LXL04_006136 | RubberDandelionOmics

Gene overview

LXL04_006136

Reference: OH-1004 Chr: Chr02 Coordinates: 2137342-2141511 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1389 bp · LXL04_006136|LXL04_006136|OH1004|cDNA

ATGCTCTCTTTAAACACTATAGCAACACCGAACATGAAGAACACATGGAATATGAAGGCCTCCATATATGGCATTTTGACCATTCTACTTCTATGGTCACCGGAACTTGGGGTCAGCGCCGCTAGAGACACCAAGCAATGGCGGCACCATGATGGCTCACGGCAGCTGATGGCAGAGACGTTTTACCCTTCGTATGGAGAGAGCATGCCGAGTTCATTACAATATAGGAAAACATCTACCATCTTTAATGTATTGAACTT...

CDS

Download CDS FASTA

1389 bp · LXL04_006136|LXL04_006136|OH1004|CDS

ATGCTCTCTTTAAACACTATAGCAACACCGAACATGAAGAACACATGGAATATGAAGGCCTCCATATATGGCATTTTGACCATTCTACTTCTATGGTCACCGGAACTTGGGGTCAGCGCCGCTAGAGACACCAAGCAATGGCGGCACCATGATGGCTCACGGCAGCTGATGGCAGAGACGTTTTACCCTTCGTATGGAGAGAGCATGCCGAGTTCATTACAATATAGGAAAACATCTACCATCTTTAATGTATTGAACTT...

Protein

Download Protein FASTA

462 aa · LXL04_006136|LXL04_006136|OH1004|PROTEIN

MLSLNTIATPNMKNTWNMKASIYGILTILLLWSPELGVSAARDTKQWRHHDGSRQLMAETFYPSYGESMPSSLQYRKTSTIFNVLNFGAKGDGISDDTKAFEAAWLAACKLEASTMIIPKGSVFLIKPISFSGPNCESNIVFQLDGKIIAPKASGNWESGLLQWVEFTKLNGITIRGSGVVDGQGSGWWTKSGTKPTAIRFYGSSDVTVTGITIQNSPQTHLKFDNCQSVQVSEITVSSPGDSPNTDGIHLQNSQDVAIH...

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_006136`
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_006136

Location Chr02:2137342-2141511 (+)

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
`At3g15720`	Probable polygalacturonase At3g15720.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006136 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005975 carbohydrate metabolic process Biological Process

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

GO:0009835 fruit ripening Biological Process

GO:0045490 pectin catabolic process Biological Process

GO:0071555 cell wall organization Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009501 amyloplast Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0016020 membrane Cellular Component

GO:0004650 polygalacturonase activity Molecular Function

KEGG gene cross-reference

ath:AT1G48100

ath:AT1G80170

ath:AT3G15720

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.

Extracellular0.765

Rank 1 · LXL04_006136 · OH-1004

Cytoplasm0.075

Rank 2 · LXL04_006136 · OH-1004

Cell membrane0.064

Rank 3 · LXL04_006136 · OH-1004

Endoplasmic reticulum0.060

Rank 4 · LXL04_006136 · OH-1004

Lysosome / Vacuole0.058

Rank 5 · LXL04_006136 · 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_epim81-129 aa

PF00295.24Glyco_hydro_28112-412 aa

PF13229.13Beta_helix194-284 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006136	`PF12708.13`	Pect-lyase_RHGA_epim	81	129	5.4e-08	33.6
LXL04_006136	`PF00295.24`	Glyco_hydro_28	112	412	4.9e-85	286.2
LXL04_006136	`PF13229.13`	Beta_helix	194	284	1.1e-06	29.1

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	48.744%	Swiss-Prot	moderate database homology
`Q94AJ5`	Arabidopsis thaliana	Probable polygalacturonase At1g80170	42.175%	Swiss-Prot	moderate database homology
`Q9LW07`	Arabidopsis thaliana	Probable polygalacturonase At3g15720	39.241%	Swiss-Prot	moderate database homology

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