LXL04_000397 | RubberDandelionOmics

Gene overview

LXL04_000397

Reference: OH-1004 Chr: Chr01 Coordinates: 7393712-7395485 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1431 bp · LXL04_000397|LXL04_000397|OH1004|cDNA

ATGCGAAACAGAAAAATGACTTTCTCTATTCAATCAGCTATTGTAACCTTGATTCTATATAGTGCAATCATCCAATCGGGATCATACACTTCCTCATCAATCCGTCTTCCTCACTCTCAATCTAGATCTCCGCCTGTTACTGTTTCCGTCACCGAATATGGGGCCACCGGCGATGGGGTCCACTACGACACCGAACCTATTCAGTCCGCAATCGACGCTTGCTCGTCCGCGGGAGGTGGTCGAGTCGTCTTCCCGCCGGG...

CDS

Download CDS FASTA

1425 bp · LXL04_000397|LXL04_000397|OH1004|CDS

ATGCGAAACAGAAAAATGACTTTCTCTATTCAATCAGCTATTGTAACCTTGATTCTATATAGTGCAATCATCCAATCGGGATCATACACTTCCTCATCAATCCGTCTTCCTCACTCTCAATCTAGATCTCCGCCTGTTACTGTTTCCGTCACCGAATATGGGGCCACCGGCGATGGGGTCCACTACGACACCGAACCTATTCAGTCCGCAATCGACGCTTGCTCGTCCGCGGGAGGTGGTCGAGTCGTCTTCCCGCCGGG...

Protein

Download Protein FASTA

474 aa · LXL04_000397|LXL04_000397|OH1004|PROTEIN

MRNRKMTFSIQSAIVTLILYSAIIQSGSYTSSSIRLPHSQSRSPPVTVSVTEYGATGDGVHYDTEPIQSAIDACSSAGGGRVVFPPGNYLTATVFLKSRVVLEVHKNATVLGGTRLEDYPVEQSRWYVVLAEDAEDVGITGGGEINGQGLEFVVRFDERKNVMVSWNQTGACSGDECRPRLVGFIRSKNVRVWDVHLTEPAYWCLHLVQCDNTYIHDISIYGDFNTPNNDGIDIDDSNNTLITRCNINTGDDAICPKTYD...

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_000397`
TK1151 ID	TkA01G614480
OH-1004 ID	LXL04_000397
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.300
Protein coverage (%)	TK1151 99.580 / OH-1004 100.000 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

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_000397

Location Chr01:7393712-7395485 (-)

Description Similar to GSVIVT00026920001: Probable polygalacturonase

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g80170`	Probable polygalacturonase At1g80170.	No verified direct reference in this release
`At1g02790`	May function in depolymerizing pectin during pollen development, germination, and tube growth.	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_000397 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005975 carbohydrate metabolic process 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:0009505 plant-type cell wall Cellular Component

GO:0016020 membrane Cellular Component

GO:0004650 polygalacturonase activity Molecular Function

GO:0033917 exo-poly-alpha-galacturonosidase activity Molecular Function

GO:0047911 galacturan 1,4-alpha-galacturonidase activity Molecular Function

KEGG gene cross-reference

ath:AT1G02790

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.

Extracellular0.325

Rank 1 · LXL04_000397 · OH-1004

Lysosome / Vacuole0.227

Rank 2 · LXL04_000397 · OH-1004

Cell membrane0.120

Rank 3 · LXL04_000397 · OH-1004

Endoplasmic reticulum0.109

Rank 4 · LXL04_000397 · OH-1004

Cytoplasm0.098

Rank 5 · LXL04_000397 · 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_epim48-99 aa

PF00295.24Glyco_hydro_2879-400 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000397	`PF12708.13`	Pect-lyase_RHGA_epim	48	99	3.8e-14	53.7
LXL04_000397	`PF00295.24`	Glyco_hydro_28	79	400	8.4e-23	81.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q94AJ5`	Arabidopsis thaliana	Probable polygalacturonase At1g80170	25.575%	Swiss-Prot	weak database homology
`P49062`	Arabidopsis thaliana	Exopolygalacturonase	23.944%	Swiss-Prot	weak database homology
`Q9LW07`	Arabidopsis thaliana	Probable polygalacturonase At3g15720	30.415%	Swiss-Prot	weak database homology

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