LXL04_036930 | RubberDandelionOmics

Gene overview

LXL04_036930

Reference: OH-1004 Chr: Chr08 Coordinates: 50261759-50262283 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

447 bp · LXL04_036930|LXL04_036930|OH1004|cDNA

CGTTTGTTTGATTATATGTAAATACAGGTCGAAAAAATGGCCGGAAAGGGCGGTAAGGGGCTATTGGCCGGGAAAACACCAGCGACCACAGCTAACAAGGACAAAGATAAGAAGCGACCGACTTCCCGATCTGCTAGAGCTGGCCTCCAGTTTCCGGTAGGGAGAATTCACCGCCATTTAAAAACACGAACCTCTGCAAACGGACGTGTTGGAGCCACCGCCGCCGTCTACTCTGCCGCTATTCTCGAGTACTTAACGGC...

CDS

Download CDS FASTA

411 bp · LXL04_036930|LXL04_036930|OH1004|CDS

ATGGCCGGAAAGGGCGGTAAGGGGCTATTGGCCGGGAAAACACCAGCGACCACAGCTAACAAGGACAAAGATAAGAAGCGACCGACTTCCCGATCTGCTAGAGCTGGCCTCCAGTTTCCGGTAGGGAGAATTCACCGCCATTTAAAAACACGAACCTCTGCAAACGGACGTGTTGGAGCCACCGCCGCCGTCTACTCTGCCGCTATTCTCGAGTACTTAACGGCTGAAGTTCTCGAGCTAGCCGGAAACGCAAGTAAAGA...

Protein

Download Protein FASTA

136 aa · LXL04_036930|LXL04_036930|OH1004|PROTEIN

MAGKGGKGLLAGKTPATTANKDKDKKRPTSRSARAGLQFPVGRIHRHLKTRTSANGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKGTIAGGGVIPHIHKSLINKTTKE

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_036930`
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_036930

Location Chr08:50261759-50262283 (+)

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
`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.

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.

Nucleus0.968

Rank 1 · LXL04_036930 · OH-1004

Cytoplasm0.068

Rank 2 · LXL04_036930 · OH-1004

Cell membrane0.012

Rank 3 · LXL04_036930 · OH-1004

Extracellular0.012

Rank 4 · LXL04_036930 · OH-1004

Endoplasmic reticulum0.007

Rank 5 · LXL04_036930 · OH-1004

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.

PF00125.31Histone20-104 aa

PF16211.11Histone_H2A_C106-135 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036930	`PF00125.31`	Histone	20	104	6.6e-20	72.0
LXL04_036930	`PF16211.11`	Histone_H2A_C	106	135	4.1e-11	43.1

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
`O23628`	Arabidopsis thaliana	Histone H2A variant 1	88.971%	Swiss-Prot	strong database homology
`Q9SII0`	Arabidopsis thaliana	Probable histone H2A variant 2	85.294%	Swiss-Prot	strong database homology
`Q84MP7`	Oryza sativa subsp. japonica	Probable histone H2A variant 3	88.321%	Swiss-Prot	strong database homology
`Q8H7Y8`	Oryza sativa subsp. japonica	Probable histone H2A variant 1	84.783%	Swiss-Prot	strong database homology
`Q8S857`	Oryza sativa subsp. japonica	Probable histone H2A variant 2	87.050%	Swiss-Prot	strong database homology

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