TkA04G010460 | RubberDandelionOmics

Gene overview

TkA04G010460

Reference: TK1151 Chr: Chr04 Coordinates: 2503122-2503968 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

755 bp · TkA04G010460|TK1151|cDNA

CAATCAGAGCCTACTTTTCCATTTCGCCTACAGAATCTCCACTATAAAGAAACCAGTTTCCCTCTTTGGATTCAATTATCATCCCTCCCATTTACAAATTACAAATCAACAAACCCTCGAAACCGCCATTCTAATTTCTACAAAGCAATGGAATCACCAAAAGCGAATAAATCCGCCGCAGGAAGAGGCAAATCCACATCCACGAAGTCCGTCTCCCGATCTTCGAAAGCCGGTCTCCAGTTCCCCGTCGGCAGAATCTC...

CDS

Download CDS FASTA

573 bp · TkA04G010460|TK1151|CDS

CAATCAGAGCCTACTTTTCCATTTCGCCTACAGAATCTCCACTATAAAGAAACCAGTTTCCCTCTTTGGATTCAATTATCATCCCTCCCATTTACAAATTACAAATCAACAAACCCTCGAAACCGCCATTCTAATTTCTACAAAGCAATGGAATCACCAAAAGCGAATAAATCCGCCGCAGGAAGAGGCAAATCCACATCCACGAAGTCCGTCTCCCGATCTTCGAAAGCCGGTCTCCAGTTCCCCGTCGGCAGAATCTC...

Protein

Download Protein FASTA

190 aa · TkA04G010460|TK1151|PROTEIN

QSEPTFPFRLQNLHYKETSFPLWIQLSSLPFTNYKSTNPRNRHSNFYKAMESPKANKSAAGRGKSTSTKSVSRSSKAGLQFPVGRISRYLKNGRYAKRVGSGSPVYLSAVLEYLAAEVLELAGNAARDNKKTRIIPRHIQLAVRNDEELSKLLGRVTIANGGVLPNIHQTLLPNKKTKGKDVIGSVSQEF

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	`TkA04G010460`
TK1151 ID	TkA04G010460
OH-1004 ID	LXL04_037017
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 74.211 / OH-1004 100.000 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA04G010460

Location Chr04:2503122-2503968 (-)

Description Similar to At1g08880: Probable histone H2AXa

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g08880`	Variant histone H2A which replaces conventional H2A in a subset of nucleosomes.	No verified direct reference in this release
`At1g54690`	Variant histone H2A which replaces conventional H2A in a subset of nucleosomes.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2XLI0`	Variant histone H2A which replaces conventional H2A in a subset of nucleosomes.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_037017 · 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:0031507 heterochromatin formation Biological Process

GO:0000786 nucleosome Cellular Component

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0030527 structural constituent of chromatin Molecular Function

GO:0046982 protein heterodimerization activity Molecular Function

KEGG gene cross-reference

ath:AT1G08880

ath:AT1G54690

cam:101514555

dosa:Os12g0530000

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

Open Annotation Module

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.

Nucleus0.964

Rank 1 · TkA04G010460 · TK1151

Cytoplasm0.093

Rank 2 · TkA04G010460 · TK1151

Cell membrane0.018

Rank 3 · TkA04G010460 · TK1151

Endoplasmic reticulum0.012

Rank 4 · TkA04G010460 · TK1151

Mitochondrion0.007

Rank 5 · TkA04G010460 · 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.

PF00125Histone66-144 aa

PF26281Histone_ABTB68-108 aa

PF00808CBFD_NFYB_HMF80-143 aa

PF22703Cdc6_lid115-142 aa

PF16211Histone_H2A_C147-180 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G010460	`PF00125`	Histone	66	144	1.1e-13	52.0
TkA04G010460	`PF26281`	Histone_ABTB	68	108	0.00038	20.8
TkA04G010460	`PF00808`	CBFD_NFYB_HMF	80	143	0.002	19.1
TkA04G010460	`PF22703`	Cdc6_lid	115	142	0.18	12.4
TkA04G010460	`PF16211`	Histone_H2A_C	147	180	1.8e-18	66.7

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
`O04848`	Arabidopsis thaliana	sp\|O04848\|H2AXA_ARATH Probable histone H2AXa	85.400%	Swiss-Prot	Medium
`Q9S9K7`	Arabidopsis thaliana	sp\|Q9S9K7\|H2AXB_ARATH Probable histone H2AXb	85.400%	Swiss-Prot	Medium
`A2XLI0`	Oryza sativa subsp. indica	sp\|A2XLI0\|H2AXA_ORYSI Probable histone H2AXa	82.300%	Swiss-Prot	Medium

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