LXL04_016397 | RubberDandelionOmics

Gene overview

LXL04_016397

Reference: OH-1004 Chr: Chr03 Coordinates: 121244926-121245447 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

399 bp · LXL04_016397|LXL04_016397|OH1004|cDNA

ATGGCCGGACGAGGGAAAACCATAGGATCTGCTGCGGCTAAGAAGGCTACATCAAGAAGTAGCAAAGCCGGCCTTCAATTTCCCGTTGGTCGTATCGCTCGTTTCCTCAAAGCCGGAAAGTATGCAGAGCGTGTCGGTGCCGGAGCTCCTGTCTATCTCGCTGCCGTTCTTGAATATCTAGCCGCCGAGGTTCTCGAATTAGCTGGAAATGCAGCAAGGGACAACAAGAAAACCAGAATCGTCCCAAGGCACATCCAATT...

CDS

Download CDS FASTA

399 bp · LXL04_016397|LXL04_016397|OH1004|CDS

ATGGCCGGACGAGGGAAAACCATAGGATCTGCTGCGGCTAAGAAGGCTACATCAAGAAGTAGCAAAGCCGGCCTTCAATTTCCCGTTGGTCGTATCGCTCGTTTCCTCAAAGCCGGAAAGTATGCAGAGCGTGTCGGTGCCGGAGCTCCTGTCTATCTCGCTGCCGTTCTTGAATATCTAGCCGCCGAGGTTCTCGAATTAGCTGGAAATGCAGCAAGGGACAACAAGAAAACCAGAATCGTCCCAAGGCACATCCAATT...

Protein

Download Protein FASTA

132 aa · LXL04_016397|LXL04_016397|OH1004|PROTEIN

MAGRGKTIGSAAAKKATSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHNLLLPKKVGGSKPSADDE

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_016397`
TK1151 ID	TkA02G146960
OH-1004 ID	LXL04_016397
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
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_016397

Location Chr03:121244926-121245447 (-)

Description Similar to At1g51060: Probable histone H2A.1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g51060`	Core component of nucleosome.	No verified direct reference in this release
`At4g27230`	Core component of nucleosome.	No verified direct reference in this release
`At5g54640`	Core component of nucleosome.	An Arabidopsis histone H2A mutant is deficient in Agrobacterium T-DNA integration.2000 · DOI: 10.1073/pnas.97.2.948 Expression of the Arabidopsis histone H2A-1 gene correlates with susceptibility to Agrobacterium transformation.2002 · DOI: 10.1046/j.1365-313x.2002.01425.x
`At3g20670`	Core component of nucleosome.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016397 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009294 DNA-mediated transformation Biological Process

GO:0009611 response to wounding Biological Process

GO:0009617 response to bacterium Biological Process

GO:0031507 heterochromatin formation Biological Process

GO:0000786 nucleosome Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0009536 plastid Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0030527 structural constituent of chromatin Molecular Function

KEGG gene cross-reference

ath:AT1G51060

ath:AT3G20670

ath:AT4G27230

ath:AT5G54640

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.

Nucleus0.971

Rank 1 · LXL04_016397 · OH-1004

Cytoplasm0.077

Rank 2 · LXL04_016397 · OH-1004

Extracellular0.013

Rank 3 · LXL04_016397 · OH-1004

Cell membrane0.013

Rank 4 · LXL04_016397 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_016397 · 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.

PF00125.31Histone12-90 aa

PF16211.11Histone_H2A_C93-126 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016397	`PF00125.31`	Histone	12	90	2.4e-14	54.2
LXL04_016397	`PF16211.11`	Histone_H2A_C	93	126	4.3e-18	65.5

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
`Q9C681`	Arabidopsis thaliana	Probable histone H2A.1	93.182%	Swiss-Prot	strong database homology
`O81826`	Arabidopsis thaliana	Probable histone H2A.3	93.130%	Swiss-Prot	strong database homology
`Q9LD28`	Arabidopsis thaliana	Histone H2A.6	94.615%	Swiss-Prot	strong database homology
`Q9LHQ5`	Arabidopsis thaliana	Probable histone H2A.2	91.667%	Swiss-Prot	strong database homology

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