LXL04_024628 | RubberDandelionOmics

Gene overview

LXL04_024628

Reference: OH-1004 Chr: Chr05 Coordinates: 95425984-95430338 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2400 bp · LXL04_024628|LXL04_024628|OH1004|cDNA

TGTATCGAAAGCCATTATAATGCGTATACACCTATACATACACACTGTACTAcactatatctatatatacacacacTTACTCTCACTCTAGATCTCAGTGTCAATGCTGTCTTGTCCAGTAAAATACGCCCCTTTCTTCGTCTTCCCCCAAACACACAAACACTTTCTCTTCGTAAATTGAGATTTTTCCTTTCGAAAAACATGAAAaccaaatgggttttgttcttcTTCATAATAACTCAACTGGGTTGTCAGGTAAT...

CDS

Download CDS FASTA

2289 bp · LXL04_024628|LXL04_024628|OH1004|CDS

TTGTCCAGTAAAATACGCCCCTTTCTTCGTCTTCCCCCAAACACACAAACACTTTCTCTTCGTAAATTGAGATTTTTCCTTTCGAAAAACATGAAAACCAAATGGGTTTTGTTCTTCTTCATAATAACTCAACTGGGTTGTCAGGTAATTGAATGCACTGTTACTTACGACAGCAAGGCCATTGTTATTAATGGCGAAAGAAGAATTCTCATCTCTGGTTCCATACATTACACCAGAAGCACCCCTGAGATGTGGGAAGA...

Protein

Download Protein FASTA

762 aa · LXL04_024628|LXL04_024628|OH1004|PROTEIN

MSSKIRPFLRLPPNTQTLSLRKLRFFLSKNMKTKWVLFFFIITQLGCQVIECTVTYDSKAIVINGERRILISGSIHYTRSTPEMWEDLVMKAKDGGLDVIDTYVFWNVHEPSPGNYNFEGRYDLVRFLKTVQKAGMYVHLRIGPYVCAEWNFGGFPVWLKYVPGISFRTDNEPFKNAMKGFTVKIVNLMKSEKMFESQGGPIILSQVENEYGSVGKAYGGAGHNYMTWAANMVVELGTGVPWVMCKQDDAPDPIINTCNG...

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_024628`
TK1151 ID	TkA06G123270
OH-1004 ID	LXL04_024628
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	98.400
Protein coverage (%)	TK1151 95.328 / 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_024628

Location Chr05:95425984-95430338 (+)

Description Similar to BGAL3: Beta-galactosidase 3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g36360`	Beta-galactosidase 3.	No verified direct reference in this release
`At1g45130`	Beta-galactosidase 5.	No verified direct reference in this release
`At3g13750`	Beta-galactosidase 1.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0165400`	Beta-galactosidase 5.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024628 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009827 plant-type cell wall modification Biological Process

GO:0019388 galactose catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005773 vacuole Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0048046 apoplast Cellular Component

GO:0004565 beta-galactosidase activity Molecular Function

GO:0030246 carbohydrate binding Molecular Function

KEGG gene cross-reference

ath:AT1G45130

ath:AT3G13750

ath:AT4G36360

dosa:Os03g0165400

sly:544167

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.

Lysosome / Vacuole0.321

Rank 1 · LXL04_024628 · OH-1004

Extracellular0.318

Rank 2 · LXL04_024628 · OH-1004

Cytoplasm0.132

Rank 3 · LXL04_024628 · OH-1004

Endoplasmic reticulum0.127

Rank 4 · LXL04_024628 · OH-1004

Cell membrane0.116

Rank 5 · LXL04_024628 · 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.

PF01301.26Glyco_hydro_3561-365 aa

PF17834.8GHD388-443 aa

PF21467.4BetaGal_gal-bd496-552 aa

PF21467.4BetaGal_gal-bd645-737 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024628	`PF01301.26`	Glyco_hydro_35	61	365	1.4e-122	410.0
LXL04_024628	`PF17834.8`	GHD	388	443	7.4e-24	84.0
LXL04_024628	`PF21467.4`	BetaGal_gal-bd	496	552	4.3e-33	114.0
LXL04_024628	`PF21467.4`	BetaGal_gal-bd	645	737	4.3e-33	114.0

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
`Q9SCV9`	Arabidopsis thaliana	Beta-galactosidase 3	72.390%	Swiss-Prot	strong database homology
`Q9MAJ7`	Arabidopsis thaliana	Beta-galactosidase 5	68.681%	Swiss-Prot	strong database homology
`Q9SCW1`	Arabidopsis thaliana	Beta-galactosidase 1	63.923%	Swiss-Prot	strong database homology
`Q10RB4`	Oryza sativa subsp. japonica	Beta-galactosidase 5	69.058%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card