LXL04_012978 | RubberDandelionOmics

Gene overview

LXL04_012978

Reference: OH-1004 Chr: Chr03 Coordinates: 21843474-21847414 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2031 bp · LXL04_012978|LXL04_012978|OH1004|cDNA

ATGGACTCCGGCGAGAGCAGTGACGAAAGTCCGGTACTAACTAAGAAGGGCAAATCGAAAACACCTCGGAAACCTAAAGCTAGTACTCTTAAACAGAAATCACCTGCTGAGTTCTTTGCGGAGAATAAGAACATTGCCGGGTTTGACAACCCTGGGAAATCCCTTTACACTACAGTGAGAGAGCTTGTTGAAAATGCACTTGATTCTGCAGAGTCCATTGCGGAGCTTCCATTAATTGAAGTAACAATTGAGGAGATTAA...

CDS

Download CDS FASTA

2031 bp · LXL04_012978|LXL04_012978|OH1004|CDS

ATGGACTCCGGCGAGAGCAGTGACGAAAGTCCGGTACTAACTAAGAAGGGCAAATCGAAAACACCTCGGAAACCTAAAGCTAGTACTCTTAAACAGAAATCACCTGCTGAGTTCTTTGCGGAGAATAAGAACATTGCCGGGTTTGACAACCCTGGGAAATCCCTTTACACTACAGTGAGAGAGCTTGTTGAAAATGCACTTGATTCTGCAGAGTCCATTGCGGAGCTTCCATTAATTGAAGTAACAATTGAGGAGATTAA...

Protein

Download Protein FASTA

676 aa · LXL04_012978|LXL04_012978|OH1004|PROTEIN

MDSGESSDESPVLTKKGKSKTPRKPKASTLKQKSPAEFFAENKNIAGFDNPGKSLYTTVRELVENALDSAESIAELPLIEVTIEEINKSKFNSMIGLIDRERIDEALYGDFETVKAREKRLAKEARFQEIQAKNSALGKKVKEPTAAKGMKGRGEASFYRVTCKDNGRGMPHDDIPNMFGRVLSGTKYGLKQTRGKFGLGAKMALIWSKMSTGLPIEISSSMKNQSYTTFCRLDIDIHRNIPHIHLHEKRDDKENWHGAE...

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_012978`
TK1151 ID	TkA02G525410
OH-1004 ID	LXL04_012978
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.700
Protein coverage (%)	TK1151 99.848 / OH-1004 99.852 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_012978

Location Chr03:21843474-21847414 (+)

Description Similar to TOP6B: DNA topoisomerase 6 subunit B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g20780`	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
`UniProt: B8BDQ4`	Component of the DNA topoisomerase VI involved in chromatin organization and progression of endoreduplication cycles.	No verified direct reference in this release
`Os09g0279600`	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_012978 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000902 cell morphogenesis Biological Process

GO:0006260 DNA replication Biological Process

GO:0006265 DNA topological change Biological Process

GO:0007389 pattern specification process Biological Process

GO:0009741 response to brassinosteroid Biological Process

GO:0010026 trichome differentiation Biological Process

GO:0042023 DNA endoreduplication Biological Process

GO:0005634 nucleus Cellular Component

GO:0005829 cytosol Cellular Component

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

GO:0015935 small ribosomal subunit Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ape:APE_0706.1

ath:AT3G20780

dosa:Os09g0279600

osa:4346606

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.

Nucleus0.830

Rank 1 · LXL04_012978 · OH-1004

Cytoplasm0.185

Rank 2 · LXL04_012978 · OH-1004

Mitochondrion0.046

Rank 3 · LXL04_012978 · OH-1004

Cell membrane0.024

Rank 4 · LXL04_012978 · OH-1004

Endoplasmic reticulum0.015

Rank 5 · LXL04_012978 · 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.

PF02518.32HATPase_c158-227 aa

PF13589.13HATPase_c_3160-235 aa

PF09239.18Topo-VIb_trans403-562 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012978	`PF02518.32`	HATPase_c	158	227	3.5e-07	31.4
LXL04_012978	`PF13589.13`	HATPase_c_3	160	235	9.4e-06	26.4
LXL04_012978	`PF09239.18`	Topo-VIb_trans	403	562	6.3e-57	192.5

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
`Q9C5V6`	Arabidopsis thaliana	DNA topoisomerase 6 subunit B	79.850%	Swiss-Prot	strong database homology
`B8BDQ4`	Oryza sativa subsp. indica	DNA topoisomerase 6 subunit B	78.582%	Swiss-Prot	strong database homology
`Q6H442`	Oryza sativa subsp. japonica	DNA topoisomerase 6 subunit B	78.428%	Swiss-Prot	strong database homology

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