TkA07G426920 | RubberDandelionOmics

Gene overview

TkA07G426920

Reference: TK1151 Chr: Chr07 Coordinates: 107952603-107953898 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1155 bp · TkA07G426920|TK1151|cDNA

TCACAATGGTCGAGTCTTCCTCAGTCGGAGGAGCCTCGCTCCCTTCAGGCCCCGATGGGAGAAAACGCCGTGTTACGTACTTCTACGAACCCTCAATCGGCGATTACTATTACGGTCAAGGTCACCCAATGAAACCCCACCGCATCCGCATGGCTCACAACCTCATCGTCCATTACTCCCTTCACCGTCGCATGGAAATCGTCCGCCCGTTTCCCGCTGGTCCAGAAGATATCCGCCGGTTTCACTCCGATGACTATGTC...

CDS

Download CDS FASTA

573 bp · TkA07G426920|TK1151|CDS

ATGGAGACGGAGTCGAAGAAGCTTTCTTCACACACTGACAGAGTAATGACAGTCTCGTTTCACAAATTTGGGGATTTCTTTTCCGGTACAGGACACATCAAAGACATCGGTGCACATCAAGGGAAATACTACGCCCTAAATGTTCCACTAAACGATGGAATGGATGATGACAGCTTCCGTGGTCTATTCAGACCAATTGTTCACAAAGTCATGGAAGTTTACCAGCCAGATGCAGTTGTTCTTCAATGTGGAGCAGATTC...

Protein

Download Protein FASTA

190 aa · TkA07G426920|TK1151|PROTEIN

METESKKLSSHTDRVMTVSFHKFGDFFSGTGHIKDIGAHQGKYYALNVPLNDGMDDDSFRGLFRPIVHKVMEVYQPDAVVLQCGADSLAGDRLGCFNLSVKGHADCLRYLRSFNVPLMVLGGGGIQSAMWPDAGVMRQQLQLVLNLKISFLIMSIMSILDLIILFMLIQVLLTIKIPKRFGENQVRLFSR

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	`TkA07G426920`
TK1151 ID	TkA07G426920
OH-1004 ID	LXL04_030734
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	99.100
Protein coverage (%)	TK1151 59.474 / OH-1004 24.094 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 TkA07G426920

Location Chr07:107952603-107953898 (-)

Description Similar to HDA6: Histone deacetylase 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g63110`	Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).	Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression.2001 · DOI: 10.1105/tpc.13.5.1047 HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA.2002 · DOI: 10.1093/emboj/cdf663 Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats.2004 · DOI: 10.1105/tpc.018754 Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance.2006 · DOI: 10.1101/gad.1417706 HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and regulates flowering in Arabidopsis.2011 · DOI: 10.1104/pp.111.174417 Histone deacetylase HDA6 is functionally associated with AS1 in repression of KNOX genes in arabidopsis.2012 · DOI: 10.1371/journal.pgen.1003114 Regulation of flowering time by the histone deacetylase HDA5 in Arabidopsis.2015 · DOI: 10.1111/tpj.12868 The arabidopsis GyraseB3 contributes to transposon silencing by promoting histone deacetylation.2025 · DOI: 10.1093/nar/gkaf985
`At4g38130`	Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).	Functional analysis of a RPD3 histone deacetylase homologue in Arabidopsis thaliana.2000 · DOI: 10.1023/a:1006498413543 HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis.2005 · DOI: 10.1105/tpc.104.028514 Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro.2006 · DOI: 10.1038/sj.cr.7310059 APETALA2 negatively regulates multiple floral organ identity genes in Arabidopsis by recruiting the co-repressor TOPLESS and the histone deacetylase HDA19.2012 · DOI: 10.1242/dev.085407 The Distinct Roles of Class I and II RPD3-Like Histone Deacetylases in Salinity Stress Response.2017 · DOI: 10.1104/pp.17.01332

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0583400`	Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).	Structure and expression of the rice class-I type histone deacetylase genes OsHDAC1-3: OsHDAC1 overexpression in transgenic plants leads to increased growth rate and altered architecture.2003 · DOI: 10.1046/j.1365-313x.2003.01650.x The histone deacetylase OsHDAC1 epigenetically regulates the OsNAC6 gene that controls seedling root growth in rice.2009 · DOI: 10.1111/j.1365-313x.2009.03908.x MODD Mediates Deactivation and Degradation of OsbZIP46 to Negatively Regulate ABA Signaling and Drought Resistance in Rice.2016 · DOI: 10.1105/tpc.16.00171
`Os02g0215200`	Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030734 · 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:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0001975 response to amphetamine Biological Process

GO:0006325 chromatin organization Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0009294 DNA-mediated transformation Biological Process

GO:0009410 response to xenobiotic stimulus Biological Process

KEGG gene cross-reference

ath:AT4G38130

ath:AT5G63110

dosa:Os06g0583400

gga:373961

osa:4341387

rno:297893

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.

Cytoplasm0.489

Rank 1 · TkA07G426920 · TK1151

Nucleus0.381

Rank 2 · TkA07G426920 · TK1151

Mitochondrion0.132

Rank 3 · TkA07G426920 · TK1151

Endoplasmic reticulum0.088

Rank 4 · TkA07G426920 · TK1151

Peroxisome0.071

Rank 5 · TkA07G426920 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

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

PF00400WD405-29 aa

PF00850Hist_deacetyl9-124 aa

PF00400WD40100-105 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G426920	`PF00400`	WD40	5	29	0.085	14.2
TkA07G426920	`PF00850`	Hist_deacetyl	9	124	1.8e-30	107.0
TkA07G426920	`PF00400`	WD40	100	105	0.085	14.2

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9FML2`	Arabidopsis thaliana	sp\|Q9FML2\|HDA6_ARATH Histone deacetylase 6	87.600%	Swiss-Prot	Medium
`O22446`	Arabidopsis thaliana	sp\|O22446\|HDA19_ARATH Histone deacetylase 19	74.300%	Swiss-Prot	Medium
`Q7Y0Y8`	Oryza sativa subsp. japonica	sp\|Q7Y0Y8\|HDAC1_ORYSJ Histone deacetylase 1	74.300%	Swiss-Prot	Medium
`Q6YV04`	Oryza sativa subsp. japonica	sp\|Q6YV04\|HDAC2_ORYSJ Histone deacetylase 2	73.500%	Swiss-Prot	Medium

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