LXL04_030807 | RubberDandelionOmics

Gene overview

LXL04_030807

Reference: OH-1004 Chr: Chr06 Coordinates: 123060458-123060754 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

297 bp · LXL04_030807|LXL04_030807|OH1004|cDNA

ATGAAGGAATGTAAGCTTGCGTTAAATGGGCTGCCGGATGAAATAGTGAAGATGAAGTGGGATGTGATTATTGTTGATGGGCCCAATGGGTATGGGCCGGATTCACCGGGAAGAATGGGCTCGATATTTATGGCGGGTATTTTAGCGAATGGGAGTAATGTTGTTGTTCATGATGTTGATCGAATGATTGAAAAGTGGTTTTCTTGGGAGTTTTTGTGTTATGAGAATTTGGTTTCTTCGAAAGGGAGATTTTTGAACTT...

CDS

Download CDS FASTA

297 bp · LXL04_030807|LXL04_030807|OH1004|CDS

ATGAAGGAATGTAAGCTTGCGTTAAATGGGCTGCCGGATGAAATAGTGAAGATGAAGTGGGATGTGATTATTGTTGATGGGCCCAATGGGTATGGGCCGGATTCACCGGGAAGAATGGGCTCGATATTTATGGCGGGTATTTTAGCGAATGGGAGTAATGTTGTTGTTCATGATGTTGATCGAATGATTGAAAAGTGGTTTTCTTGGGAGTTTTTGTGTTATGAGAATTTGGTTTCTTCGAAAGGGAGATTTTTGAACTT...

Protein

Download Protein FASTA

98 aa · LXL04_030807|LXL04_030807|OH1004|PROTEIN

MKECKLALNGLPDEIVKMKWDVIIVDGPNGYGPDSPGRMGSIFMAGILANGSNVVVHDVDRMIEKWFSWEFLCYENLVSSKGRFLNFRRLETIVGNFV

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_030807`
TK1151 ID	TkA07G432840
OH-1004 ID	LXL04_030807
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	98.900
Protein coverage (%)	TK1151 73.643 / OH-1004 96.939 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_030807

Location Chr06:123060458-123060754 (-)

Description Similar to At1g27930: Probable methyltransferase At1g27930

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`At5g67210`	Required for xylan biosynthesis, but not directly involved in catalyzing the addition of sugars to the growing polymer.	The DUF579 domain containing proteins IRX15 and IRX15-L affect xylan synthesis in Arabidopsis.2011 · DOI: 10.1111/j.1365-313x.2010.04475.x
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030807 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006479 protein methylation 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

GO:0005768 endosome Cellular Component

GO:0005794 Golgi apparatus Cellular Component

KEGG gene cross-reference

ath:AT1G09610

ath:AT1G27930

ath:AT1G67330

ath:AT4G09990

ath:AT5G67210

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.

Extracellular0.467

Rank 1 · LXL04_030807 · OH-1004

Cytoplasm0.115

Rank 2 · LXL04_030807 · OH-1004

Endoplasmic reticulum0.099

Rank 3 · LXL04_030807 · OH-1004

Lysosome / Vacuole0.083

Rank 4 · LXL04_030807 · OH-1004

Golgi apparatus0.061

Rank 5 · LXL04_030807 · 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.

PF21729.4IRX15_IRX15L_GXM2-87 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030807	`PF21729.4`	IRX15_IRX15L_GXM	2	87	1.6e-31	110.1

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
`Q9C7F9`	Arabidopsis thaliana	Arabinogalactan O-methyltransferase 1	44.565%	Swiss-Prot	moderate database homology
`Q9FYG0`	Arabidopsis thaliana	Arabinogalactan O-methyltransferase 2	44.565%	Swiss-Prot	moderate database homology
`Q9FH92`	Arabidopsis thaliana	Protein IRX15-LIKE	50.588%	Swiss-Prot	strong database homology
`Q6NMK1`	Arabidopsis thaliana	Glucuronoxylan 4-O-methyltransferase 1	45.556%	Swiss-Prot	moderate database homology
`Q9T0F7`	Arabidopsis thaliana	Glucuronoxylan 4-O-methyltransferase 2	40.659%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card