidopsis thaliana	sp\|Q9STM3\|REF6_ARATH Lysine-specific demethylase REF6	46.100%	Swiss-Prot	Medium
`Q6BDA0`	Arabidopsis thaliana	sp\|Q6BDA0\|ELF6_ARATH Lysine-specific demethylase ELF6	43.100%	Swiss-Prot	Low
`F4KIX0`	Arabidopsis thaliana	sp\|F4KIX0\|JMJ13_ARATH Lysine-specific demethylase JMJ13	51.200%	Swiss-Prot	Low
`Q5N712`	Oryza sativa subsp. japonica	sp\|Q5N712\|JM705_ORYSJ Lysine-specific demethylase JMJ705	36.400%	Swiss-Prot	Medium
`Q10RP4`	Oryza sativa subsp. japonica	sp\|Q10RP4\|SE14_ORYSJ Probable lysine-specific demethylase SE14	37.300%	Swiss-Prot	Medium

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