LXL04_032021 | RubberDandelionOmics

Gene overview

LXL04_032021

Reference: OH-1004 Chr: Chr07 Coordinates: 15091576-15098208 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2838 bp · LXL04_032021|LXL04_032021|OH1004|cDNA

ATGGCGTCTAGATCGTCTGGTTTTTCAGGCATACAACTCGAGATCGAGTTGATGGACGCAGGGAAGAGGCTATTACTTCTGCCATCTTCATTTTCAGATGTTCTCGACGTTCTTGCACATATGGAGCGAACTCTATCCAAAGTGCAACAAGTGCCATCCGAATCAATGAAGTATGCCCTGCATCCAATAATCGATGCACTAATAGCCAAAGAACTGGTAACACATCCGGATACGAATGTAAACATCTTAGTTTCATGTTG...

CDS

Download CDS FASTA

2838 bp · LXL04_032021|LXL04_032021|OH1004|CDS

ATGGCGTCTAGATCGTCTGGTTTTTCAGGCATACAACTCGAGATCGAGTTGATGGACGCAGGGAAGAGGCTATTACTTCTGCCATCTTCATTTTCAGATGTTCTCGACGTTCTTGCACATATGGAGCGAACTCTATCCAAAGTGCAACAAGTGCCATCCGAATCAATGAAGTATGCCCTGCATCCAATAATCGATGCACTAATAGCCAAAGAACTGGTAACACATCCGGATACGAATGTAAACATCTTAGTTTCATGTTG...

Protein

Download Protein FASTA

945 aa · LXL04_032021|LXL04_032021|OH1004|PROTEIN

MASRSSGFSGIQLEIELMDAGKRLLLLPSSFSDVLDVLAHMERTLSKVQQVPSESMKYALHPIIDALIAKELVTHPDTNVNILVSCCISEILRIMAPNSPYNNQQMKDFFELATMTFEKLSSSSSGCYAKMTKVLQIFTTVRLPVIMLDLQLDKLVVRLFKQFLTVADFNYSEVIVEMEKIMTMIIEESEQPKIELVGLLVMSVRNYNQINSPVSWQLGEKVLKKCASKLKHQLPDFVQKMGIHLLDYSKVVSDICIGMP...

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_032021`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_032021

Location Chr07:15091576-15098208 (+)

Description Similar to SDF2: Stromal cell-derived factor 2-like protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g25110`	Involved in the endoplasmic reticulum (ER) protein quality control and unfolded protein response.	Control of the pattern-recognition receptor EFR by an ER protein complex in plant immunity.2009 · DOI: 10.1038/emboj.2009.262 Arabidopsis stromal-derived Factor2 (SDF2) is a crucial target of the unfolded protein response in the endoplasmic reticulum.2010 · DOI: 10.1074/jbc.m110.117176
`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
`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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032021 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002221 pattern recognition receptor signaling pathway Biological Process

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:0042742 defense response to bacterium Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0051301 cell division Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G80810

ath:AT2G25110

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.

Nucleus0.445

Rank 1 · LXL04_032021 · OH-1004

Cytoplasm0.329

Rank 2 · LXL04_032021 · OH-1004

Cell membrane0.158

Rank 3 · LXL04_032021 · OH-1004

Endoplasmic reticulum0.099

Rank 4 · LXL04_032021 · OH-1004

Plastid0.069

Rank 5 · LXL04_032021 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF20168.5PDS534-260 aa

PF21743.4PTM_DIR17_Tudor336-380 aa

PF05278.18PEARLI-4379-559 aa

PF02815.26MIR783-929 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032021	`PF20168.5`	PDS5	34	260	8e-39	133.9
LXL04_032021	`PF21743.4`	PTM_DIR17_Tudor	336	380	4.5e-07	30.3
LXL04_032021	`PF05278.18`	PEARLI-4	379	559	3.7e-15	56.9
LXL04_032021	`PF02815.26`	MIR	783	929	3.2e-17	63.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q93ZE8`	Arabidopsis thaliana	Stromal cell-derived factor 2-like protein	76.056%	Swiss-Prot	weak database homology
`Q8GUP3`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog C	40.239%	Swiss-Prot	weak database homology
`A8MRD9`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog D	40.239%	Swiss-Prot	weak database homology
`Q9S9P0`	Arabidopsis thaliana	Sister chromatid cohesion protein PDS5 homolog E	39.419%	Swiss-Prot	weak database homology

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