TkA03G409440 | RubberDandelionOmics

Gene overview

TkA03G409440

Reference: TK1151 Chr: Chr03 Coordinates: 101794971-101798437 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2119 bp · TkA03G409440|TK1151|cDNA

GTAAATTTCCTCGGATAAAATCATCAAAGGTCGACACCTGGAACCCGCAATCAAAACCCCACGGCGCCTCTCACGCAGCCTTCAATCTCCAAATTCTCGAAAAATCGGCAGGCTCGTATGTACGAGTTCGGAATTCCGATATCGGTTTTCTTCAACTTCCGGCACAGATTTGACGTAGCGATTGATTCGAATCGATAAACCCTTTGCCTTTGTAAACACAGACACATACATACCTGCGTAAAGTCAAATCAACATTTTGG...

CDS

Download CDS FASTA

1641 bp · TkA03G409440|TK1151|CDS

ATGGACTATGTTTGTCCAGTTAATGGAGTGGAGCAGCAGCTTAAAGTAGCTGGTGAACAGCTTGCATTGCCCCCTTCTTCCACCAAGGACCTTCTAGACCTCCTCGATAACACCGAGCAACTATTGGCATTTGTGGGTCAAGCTCCAAATCTCAGAATGCAAGGTGCACTTGTGCCTTCAATGGGGGCATTAATTTCCCATGATCTCTTAAAGCATTCAGATATGGATGTCAAAGTTTCAGTAGCATCATGTCTTTGTGA...

Protein

Download Protein FASTA

546 aa · TkA03G409440|TK1151|PROTEIN

MDYVCPVNGVEQQLKVAGEQLALPPSSTKDLLDLLDNTEQLLAFVGQAPNLRMQGALVPSMGALISHDLLKHSDMDVKVSVASCLCEVSRITAPEPPYKDDIMKDIFQLNVQAFGELSNVTGRNYYKAIHILESVAKVKSCLLMLDLECDALILEMFEQFLSRIRTNHPQSVFSDMENIMTLVLEESDEIASQLLSLLISHVRKENQNLSPAPWKLAEKVLRNCYNTLKPYSSTLIELIEADADEYAEIVATLCQNDYEN...

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	`TkA03G409440`
TK1151 ID	TkA03G409440
OH-1004 ID	LXL04_009211
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
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 TkA03G409440

Location Chr03:101794971-101798437 (+)

Description Similar to pds5b-b: Sister chromatid cohesion protein PDS5 homolog B-B

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g80810`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	No verified direct reference in this release
`At4g31880`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana.2015 · DOI: 10.3389/fpls.2015.01034
`At1g15940`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana.2015 · DOI: 10.3389/fpls.2015.01034
`At5g47690`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana.2015 · DOI: 10.3389/fpls.2015.01034
`At1g77600`	Cohesin cofactor dispensable during the meiotic division but playing an important role in DNA repair by homologous recombination (HR) probably by helping SMC5/SMC6 complex.	Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants.2014 · DOI: 10.1111/tpj.12595 Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana.2015 · DOI: 10.3389/fpls.2015.01034

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009211 · 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:0006281 DNA repair Biological Process

GO:0006310 DNA recombination Biological Process

GO:0007064 mitotic sister chromatid cohesion Biological Process

GO:0009556 microsporogenesis Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0035825 homologous recombination Biological Process

GO:0051301 cell division Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005874 microtubule Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0043565 sequence-specific DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G15940

ath:AT1G80810

ath:AT4G31880

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.

Nucleus0.940

Rank 1 · TkA03G409440 · TK1151

Cytoplasm0.142

Rank 2 · TkA03G409440 · TK1151

Cell membrane0.026

Rank 3 · TkA03G409440 · TK1151

Endoplasmic reticulum0.013

Rank 4 · TkA03G409440 · TK1151

Mitochondrion0.011

Rank 5 · TkA03G409440 · 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.

PF20168PDS530-234 aa

PF12374Dmrt1267-323 aa

PF21743PTM_DIR17_Tudor369-411 aa

PF09465LBR_tudor375-406 aa

PF12374Dmrt1428-439 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G409440	`PF20168`	PDS5	30	234	1.5e-47	162.8
TkA03G409440	`PF12374`	Dmrt1	267	323	3.1	9.0
TkA03G409440	`PF21743`	PTM_DIR17_Tudor	369	411	1.1e-05	25.9
TkA03G409440	`PF09465`	LBR_tudor	375	406	0.0096	16.4
TkA03G409440	`PF12374`	Dmrt1	428	439	3.1	9.0

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
`A8MRD9`	Arabidopsis thaliana	sp\|A8MRD9\|PDS5D_ARATH Sister chromatid cohesion protein PDS5 homolog D	52.200%	Swiss-Prot	Low
`Q8GUP3`	Arabidopsis thaliana	sp\|Q8GUP3\|PDS5C_ARATH Sister chromatid cohesion protein PDS5 homolog C	49.400%	Swiss-Prot	Low
`Q9S9P0`	Arabidopsis thaliana	sp\|Q9S9P0\|PDS5E_ARATH Sister chromatid cohesion protein PDS5 homolog E	48.400%	Swiss-Prot	Low
`B6EUB3`	Arabidopsis thaliana	sp\|B6EUB3\|PDS5A_ARATH Sister chromatid cohesion protein PDS5 homolog A	45.300%	Swiss-Prot	Low
`F4I735`	Arabidopsis thaliana	sp\|F4I735\|PDS5B_ARATH Sister chromatid cohesion protein PDS5 homolog B	32.000%	Swiss-Prot	Low

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