LXL04_005516 | RubberDandelionOmics

Gene overview

LXL04_005516

Reference: OH-1004 Chr: Chr01 Coordinates: 166391807-166394461 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1146 bp · LXL04_005516|LXL04_005516|OH1004|cDNA

ATGGAGGACGTGCGCAGATCCACCATCTTCTTCACCGAGCAACACCTATCCTACGCCGATATCCTTACACCTCTTGAGGTCCGAGCTAGAATCGAAATAGCAGTCCTGAATTTCCTCAAGGATTTGAACTCTCCAACTCCAGCCATCTCAAACCTCCCTATGATCAACCGTAAATCAAGTAACAGCCGAGTGAATCAGAGTCTATTAACTGACGTTTCGTGGATCTTCCTGTCACGTTCATTCTGCACAAAATCATTGAC...

CDS

Download CDS FASTA

1146 bp · LXL04_005516|LXL04_005516|OH1004|CDS

ATGGAGGACGTGCGCAGATCCACCATCTTCTTCACCGAGCAACACCTATCCTACGCCGATATCCTTACACCTCTTGAGGTCCGAGCTAGAATCGAAATAGCAGTCCTGAATTTCCTCAAGGATTTGAACTCTCCAACTCCAGCCATCTCAAACCTCCCTATGATCAACCGTAAATCAAGTAACAGCCGAGTGAATCAGAGTCTATTAACTGACGTTTCGTGGATCTTCCTGTCACGTTCATTCTGCACAAAATCATTGAC...

Protein

Download Protein FASTA

381 aa · LXL04_005516|LXL04_005516|OH1004|PROTEIN

MEDVRRSTIFFTEQHLSYADILTPLEVRARIEIAVLNFLKDLNSPTPAISNLPMINRKSSNSRVNQSLLTDVSWIFLSRSFCTKSLTRENSAKAFIRVWKVMEMCYGILLLEKRVTQRELFYKLLCSSPDYFTSQLQVNQTIQDVVALLRCSRFSLGIMASSRGIIAGRLLLQEPGEETVDCTKCGSSGYAISGDLNLLEKLVMKTDANYIIVIEKHAIFQRLAEDKVFNQIPCILITAKGYPDLATRFLLHRMSRAFPE...

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_005516`
TK1151 ID	TkA01G038440
OH-1004 ID	LXL04_005516
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
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_005516

Location Chr01:166391807-166394461 (+)

Description Similar to SPO11-2: Meiotic recombination protein SPO11-2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g63990`	Component of a topoisomerase 6 complex specifically required for meiotic recombination.	Arabidopsis SPO11-2 functions with SPO11-1 in meiotic recombination.2006 · DOI: 10.1111/j.1365-313x.2006.02867.x The catalytically active tyrosine residues of both SPO11-1 and SPO11-2 are required for meiotic double-strand break induction in Arabidopsis.2007 · DOI: 10.1105/tpc.107.054817 A high throughput genetic screen identifies new early meiotic recombination functions in Arabidopsis thaliana.2009 · DOI: 10.1371/journal.pgen.1000654 A DNA topoisomerase VI-like complex initiates meiotic recombination.2016 · DOI: 10.1126/science.aad5196

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q5ZPI9`	Required for meiotic recombination.	No verified direct reference in this release
`Os08g0156900`	Required for meiotic recombination.	No verified direct reference in this release
`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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005516 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0006265 DNA topological change Biological Process

GO:0007059 chromosome segregation Biological Process

GO:0007129 homologous chromosome pairing at meiosis Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

GO:0009553 embryo sac development Biological Process

GO:0009555 pollen development Biological Process

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

GO:0048316 seed development Biological Process

GO:0051026 chiasma assembly Biological Process

GO:0051321 meiotic cell cycle Biological Process

GO:0000228 nuclear chromosome Cellular Component

KEGG gene cross-reference

ath:AT1G63990

dosa:Os03g0284800

dosa:Os08g0156900

osa:4332468

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.

Nucleus0.496

Rank 1 · LXL04_005516 · OH-1004

Cytoplasm0.450

Rank 2 · LXL04_005516 · OH-1004

Mitochondrion0.083

Rank 3 · LXL04_005516 · OH-1004

Cell membrane0.068

Rank 4 · LXL04_005516 · OH-1004

Endoplasmic reticulum0.045

Rank 5 · LXL04_005516 · 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.

PF04406.20TP6A_N94-158 aa

PF21180.4TOP6A-Spo11_Toprim210-375 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005516	`PF04406.20`	TP6A_N	94	158	1e-14	54.8
LXL04_005516	`PF21180.4`	TOP6A-Spo11_Toprim	210	375	2.7e-41	142.1

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9M4A1`	Arabidopsis thaliana	Meiotic recombination protein SPO11-2	73.067%	Swiss-Prot	strong database homology
`Q5ZPI9`	Oryza sativa subsp. indica	Meiotic recombination protein SPO11-2	65.526%	Swiss-Prot	strong database homology
`Q6ZD95`	Oryza sativa subsp. japonica	Meiotic recombination protein SPO11-2	65.263%	Swiss-Prot	strong database homology
`Q0DSV9`	Oryza sativa subsp. japonica	Topoisomerase 6 subunit A3	34.451%	Swiss-Prot	moderate database homology
`A2XFC1`	Oryza sativa subsp. indica	DNA topoisomerase 6 subunit A3	34.451%	Swiss-Prot	moderate database homology

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