LXL04_016979 | RubberDandelionOmics

Gene overview

LXL04_016979

Reference: OH-1004 Chr: Chr03 Coordinates: 138316624-138317511 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

888 bp · LXL04_016979|LXL04_016979|OH1004|cDNA

ATGAGGTCAAGAACACAATTCCCAGTGAACACCAAGCTTCTTGTCATTAGCATCATCGTCGTGTTCTTTCTTCTCTTTGTATTCAGATCGACATTTTCATCATCTTCCAACGATCAAATTTCATCATCTCAAATCGCGCAAAAAGTCCTTCCAAAATCAGTTTCAGATTCTCTCAGAAACATTCAAACATCTCCAAAATGCTCACCAACCTGCAACAAAATCCCACCTTCATTAGCGCAAGCTCTAGTCCACTACTCAAC...

CDS

Download CDS FASTA

888 bp · LXL04_016979|LXL04_016979|OH1004|CDS

ATGAGGTCAAGAACACAATTCCCAGTGAACACCAAGCTTCTTGTCATTAGCATCATCGTCGTGTTCTTTCTTCTCTTTGTATTCAGATCGACATTTTCATCATCTTCCAACGATCAAATTTCATCATCTCAAATCGCGCAAAAAGTCCTTCCAAAATCAGTTTCAGATTCTCTCAGAAACATTCAAACATCTCCAAAATGCTCACCAACCTGCAACAAAATCCCACCTTCATTAGCGCAAGCTCTAGTCCACTACTCAAC...

Protein

Download Protein FASTA

295 aa · LXL04_016979|LXL04_016979|OH1004|PROTEIN

MRSRTQFPVNTKLLVISIIVVFFLLFVFRSTFSSSSNDQISSSQIAQKVLPKSVSDSLRNIQTSPKCSPTCNKIPPSLAQALVHYSTSTITPQQTSKEISVTKTILDKKSPCNFLVFGLGHDSLMWSSLNFNGRTVFLEEDEAWIEQIRKRFPMLESYHVRYDSKVNQADGLMEAGKGPECTAVGEARHSVCQLALKGLPEDVYETNWDLIMVDAPTGYYDEAPGRMSAIYTAGMMARNRAEGETDVFVHDVNRVVEDKF...

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_016979`
TK1151 ID	TkA08G130790
OH-1004 ID	LXL04_016979
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	69.800
Protein coverage (%)	TK1151 99.422 / OH-1004 57.966 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_016979

Location Chr03:138316624-138317511 (-)

Description Similar to GXM1: Glucuronoxylan 4-O-methyltransferase 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g09610`	Methyltransferase catalyzing 4-O-methylation of glucuronic acid side chains on xylan.	Three Arabidopsis DUF579 domain-containing GXM proteins are methyltransferases catalyzing 4-o-methylation of glucuronic acid on xylan.2012 · DOI: 10.1093/pcp/pcs138
`At4g09990`	Methyltransferase catalyzing 4-O-methylation of glucuronic acid side chains on xylan.	Three Arabidopsis DUF579 domain-containing GXM proteins are methyltransferases catalyzing 4-o-methylation of glucuronic acid on xylan.2012 · DOI: 10.1093/pcp/pcs138
`At1g33800`	Methyltransferase catalyzing 4-O-methylation of glucuronic acid side chains on xylan.	Three Arabidopsis DUF579 domain-containing GXM proteins are methyltransferases catalyzing 4-o-methylation of glucuronic acid on xylan.2012 · DOI: 10.1093/pcp/pcs138
`At1g67330`	Involved in the methylation of glucuronic acid of different plant cell wall component, but mainly on side chains of arabinogalactans.	Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis.2019 · DOI: 10.1002/pld3.117
`At1g27930`	Involved in the methylation of glucuronic acid of different plant cell wall component, but mainly on side chains of arabinogalactans.	Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis.2019 · DOI: 10.1002/pld3.117

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016979 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005976 polysaccharide metabolic process Biological Process

GO:0006479 protein methylation Biological Process

GO:0009808 lignin metabolic process Biological Process

GO:0009827 plant-type cell wall modification Biological Process

GO:0009834 plant-type secondary cell wall biogenesis Biological Process

GO:0032259 methylation Biological Process

GO:0045491 xylan metabolic process Biological Process

GO:0045492 xylan biosynthetic process Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G09610

ath:AT1G27930

ath:AT1G33800

ath:AT1G67330

ath:AT4G09990

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.

Golgi apparatus0.785

Rank 1 · LXL04_016979 · OH-1004

Endoplasmic reticulum0.076

Rank 2 · LXL04_016979 · OH-1004

Extracellular0.059

Rank 3 · LXL04_016979 · OH-1004

Cell membrane0.058

Rank 4 · LXL04_016979 · OH-1004

Cytoplasm0.043

Rank 5 · LXL04_016979 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF21729.4IRX15_IRX15L_GXM97-280 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016979	`PF21729.4`	IRX15_IRX15L_GXM	97	280	3.1e-79	265.6

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
`Q6NMK1`	Arabidopsis thaliana	Glucuronoxylan 4-O-methyltransferase 1	70.819%	Swiss-Prot	strong database homology
`Q9T0F7`	Arabidopsis thaliana	Glucuronoxylan 4-O-methyltransferase 2	59.933%	Swiss-Prot	strong database homology
`Q9LQ32`	Arabidopsis thaliana	Glucuronoxylan 4-O-methyltransferase 3	69.778%	Swiss-Prot	strong database homology
`Q9FYG0`	Arabidopsis thaliana	Arabinogalactan O-methyltransferase 2	51.101%	Swiss-Prot	strong database homology
`Q9C7F9`	Arabidopsis thaliana	Arabinogalactan O-methyltransferase 1	53.774%	Swiss-Prot	strong database homology

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