LXL04_004007 | RubberDandelionOmics

Gene overview

LXL04_004007

Reference: OH-1004 Chr: Chr01 Coordinates: 121502300-121508243 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2598 bp · LXL04_004007|LXL04_004007|OH1004|cDNA

ATGCAACACGGAATTCTAATTTGGCTCCAATGGCTGGCAATGGCGTTGACTGTAACCATTGGCATGGTAACCGGCGAATACTTTAAGCCGTTCAATGTTAGCTACGATCACAGAGCACTGATTATTGATGGACAAAGGAGAATGCTTGTTTCCGCAGGAATTCACTATCCTCGAGCCACACCTGAGATGTGGCCTGACCTGATTGCCAAGAGTAAGGATGGTGGTGCTGATGTCGTTCAGACTTATGTATTCTGGAGTGG...

CDS

Download CDS FASTA

2598 bp · LXL04_004007|LXL04_004007|OH1004|CDS

ATGCAACACGGAATTCTAATTTGGCTCCAATGGCTGGCAATGGCGTTGACTGTAACCATTGGCATGGTAACCGGCGAATACTTTAAGCCGTTCAATGTTAGCTACGATCACAGAGCACTGATTATTGATGGACAAAGGAGAATGCTTGTTTCCGCAGGAATTCACTATCCTCGAGCCACACCTGAGATGTGGCCTGACCTGATTGCCAAGAGTAAGGATGGTGGTGCTGATGTCGTTCAGACTTATGTATTCTGGAGTGG...

Protein

Download Protein FASTA

865 aa · LXL04_004007|LXL04_004007|OH1004|PROTEIN

MQHGILIWLQWLAMALTVTIGMVTGEYFKPFNVSYDHRALIIDGQRRMLVSAGIHYPRATPEMWPDLIAKSKDGGADVVQTYVFWSGHEPVKGQYNFEGRYDLVKFVKLVGSSGLYLHLRIGPYVCAEWNFGGFPVWLRDIPGIVFRTDNAPFKEEMQRFVKKIVDLMREESLFSWQGGPIIMLQIENEYGNIEGSFGQKGKAYVKWAAEMAVGLGAGVPWVMCKQTDAPEYIIDACNGYYCDGFKPNSNKKPIFWTENW...

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_004007`
TK1151 ID	TkA01G215240
OH-1004 ID	LXL04_004007
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_004007

Location Chr01:121502300-121508243 (+)

Description Similar to BGAL9: Beta-galactosidase 9

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g32810`	Beta-galactosidase 9.	No verified direct reference in this release
`At2g28470`	Beta-galactosidase 8.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os12g0429200`	Beta-galactosidase 15.	No verified direct reference in this release
`Os03g0255100`	Releases galactose by hydrolysis of plant cell wall galactose-containing polysaccharides such as galacto-xyloglucan, pectic galactan and galactan (in vitro).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004007 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005975 carbohydrate metabolic process Biological Process

GO:0009827 plant-type cell wall modification Biological Process

GO:0010345 suberin biosynthetic process Biological Process

GO:0019388 galactose catabolic process Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005576 extracellular region Cellular Component

GO:0005773 vacuole Cellular Component

GO:0009505 plant-type cell wall 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:AT2G28470

ath:AT2G32810

dosa:Os03g0255100

dosa:Os12g0429200

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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 / Vacuole0.386

Rank 1 · LXL04_004007 · OH-1004

Extracellular0.283

Rank 2 · LXL04_004007 · OH-1004

Cytoplasm0.158

Rank 3 · LXL04_004007 · OH-1004

Endoplasmic reticulum0.146

Rank 4 · LXL04_004007 · OH-1004

Cell membrane0.132

Rank 5 · LXL04_004007 · 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_3540-344 aa

PF17834.8GHD368-424 aa

PF21467.4BetaGal_gal-bd637-724 aa

PF02140.24SUEL_Lectin778-854 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004007	`PF01301.26`	Glyco_hydro_35	40	344	6.1e-118	394.7
LXL04_004007	`PF17834.8`	GHD	368	424	3e-25	88.4
LXL04_004007	`PF21467.4`	BetaGal_gal-bd	637	724	4.9e-28	97.8
LXL04_004007	`PF02140.24`	SUEL_Lectin	778	854	2.9e-22	79.5

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SCV3`	Arabidopsis thaliana	Beta-galactosidase 9	70.709%	Swiss-Prot	strong database homology
`Q9SCV4`	Arabidopsis thaliana	Beta-galactosidase 8	55.529%	Swiss-Prot	strong database homology
`Q0INM3`	Oryza sativa subsp. japonica	Beta-galactosidase 15	63.435%	Swiss-Prot	strong database homology
`Q10NX8`	Oryza sativa subsp. japonica	Beta-galactosidase 6	52.913%	Swiss-Prot	strong database homology

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