LXL04_029300 | RubberDandelionOmics

Gene overview

LXL04_029300

Reference: OH-1004 Chr: Chr06 Coordinates: 86570442-86574686 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2652 bp · LXL04_029300|LXL04_029300|OH1004|cDNA

ATGGCATCTTCAGAGGCTGAGTTAGAGCAACTGCTTAAGGAGGCAGGGAAACAGCTATTACATCCCCCGGACTCCGTCGACGACCTTCTTCCTGTTCTTGACAAAGTAGAGAAACTTCTATCAAAAGTTGACCAGTCTCCGAAAAAGTCAATGCTAGATGCACTCAAACCATCAATGAGGGCATTGATTCACGACAGTCTTTCATCACATTCAGATGTTGATGTTAAGGTTGCAGTCGCTTCATGCATCAGTGAAATAAC...

CDS

Download CDS FASTA

2652 bp · LXL04_029300|LXL04_029300|OH1004|CDS

ATGGCATCTTCAGAGGCTGAGTTAGAGCAACTGCTTAAGGAGGCAGGGAAACAGCTATTACATCCCCCGGACTCCGTCGACGACCTTCTTCCTGTTCTTGACAAAGTAGAGAAACTTCTATCAAAAGTTGACCAGTCTCCGAAAAAGTCAATGCTAGATGCACTCAAACCATCAATGAGGGCATTGATTCACGACAGTCTTTCATCACATTCAGATGTTGATGTTAAGGTTGCAGTCGCTTCATGCATCAGTGAAATAAC...

Protein

Download Protein FASTA

883 aa · LXL04_029300|LXL04_029300|OH1004|PROTEIN

MASSEAELEQLLKEAGKQLLHPPDSVDDLLPVLDKVEKLLSKVDQSPKKSMLDALKPSMRALIHDSLSSHSDVDVKVAVASCISEITRITAPDAPYNDDQMRDVFQLIVSSFEGLADQSSRSYNKRASILETVSKVRSCVIMLDLECEGLIVEMFEYFLRSVRDYHLESIYLSMENIMVLVLEESEEISVDLLKPILASVKKDSEGVLPIARKLAEGVLLKSASKVKPYLMPAVESIGDTLDMYTQAVASICEETTATIE...

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_029300`
TK1151 ID	TkA07G298500
OH-1004 ID	LXL04_029300
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	93.500
Protein coverage (%)	TK1151 88.757 / OH-1004 34.881 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_029300

Location Chr06:86570442-86574686 (-)

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
`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

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Functional annotation source: OH1004 · LXL04_029300 · 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:0009954 proximal/distal pattern formation Biological Process

GO:0009965 leaf morphogenesis 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:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G15940

ath:AT1G77600

ath:AT4G31880

ath:AT5G47690

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.

Nucleus0.973

Rank 1 · LXL04_029300 · OH-1004

Cytoplasm0.080

Rank 2 · LXL04_029300 · OH-1004

Cell membrane0.025

Rank 3 · LXL04_029300 · OH-1004

Endoplasmic reticulum0.016

Rank 4 · LXL04_029300 · OH-1004

Extracellular0.007

Rank 5 · LXL04_029300 · 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.

PF20168.5PDS527-230 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029300	`PF20168.5`	PDS5	27	230	2.6e-51	175.3

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
`Q8GUP3`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog C	38.194%	Swiss-Prot	moderate database homology
`Q9S9P0`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog E	50.000%	Swiss-Prot	weak database homology
`B6EUB3`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog A	48.165%	Swiss-Prot	weak database homology
`F4I735`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog B	31.660%	Swiss-Prot	weak database homology

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