LXL04_014917 | RubberDandelionOmics

Gene overview

LXL04_014917

Reference: OH-1004 Chr: Chr03 Coordinates: 59604927-59606217 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

960 bp · LXL04_014917|LXL04_014917|OH1004|cDNA

ATGTATATGAGTCAAACTTTGATATGGAACGCGCAATTCGGCCAATCATCAGACTACCTCAATACAACAAAGACAAGACCGACTTTGGAATTCCAAATACGTGCAGACCTTGAAAACCTGGTAGCTGCTATGAAGAAGAATTCAGCTCAAATATCTCAAAAACCATCCCTCACCGATCTCGGCTTTACAGGAAACTTCGTTCAACTAACCGCCTTAGAGCCAAAAGTGGTACTAAAAGCCATACATGACCTGGATTTTGT...

CDS

Download CDS FASTA

960 bp · LXL04_014917|LXL04_014917|OH1004|CDS

ATGTATATGAGTCAAACTTTGATATGGAACGCGCAATTCGGCCAATCATCAGACTACCTCAATACAACAAAGACAAGACCGACTTTGGAATTCCAAATACGTGCAGACCTTGAAAACCTGGTAGCTGCTATGAAGAAGAATTCAGCTCAAATATCTCAAAAACCATCCCTCACCGATCTCGGCTTTACAGGAAACTTCGTTCAACTAACCGCCTTAGAGCCAAAAGTGGTACTAAAAGCCATACATGACCTGGATTTTGT...

Protein

Download Protein FASTA

319 aa · LXL04_014917|LXL04_014917|OH1004|PROTEIN

MYMSQTLIWNAQFGQSSDYLNTTKTRPTLEFQIRADLENLVAAMKKNSAQISQKPSLTDLGFTGNFVQLTALEPKVVLKAIHDLDFVGKVRGQGYYFKIPSRAKCNCSYIEEYDQVLLREKFITRSLDSESTNSKALMTSCILSIVATALKDNVVLTKCEVFYMNTTLFEKQYNSDSVIEDVACLLKCTRGSLSIMASERGTVIGNLVFSKDEQIFDCTKQGSNPKRSEKCDISVNQSILCIASAIFSRLAMDSFYDRST...

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_014917`
TK1151 ID	TkA02G384070
OH-1004 ID	LXL04_014917
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	91.400
Protein coverage (%)	TK1151 98.936 / OH-1004 58.307 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_014917

Location Chr03:59604927-59606217 (-)

Description Similar to TOP6A: DNA topoisomerase 6 subunit A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g02820`	Component of the DNA topoisomerase VI involved in chromatin organization and progression of endoreduplication cycles.	A crucial role for the putative Arabidopsis topoisomerase VI in plant growth and development.2002 · DOI: 10.1073/pnas.152337599 DNA topoisomerase VI is essential for endoreduplication in Arabidopsis.2002 · DOI: 10.1016/s0960-9822(02)01198-3

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0284800`	Component of the DNA topoisomerase VI involved in chromatin organization and progression of endoreduplication cycles.	No verified direct reference in this release
`UniProt: A2XFC1`	Component of the DNA topoisomerase VI involved in chromatin organization and progression of endoreduplication cycles.	No verified direct reference in this release
`Os12g0622500`	Required for meiotic recombination.	OsSpo11-4, a rice homologue of the archaeal TopVIA protein, mediates double-strand DNA cleavage and interacts with OsTopVIB.2011 · DOI: 10.1371/journal.pone.0020327

Functional annotation source

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Functional annotation source: OH1004 · LXL04_014917 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000706 meiotic DNA double-strand break processing Biological Process

GO:0006260 DNA replication Biological Process

GO:0006265 DNA topological change Biological Process

GO:0006302 double-strand break repair Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

GO:0042138 meiotic DNA double-strand break formation Biological Process

GO:0090628 plant epidermal cell fate specification Biological Process

GO:0000228 nuclear chromosome Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005694 chromosome Cellular Component

GO:0009330 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex Cellular Component

GO:0000287 magnesium ion binding Molecular Function

KEGG gene cross-reference

ath:AT5G02820

dosa:Os03g0284800

dosa:Os12g0622500

osa:4332468

pfu:PF1578

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.

Cytoplasm0.438

Rank 1 · LXL04_014917 · OH-1004

Nucleus0.424

Rank 2 · LXL04_014917 · OH-1004

Mitochondrion0.117

Rank 3 · LXL04_014917 · OH-1004

Cell membrane0.053

Rank 4 · LXL04_014917 · OH-1004

Endoplasmic reticulum0.044

Rank 5 · LXL04_014917 · 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.

PF04406.20TP6A_N136-195 aa

PF21180.4TOP6A-Spo11_Toprim259-313 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014917	`PF04406.20`	TP6A_N	136	195	2.3e-14	53.7
LXL04_014917	`PF21180.4`	TOP6A-Spo11_Toprim	259	313	1.1e-07	32.7

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
`Q9LZ03`	Arabidopsis thaliana	DNA topoisomerase 6 subunit A	33.096%	Swiss-Prot	moderate database homology
`Q0DSV9`	Oryza sativa subsp. japonica	Topoisomerase 6 subunit A3	33.452%	Swiss-Prot	moderate database homology
`A2XFC1`	Oryza sativa subsp. indica	DNA topoisomerase 6 subunit A3	33.452%	Swiss-Prot	moderate database homology
`Q2QM00`	Oryza sativa subsp. japonica	Meiotic recombination protein SPO11-4	34.746%	Swiss-Prot	weak database homology

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