TkA01G323060 | RubberDandelionOmics

Gene overview

TkA01G323060

Reference: TK1151 Chr: Chr01 Coordinates: 80369608-80371011 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

870 bp · TkA01G323060|TK1151|cDNA

ATGCATTCAGGTGTTGAAGTTAAACCTGGTGTACCACTTAAGGTCACACCTGAATCTGGAAGACTGATTCATATCTCCCAGGCGGCACTAGGTGAGGTGAAGGATGCAAAGTCTGCGAAGAATGTTCCTCTTCGGTTGAAGATCGACAATAAGAATTTCATCATTGGATCTCTTGCAGCTGAAGATAGGACTCAAATAATGTTTGATTTGGTATTCGAGAGGGAGTTTGAACTCTCCCATGACTGCAAGAATGGCAGTGT...

CDS

Download CDS FASTA

870 bp · TkA01G323060|TK1151|CDS

ATGCATTCAGGTGTTGAAGTTAAACCTGGTGTACCACTTAAGGTCACACCTGAATCTGGAAGACTGATTCATATCTCCCAGGCGGCACTAGGTGAGGTGAAGGATGCAAAGTCTGCGAAGAATGTTCCTCTTCGGTTGAAGATCGACAATAAGAATTTCATCATTGGATCTCTTGCAGCTGAAGATAGGACTCAAATAATGTTTGATTTGGTATTCGAGAGGGAGTTTGAACTCTCCCATGACTGCAAGAATGGCAGTGT...

Protein

Download Protein FASTA

289 aa · TkA01G323060|TK1151|PROTEIN

MHSGVEVKPGVPLKVTPESGRLIHISQAALGEVKDAKSAKNVPLRLKIDNKNFIIGSLAAEDRTQIMFDLVFEREFELSHDCKNGSVYFIGYLADEPVSVYGEEFSDFDDVSEDELVAAEENGKIVPKSKDVKAAKGILAAAAAAANGKSKAGKKKEEQPESDDDDDESDSDEEMALDGLQGDDSSDASGDDSEDDDDDLSEEEELPKVQESKKRGAESAQKTPASKKAKSATPDKSGKKAHTATPIPSKASAGSKSKEQ...

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	`TkA01G323060`
TK1151 ID	TkA01G323060
OH-1004 ID	LXL04_009348
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	48.400
Protein coverage (%)	TK1151 43.599 / OH-1004 47.200 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G323060

Location Chr01:80369608-80371011 (-)

Description Similar to HDT1: Histone deacetylase HDT1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g44750`	Probably mediates the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).	Functional analysis of HD2 histone deacetylase homologues in Arabidopsis thaliana.2000 · DOI: 10.1046/j.1365-313x.2000.00711.x Repression of gene expression by Arabidopsis HD2 histone deacetylases.2003 · DOI: 10.1046/j.1365-313x.2003.01714.x Expression and function of HD2-type histone deacetylases in Arabidopsis development.2004 · DOI: 10.1111/j.1365-313x.2004.02083.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009348 · 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:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009294 DNA-mediated transformation Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009944 polarity specification of adaxial/abaxial axis Biological Process

GO:0010162 seed dormancy process Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0048364 root development Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT3G44750

ath:AT5G03740

gmx:547649

zma:542636

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.

Nucleus0.954

Rank 1 · TkA01G323060 · TK1151

Cytoplasm0.136

Rank 2 · TkA01G323060 · TK1151

Cell membrane0.021

Rank 3 · TkA01G323060 · TK1151

Endoplasmic reticulum0.014

Rank 4 · TkA01G323060 · TK1151

Mitochondrion0.014

Rank 5 · TkA01G323060 · 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.

PF17800NPL4-93 aa

PF05764YL1107-155 aa

PF04889Cwf_Cwc_15115-230 aa

PF04147Nop14133-235 aa

PF30191LAG2_N145-211 aa

PF06524NOA36149-212 aa

PF14996RMP149-172 aa

PF02724CDC45150-236 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G323060	`PF17800`	NPL	4	93	1.6e-14	55.1
TkA01G323060	`PF05764`	YL1	107	155	3.1	8.6
TkA01G323060	`PF04889`	Cwf_Cwc_15	115	230	0.0016	19.0
TkA01G323060	`PF04147`	Nop14	133	235	1.8	7.4
TkA01G323060	`PF30191`	LAG2_N	145	211	0.23	11.2
TkA01G323060	`PF06524`	NOA36	149	212	1.0	9.4
TkA01G323060	`PF14996`	RMP	149	172	9.0	7.2
TkA01G323060	`PF02724`	CDC45	150	236	0.46	9.4
TkA01G323060	`PF25695`	BKRF4	151	258	0.057	14.2
TkA01G323060	`PF05764`	YL1	162	260	3.1	8.6
TkA01G323060	`PF14996`	RMP	202	278	9.0	7.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FVE6`	Arabidopsis thaliana	sp\|Q9FVE6\|HDT1_ARATH Histone deacetylase HDT1	55.100%	Swiss-Prot	Low

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