LXL04_011333 | RubberDandelionOmics

Gene overview

LXL04_011333

Reference: OH-1004 Chr: Chr02 Coordinates: 162645727-162647744 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1221 bp · LXL04_011333|LXL04_011333|OH1004|cDNA

ATGGCGGGAAAGGGTGGGAAAGGTCTCTTAGCTGGAAAAACAACCGCCGCAGCTGCTGTCGTTGCTAGTAAGGACAAAGATAAGAAGAGGCCAACATCCAGATCTTCTCGAGCTGAACTTCCGCCATACTCAGCCGCCATTCTGGAGTACTTAACTGCTGAAGTGCTTGAGCTGGCAGGAAACGCCAGCAAGGATTTGAAAGTGAAGAGGATCACGCCACGTCACTTACAGCTGGCGATCCGTGGTGACGAAGAGCTTGA...

CDS

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1221 bp · LXL04_011333|LXL04_011333|OH1004|CDS

ATGGCGGGAAAGGGTGGGAAAGGTCTCTTAGCTGGAAAAACAACCGCCGCAGCTGCTGTCGTTGCTAGTAAGGACAAAGATAAGAAGAGGCCAACATCCAGATCTTCTCGAGCTGAACTTCCGCCATACTCAGCCGCCATTCTGGAGTACTTAACTGCTGAAGTGCTTGAGCTGGCAGGAAACGCCAGCAAGGATTTGAAAGTGAAGAGGATCACGCCACGTCACTTACAGCTGGCGATCCGTGGTGACGAAGAGCTTGA...

Protein

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406 aa · LXL04_011333|LXL04_011333|OH1004|PROTEIN

MAGKGGKGLLAGKTTAAAAVVASKDKDKKRPTSRSSRAELPPYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKGLILIIFQLIFLPSMYELRIPILKKEVEHVKGLLSDNEKEWAEKGCSILSDGWRDSVVQKDIINFMVNSPKGSVFVRSVDASNVSKDADLLFRVLDQMVEAVGEENVVQVVTDNASAYVKAGRLLEAKRQHLYWTPCAAHCLDLMLEEIGKEIPKVKIAIKKAMLAIGY...

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	`LXL04_011333`
TK1151 ID	TkA05G087350
OH-1004 ID	LXL04_011333
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	80.500
Protein coverage (%)	TK1151 100.000 / OH-1004 30.788 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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_011333

Location Chr02:162645727-162647744 (-)

Description Similar to Os03g0743400: Probable histone H2A variant 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At3g54560`	Variant histone H2A which may replace conventional H2A in a subset of nucleosomes.	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
`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
`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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011333 · GCA_047496595.1_OSU_TarKok_2.0.

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.

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Gene expression

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

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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.

Nucleus0.798

Rank 1 · LXL04_011333 · OH-1004

Cytoplasm0.165

Rank 2 · LXL04_011333 · OH-1004

Extracellular0.031

Rank 3 · LXL04_011333 · OH-1004

Endoplasmic reticulum0.030

Rank 4 · LXL04_011333 · OH-1004

Cell membrane0.028

Rank 5 · LXL04_011333 · OH-1004

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.

PF00125.31Histone37-82 aa

PF04937.21DUF659104-254 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011333	`PF00125.31`	Histone	37	82	3.7e-08	34.3
LXL04_011333	`PF04937.21`	DUF659	104	254	6.4e-56	188.9

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
`Q9SII0`	Arabidopsis thaliana	Probable histone H2A variant 2	60.504%	Swiss-Prot	weak database homology
`O23628`	Arabidopsis thaliana	Histone H2A variant 1	59.664%	Swiss-Prot	weak database homology
`Q84MP7`	Oryza sativa subsp. japonica	Probable histone H2A variant 3	65.546%	Swiss-Prot	weak database homology
`Q8S857`	Oryza sativa subsp. japonica	Probable histone H2A variant 2	64.706%	Swiss-Prot	weak database homology
`Q8H7Y8`	Oryza sativa subsp. japonica	Probable histone H2A variant 1	63.025%	Swiss-Prot	weak database homology

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