LXL04_005302 | RubberDandelionOmics

Gene overview

LXL04_005302

Reference: OH-1004 Chr: Chr01 Coordinates: 159980046-159982342 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1194 bp · LXL04_005302|LXL04_005302|OH1004|cDNA

ATGGGCTTCTTGATGTTAGTCTTGTTAACCTTGTTTTGTGTCTCATTGGGTCCGAAAATCACAAGTGCTACCACCTATGATGTAACATCTTATGGTGCAAAAGGAGATGGGAATACAGACGATTCCAATGCTTTCCTTCGAGCATGGAATGATTTATGCCGTGATAAGTCGCCAGGACCAACATTGATAATACCAACAGGCAAAACATTTTTAATAAGTCCGGTGGCATTCAATGGCCCATGCAAATCCTCAAGTGTAGA...

CDS

Download CDS FASTA

1194 bp · LXL04_005302|LXL04_005302|OH1004|CDS

ATGGGCTTCTTGATGTTAGTCTTGTTAACCTTGTTTTGTGTCTCATTGGGTCCGAAAATCACAAGTGCTACCACCTATGATGTAACATCTTATGGTGCAAAAGGAGATGGGAATACAGACGATTCCAATGCTTTCCTTCGAGCATGGAATGATTTATGCCGTGATAAGTCGCCAGGACCAACATTGATAATACCAACAGGCAAAACATTTTTAATAAGTCCGGTGGCATTCAATGGCCCATGCAAATCCTCAAGTGTAGA...

Protein

Download Protein FASTA

397 aa · LXL04_005302|LXL04_005302|OH1004|PROTEIN

MGFLMLVLLTLFCVSLGPKITSATTYDVTSYGAKGDGNTDDSNAFLRAWNDLCRDKSPGPTLIIPTGKTFLISPVAFNGPCKSSSVDIKLSGNILAPKTLDGWKGCIEEHFWIYFRSVQRLTIQGPGQIDGQGSIWWKNGGQTKTTTCNRPSALHFHDCDGLQLRGTKHINSPKMHISINGCDGVDIGNVQILAPGDSPNTDGIDISGSSHVNIHDSNIQTGDDCVAINGGTNDINVTRVLCGPGHGISIGSLGENGAHD...

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_005302`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_005302

Location Chr01:159980046-159982342 (-)

Description Similar to At3g15720: Probable polygalacturonase At3g15720

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g15720`	Probable polygalacturonase At3g15720.	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
`At3g07970`	Polygalacturonase required for cell type-specific pectin degradation to separate microspores.	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 Tetrad analysis possible in Arabidopsis with mutation of the QUARTET (QRT) genes.1994 · DOI: 10.1126/science.8197459

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005302 · 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: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:0048235 pollen sperm cell differentiation Biological Process

GO:0071555 cell wall organization Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009505 plant-type cell wall Cellular Component

KEGG gene cross-reference

ath:AT3G07970

ath:AT3G15720

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.

Extracellular0.769

Rank 1 · LXL04_005302 · OH-1004

Cytoplasm0.092

Rank 2 · LXL04_005302 · OH-1004

Lysosome / Vacuole0.063

Rank 3 · LXL04_005302 · OH-1004

Endoplasmic reticulum0.059

Rank 4 · LXL04_005302 · OH-1004

Cell membrane0.058

Rank 5 · LXL04_005302 · 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_epim27-243 aa

PF00295.24Glyco_hydro_2861-387 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005302	`PF12708.13`	Pect-lyase_RHGA_epim	27	243	4.8e-08	33.8
LXL04_005302	`PF00295.24`	Glyco_hydro_28	61	387	8.8e-90	301.8

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
`Q9LW07`	Arabidopsis thaliana	Probable polygalacturonase At3g15720	44.697%	Swiss-Prot	moderate database homology
`O23147`	Arabidopsis thaliana	Polygalacturonase ADPG1	39.175%	Swiss-Prot	moderate database homology
`Q9SFB7`	Arabidopsis thaliana	Polygalacturonase QRT2	39.353%	Swiss-Prot	moderate database homology

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