LXL04_032309 | RubberDandelionOmics

Gene overview

LXL04_032309

Reference: OH-1004 Chr: Chr07 Coordinates: 20198560-20200785 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1455 bp · LXL04_032309|LXL04_032309|OH1004|cDNA

ATGAACATCTCTCAAGGATTTTCAACCTTCTTCCTAGCTCTCTTAGTTTTTTTCTCTATCAATGTGGAAGGAAGATATCATTTCCACAAGAATAAAAAGAACGGTTCTTCCGGTGATCCTAATGCGCCTATTCCTCAACCTCCCGTTTACCCGCCGTCAGTTCCATCCGACCCGAGTTCTGCTCCGTCCGACCCTGGTTCGGCTCCACCTGACCCGGATTTGGCTCCACCTGACCCGGATTCCGCTCCATCTGGTCCTTG...

CDS

Download CDS FASTA

1455 bp · LXL04_032309|LXL04_032309|OH1004|CDS

ATGAACATCTCTCAAGGATTTTCAACCTTCTTCCTAGCTCTCTTAGTTTTTTTCTCTATCAATGTGGAAGGAAGATATCATTTCCACAAGAATAAAAAGAACGGTTCTTCCGGTGATCCTAATGCGCCTATTCCTCAACCTCCCGTTTACCCGCCGTCAGTTCCATCCGACCCGAGTTCTGCTCCGTCCGACCCTGGTTCGGCTCCACCTGACCCGGATTTGGCTCCACCTGACCCGGATTCCGCTCCATCTGGTCCTTG...

Protein

Download Protein FASTA

484 aa · LXL04_032309|LXL04_032309|OH1004|PROTEIN

MNISQGFSTFFLALLVFFSINVEGRYHFHKNKKNGSSGDPNAPIPQPPVYPPSVPSDPSSAPSDPGSAPPDPDLAPPDPDSAPSGPCVFDVTDYGAIGDGSTDDTPAFKAAWKEACAVESATILVPAGCTFLITSTIFSGPCKPGLVFQVDGILTPPAGPDCWPEKDSKKQWLVFYKLDNMTLTGTGTIEGNGQDWWDLPCKPHKGPGGKTLPGPCDSPTLIRFFMSTNLQMTRLRIQNSPMFHVKFDGCEGVMIDKVSI...

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_032309`
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_032309

Location Chr07:20198560-20200785 (-)

Description Similar to At1g48100: Polygalacturonase At1g48100

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g48100`	Polygalacturonase not involved in the final stages of pod shatter.	No verified direct reference in this release
`At1g80170`	Probable polygalacturonase At1g80170.	No verified direct reference in this release
`At3g57510`	Polygalacturonase involved in cell separation in the final stages of pod shatter and in anther dehiscence.	ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE1 (ADPG1), ADPG2, and QUARTET2 are Polygalacturonases required for cell separation during reproductive development in Arabidopsis.2009 · DOI: 10.1105/tpc.108.063768

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032309 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005975 carbohydrate metabolic process Biological Process

GO:0009830 cell wall modification involved in abscission Biological Process

GO:0009831 plant-type cell wall modification involved in multidimensional cell growth Biological Process

GO:0009835 fruit ripening Biological Process

GO:0009901 anther dehiscence Biological Process

GO:0010047 fruit dehiscence Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0071555 cell wall organization Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009501 amyloplast Cellular Component

GO:0009505 plant-type cell wall Cellular Component

KEGG gene cross-reference

ath:AT1G48100

ath:AT1G80170

ath:AT3G57510

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.

Extracellular0.463

Rank 1 · LXL04_032309 · OH-1004

Lysosome / Vacuole0.192

Rank 2 · LXL04_032309 · OH-1004

Cytoplasm0.137

Rank 3 · LXL04_032309 · OH-1004

Endoplasmic reticulum0.127

Rank 4 · LXL04_032309 · OH-1004

Cell membrane0.084

Rank 5 · LXL04_032309 · 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.

PF12708.13Pect-lyase_RHGA_epim89-137 aa

PF00295.24Glyco_hydro_28120-436 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032309	`PF12708.13`	Pect-lyase_RHGA_epim	89	137	4.4e-10	40.4
LXL04_032309	`PF00295.24`	Glyco_hydro_28	120	436	5e-88	296.0

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
`Q949Z1`	Arabidopsis thaliana	Polygalacturonase At1g48100	67.382%	Swiss-Prot	strong database homology
`Q94AJ5`	Arabidopsis thaliana	Probable polygalacturonase At1g80170	42.347%	Swiss-Prot	moderate database homology
`O23147`	Arabidopsis thaliana	Polygalacturonase ADPG1	42.703%	Swiss-Prot	moderate database homology

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