LXL04_009211 | RubberDandelionOmics

Gene overview

LXL04_009211

Reference: OH-1004 Chr: Chr02 Coordinates: 120524178-120527273 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1647 bp · LXL04_009211|LXL04_009211|OH1004|cDNA

ATGGACTATGTTTGTCCAGTTAATGGAGTGGAGCAGCAGCTTAAAGTAGCTGGTGAACAGCTTGCATTGCCCCCTTCTTCCACCAAGGACCTTCTAGACCTCCTCGATAACACCGAGCAACTATTGGCATTTGTGGGTCAAGCACCAAATCTCAGAATGCAAGGTGCACTTGTGCCTTCAATGGGGGCATTAATTTCCCATGATCTTTTAAAGCATTCAGATATGGATGTCAAAGTTTCAGTAGCATCATGTCTTTGTGA...

CDS

Download CDS FASTA

1647 bp · LXL04_009211|LXL04_009211|OH1004|CDS

ATGGACTATGTTTGTCCAGTTAATGGAGTGGAGCAGCAGCTTAAAGTAGCTGGTGAACAGCTTGCATTGCCCCCTTCTTCCACCAAGGACCTTCTAGACCTCCTCGATAACACCGAGCAACTATTGGCATTTGTGGGTCAAGCACCAAATCTCAGAATGCAAGGTGCACTTGTGCCTTCAATGGGGGCATTAATTTCCCATGATCTTTTAAAGCATTCAGATATGGATGTCAAAGTTTCAGTAGCATCATGTCTTTGTGA...

Protein

Download Protein FASTA

548 aa · LXL04_009211|LXL04_009211|OH1004|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	`LXL04_009211`
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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_009211

Location Chr02:120524178-120527273 (+)

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

Arabidopsis / Rice Reference Genes and Papers

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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.

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.

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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.

Nucleus0.940

Rank 1 · LXL04_009211 · OH-1004

Cytoplasm0.142

Rank 2 · LXL04_009211 · OH-1004

Cell membrane0.026

Rank 3 · LXL04_009211 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_009211 · OH-1004

Mitochondrion0.011

Rank 5 · LXL04_009211 · 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.

PF20168.5PDS530-234 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009211	`PF20168.5`	PDS5	30	234	1.6e-47	162.8

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	Sister chromatid cohesion protein PDS5 homolog D	45.938%	Swiss-Prot	moderate database homology
`Q8GUP3`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog C	49.398%	Swiss-Prot	weak database homology
`Q9S9P0`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog E	48.387%	Swiss-Prot	weak database homology
`B6EUB3`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog A	45.327%	Swiss-Prot	weak database homology
`F4I735`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog B	32.018%	Swiss-Prot	weak database homology

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