TkA01G095000 | RubberDandelionOmics

Gene overview

TkA01G095000

Reference: TK1151 Chr: Chr01 Coordinates: 24011512-24013356 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1723 bp · TkA01G095000|TK1151|cDNA

TTTACAGTTGTTAGACTTCGTTCGATGTTCAATAGTGCTAACAGATTCAAACAAATGCATATGAGTTGAATGCTCCAATGAAGGAACATGTTCAATCAAAGGAATATTAGTCTCATACTTCAAATAAGGAACTTCACAGCCAAACACCCTTTCGGCCCAGCCGGGCTTTCGTCTTCGTCCGGAAGAACCACAGAAACGTTCGTCAATATCATTTCCTTTACATTTTCCCGCCATCTGCCCCCACTCACTACACAATGGCG...

CDS

Download CDS FASTA

1266 bp · TkA01G095000|TK1151|CDS

ATGGCGGATAAGAAAAAACGCCGACGAGCAGACGCCGATTCCGATGACGAATCTGCTCGCCTCCCTTTCAAAAACCGTCTCAAACCAGACGCCGCCATCCTATCAATACTCAAAACCCTAACCGAAGCCACCAAGTCAGCTTCAACTTCTAAAACCCTAACTCTCTCCGATCTCAACCTCGCTTCCGCTTGCCGTGAAGTCACCGACTTAACCTTATCCTCTGTCCAAACCGAGATCCAAACACTAGCCATCTCTCTCGC...

Protein

Download Protein FASTA

421 aa · TkA01G095000|TK1151|PROTEIN

MADKKKRRRADADSDDESARLPFKNRLKPDAAILSILKTLTEATKSASTSKTLTLSDLNLASACREVTDLTLSSVQTEIQTLAISLAKSILAGNGFSFSVPSRAATNQLYVPELDRIVLKDKTSVRPYASVSTVRKTTITARILSLIHQLSLKNIHVTKRDLFYTDVKLFQDQTQSDAVLDDVSCILGCTRSSLNVVAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMSSDALFILLVEKDAAYMRLAE...

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	`TkA01G095000`
TK1151 ID	TkA01G095000
OH-1004 ID	LXL04_004941
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
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	TK1151 / GWHBCHF00000000

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G095000

Location Chr01:24011512-24013356 (-)

Description Similar to TOP6A: DNA topoisomerase 6 subunit A

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`At3g13170`	DNA endonuclease, which specifically mediates DNA cleavage that forms the double-strand breaks (DSB) that initiate meiotic recombination.	AtSPO11-1 is necessary for efficient meiotic recombination in plants.2001 · DOI: 10.1093/emboj/20.3.589 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: A2XFC1`	Component of the DNA topoisomerase VI involved in chromatin organization and progression of endoreduplication cycles.	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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004941 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

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

GO:0006265 DNA topological change Biological Process

GO:0007129 homologous chromosome pairing at meiosis Biological Process

GO:0007130 synaptonemal complex assembly Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

GO:0007141 male meiosis I Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0007286 spermatid development Biological Process

GO:0007292 female gamete generation Biological Process

GO:0034502 protein localization to chromosome Biological Process

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

GO:0045141 meiotic telomere clustering Biological Process

KEGG gene cross-reference

ath:AT5G02820

dosa:Os03g0284800

hsa:23626

mmu:26972

osa:4332468

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.

Nucleus0.691

Rank 1 · TkA01G095000 · TK1151

Cytoplasm0.238

Rank 2 · TkA01G095000 · TK1151

Cell membrane0.046

Rank 3 · TkA01G095000 · TK1151

Mitochondrion0.042

Rank 4 · TkA01G095000 · TK1151

Plastid0.041

Rank 5 · TkA01G095000 · TK1151

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.

PF04406TP6A_N135-196 aa

PF20768Topo_VI_alpha200-236 aa

PF21180TOP6A-Spo11_Toprim245-415 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G095000	`PF04406`	TP6A_N	135	196	1.2e-21	77.0
TkA01G095000	`PF20768`	Topo_VI_alpha	200	236	1.7e-05	25.2
TkA01G095000	`PF21180`	TOP6A-Spo11_Toprim	245	415	4e-68	229.4

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	sp\|Q9LZ03\|TOP6A_ARATH DNA topoisomerase 6 subunit A	82.600%	Swiss-Prot	High
`Q9M4A2`	Arabidopsis thaliana	sp\|Q9M4A2\|SPO11_ARATH Meiotic recombination protein SPO11-1	41.400%	Swiss-Prot	Medium
`A2XFC1`	Oryza sativa subsp. indica	sp\|A2XFC1\|TOP6A_ORYSI DNA topoisomerase 6 subunit A3	69.900%	Swiss-Prot	High
`Q0DSV9`	Oryza sativa subsp. japonica	sp\|Q0DSV9\|TOP6A_ORYSJ Topoisomerase 6 subunit A3	69.900%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card