LXL04_032092 | RubberDandelionOmics

Gene overview

LXL04_032092

Reference: OH-1004 Chr: Chr07 Coordinates: 16674137-16674889 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

420 bp · LXL04_032092|LXL04_032092|OH1004|cDNA

ATGTCGGGAAAAGGAGCAAAAGGTCTGATAATGGGGAAATCCTCCTCTTCCGTGAATGGATCAAGCAGCAAAGATAAAGACAAGAAGAAATCCGTCACCCGCTCTTCGCGCGCCGGTCTCCAGTTTCCTGTGGGTAGAGTTCATCGTCTTTTGAAGATGAGAGCTATGTCTAACGGAAGAGTTGGAGCAACTGCCGCAGTCTACACAGCAGCTATTCTAGAGTATCTCACAGCTGAAGTTCTCGAGTTAGCTGGAAACGC...

CDS

Download CDS FASTA

420 bp · LXL04_032092|LXL04_032092|OH1004|CDS

ATGTCGGGAAAAGGAGCAAAAGGTCTGATAATGGGGAAATCCTCCTCTTCCGTGAATGGATCAAGCAGCAAAGATAAAGACAAGAAGAAATCCGTCACCCGCTCTTCGCGCGCCGGTCTCCAGTTTCCTGTGGGTAGAGTTCATCGTCTTTTGAAGATGAGAGCTATGTCTAACGGAAGAGTTGGAGCAACTGCCGCAGTCTACACAGCAGCTATTCTAGAGTATCTCACAGCTGAAGTTCTCGAGTTAGCTGGAAACGC...

Protein

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139 aa · LXL04_032092|LXL04_032092|OH1004|PROTEIN

MSGKGAKGLIMGKSSSSVNGSSSKDKDKKKSVTRSSRAGLQFPVGRVHRLLKMRAMSNGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKGTIAGGGVIPHIHKSLINKSSKE

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_032092`
TK1151 ID	TkA08G149830
OH-1004 ID	LXL04_032092
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / 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	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_032092

Location Chr07:16674137-16674889 (+)

Description Similar to At1g52740: Probable histone H2A variant 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g52740`	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
`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

Functional annotation source

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Functional annotation source: OH1004 · LXL04_032092 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006970 response to osmotic stress Biological Process

GO:0009266 response to temperature stimulus 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:0000325 plant-type vacuole Cellular Component

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

KEGG gene cross-reference

ath:AT1G52740

ath:AT2G38810

ath:AT3G54560

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.

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.

Nucleus0.975

Rank 1 · LXL04_032092 · OH-1004

Cytoplasm0.072

Rank 2 · LXL04_032092 · OH-1004

Cell membrane0.014

Rank 3 · LXL04_032092 · OH-1004

Endoplasmic reticulum0.008

Rank 4 · LXL04_032092 · OH-1004

Extracellular0.006

Rank 5 · LXL04_032092 · 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.

PF00125.31Histone22-107 aa

PF16211.11Histone_H2A_C109-138 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032092	`PF00125.31`	Histone	22	107	7.4e-19	68.6
LXL04_032092	`PF16211.11`	Histone_H2A_C	109	138	1.7e-10	41.1

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
`Q9C944`	Arabidopsis thaliana	Probable histone H2A variant 3	87.770%	Swiss-Prot	strong database homology
`Q9SII0`	Arabidopsis thaliana	Probable histone H2A variant 2	76.978%	Swiss-Prot	strong database homology
`O23628`	Arabidopsis thaliana	Histone H2A variant 1	78.417%	Swiss-Prot	strong database homology
`Q84MP7`	Oryza sativa subsp. japonica	Probable histone H2A variant 3	81.295%	Swiss-Prot	strong database homology
`Q8S857`	Oryza sativa subsp. japonica	Probable histone H2A variant 2	77.698%	Swiss-Prot	strong database homology

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