TkA04G016780 | RubberDandelionOmics

Gene overview

TkA04G016780

Reference: TK1151 Chr: Chr04 Coordinates: 4180429-4181292 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

786 bp · TkA04G016780|TK1151|cDNA

GGCGGAATTTGTTCGGAGAATCAAGTTGAAGTTTTGGCCGGTAAGGGCGGTAAGGGGCTATTGGCCGGGAAAACACCAGCGACCACAGCTAACAAGGACAAAGATAAGAAGCGACCGACTTCCCGATCTGCTAGAGCTGGCCTCCAGTTTCCGGTAGGGAGAATTCACCGCCATTTAAAAACACGAACCTCTGCAAACGGACGTGTTGGAGCCACCGCCGCCGTCTACTCTGCCGCTATTCTCGAGTACTTAACGGCTGA...

CDS

Download CDS FASTA

444 bp · TkA04G016780|TK1151|CDS

GGCGGAATTTGTTCGGAGAATCAAGTTGAAGTTTTGGCCGGTAAGGGCGGTAAGGGGCTATTGGCCGGGAAAACACCAGCGACCACAGCTAACAAGGACAAAGATAAGAAGCGACCGACTTCCCGATCTGCTAGAGCTGGCCTCCAGTTTCCGGTAGGGAGAATTCACCGCCATTTAAAAACACGAACCTCTGCAAACGGACGTGTTGGAGCCACCGCCGCCGTCTACTCTGCCGCTATTCTCGAGTACTTAACGGCTGA...

Protein

Download Protein FASTA

147 aa · TkA04G016780|TK1151|PROTEIN

GGICSENQVEVLAGKGGKGLLAGKTPATTANKDKDKKRPTSRSARAGLQFPVGRIHRHLKTRTSANGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKGTIAGGGVIPHIHKSLINKTTKE

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	`TkA04G016780`
TK1151 ID	TkA04G016780
OH-1004 ID	LXL04_036930
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.300
Protein coverage (%)	TK1151 92.517 / 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 TkA04G016780

Location Chr04:4180429-4181292 (-)

Description Similar to Os03g0743400: Probable histone H2A variant 3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g54560`	Variant histone H2A which may replace conventional H2A in a subset of nucleosomes.	No verified direct reference in this release
`At2g38810`	Variant histones H2A are synthesized throughout the cell cycle and are very different from classical S-phase regulated H2A.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0743400`	Variant histones H2A are synthesized throughout the cell cycle and are very different from classical S-phase regulated H2A.	No verified direct reference in this release
`Os03g0162200`	Variant histones H2A are synthesized throughout the cell cycle and are very different from classical S-phase regulated H2A.	No verified direct reference in this release
`Os10g0418000`	Variant histones H2A are synthesized throughout the cell cycle and are very different from classical S-phase regulated H2A.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_036930 · 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:0006970 response to osmotic stress Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0016048 detection of temperature stimulus Biological Process

GO:0031507 heterochromatin formation Biological Process

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

GO:0000786 nucleosome 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:AT2G38810

ath:AT3G54560

dosa:Os03g0162200

dosa:Os03g0743400

dosa:Os10g0418000

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.

Nucleus0.963

Rank 1 · TkA04G016780 · TK1151

Cytoplasm0.080

Rank 2 · TkA04G016780 · TK1151

Cell membrane0.014

Rank 3 · TkA04G016780 · TK1151

Mitochondrion0.009

Rank 4 · TkA04G016780 · TK1151

Extracellular0.008

Rank 5 · TkA04G016780 · 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.

PF00125Histone31-115 aa

PF26281Histone_ABTB38-76 aa

PF00808CBFD_NFYB_HMF49-113 aa

PF16211Histone_H2A_C117-146 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G016780	`PF00125`	Histone	31	115	8.1e-20	71.7
TkA04G016780	`PF26281`	Histone_ABTB	38	76	0.00017	22.0
TkA04G016780	`PF00808`	CBFD_NFYB_HMF	49	113	0.034	15.2
TkA04G016780	`PF16211`	Histone_H2A_C	117	146	4.7e-11	42.9

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
`O23628`	Arabidopsis thaliana	sp\|O23628\|H2AV1_ARATH Histone H2A variant 1	86.800%	Swiss-Prot	High
`Q9SII0`	Arabidopsis thaliana	sp\|Q9SII0\|H2AV2_ARATH Probable histone H2A variant 2	84.600%	Swiss-Prot	High
`Q84MP7`	Oryza sativa subsp. japonica	sp\|Q84MP7\|H2AV3_ORYSJ Probable histone H2A variant 3	88.300%	Swiss-Prot	High
`Q8H7Y8`	Oryza sativa subsp. japonica	sp\|Q8H7Y8\|H2AV1_ORYSJ Probable histone H2A variant 1	88.400%	Swiss-Prot	High
`Q8S857`	Oryza sativa subsp. japonica	sp\|Q8S857\|H2AV2_ORYSJ Probable histone H2A variant 2	86.300%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card