LXL04_016239 | RubberDandelionOmics

Gene overview

LXL04_016239

Reference: OH-1004 Chr: Chr03 Coordinates: 116264397-116266669 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1425 bp · LXL04_016239|LXL04_016239|OH1004|cDNA

ATGGAGGGGCGTCGAAGGGTGATTTGTGGTGCAACTCAAACAATTGGTTTACTTGCATTCATCTACTTGTTTTACACTCAATCTTTTGCATTCAACCCCATGACATTTTGCTTTGGCAAACGAAATTTGTCTAAGTGGAATGCTGCATTAATGGATGAAGTTGGTGTTCGACACGATGACTTTCAACCATCTCTACAATCTCTTGTAGGAGATTATGATCTACGAAAGCTTGAAACGAGTGGGTTTGCTTGTAATGCGAC...

CDS

Download CDS FASTA

1425 bp · LXL04_016239|LXL04_016239|OH1004|CDS

ATGGAGGGGCGTCGAAGGGTGATTTGTGGTGCAACTCAAACAATTGGTTTACTTGCATTCATCTACTTGTTTTACACTCAATCTTTTGCATTCAACCCCATGACATTTTGCTTTGGCAAACGAAATTTGTCTAAGTGGAATGCTGCATTAATGGATGAAGTTGGTGTTCGACACGATGACTTTCAACCATCTCTACAATCTCTTGTAGGAGATTATGATCTACGAAAGCTTGAAACGAGTGGGTTTGCTTGTAATGCGAC...

Protein

Download Protein FASTA

474 aa · LXL04_016239|LXL04_016239|OH1004|PROTEIN

MEGRRRVICGATQTIGLLAFIYLFYTQSFAFNPMTFCFGKRNLSKWNAALMDEVGVRHDDFQPSLQSLVGDYDLRKLETSGFACNATVHYPLVCVAINHLKIDIKTMEIYISTRLNSTNGTDLLVKEKKEAVQVRPYAWSQFDLLKSVTPVKILREPPQTPARYCDYNHRVPAVVFSSGGFAGNLFHEFNEIIIPLFITSRVFKSRVQFILVNYNSYLVEKYKSIFTSLSQYEVLNPMVNTSIHCFPGAVVGLKFHSFLA...

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_016239`
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_016239

Location Chr03:116264397-116266669 (+)

Description Similar to XAT2: Alpha-1,3-arabinosyltransferase XAT2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g10320`	Glycosyletransferase required for the proper composition and structural properties of released seed coat mucilage.	Highly Branched Xylan Made by IRREGULAR XYLEM14 and MUCILAGE-RELATED21 Links Mucilage to Arabidopsis Seeds.2015 · DOI: 10.1104/pp.15.01441 Xylans Provide the Structural Driving Force for Mucilage Adhesion to the Arabidopsis Seed Coat.2016 · DOI: 10.1104/pp.16.00211

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0330200`	Glycosyltransferase involved in the arabinosylation of xylan, the major hemicellulose (non-cellulosic component) of primary and secondary walls of angiosperms.	No verified direct reference in this release
`Os03g0567600`	Glycosyltransferase involved in the arabinosylation of xylan, the major hemicellulose (non-cellulosic component) of primary and secondary walls of angiosperms.	No verified direct reference in this release
`Os02g0329800`	Glycosyltransferase involved in the xylosylation of xylan, the major hemicellulose (non-cellulosic component) of primary and secondary walls of angiosperms.	XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan.2012 · DOI: 10.1073/pnas.1202079109
`Os06g0707000`	Glycosyltransferase involved in the xylosylation of xylan, the major hemicellulose (non-cellulosic component) of primary and secondary walls of angiosperms.	A Novel Rice Xylosyltransferase Catalyzes the Addition of 2-O-Xylosyl Side Chains onto the Xylan Backbone.2018 · DOI: 10.1093/pcp/pcy003

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016239 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009664 plant-type cell wall organization Biological Process

GO:0010192 mucilage biosynthetic process Biological Process

GO:0048354 mucilage biosynthetic process involved in seed coat development Biological Process

GO:0071555 cell wall organization Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0016757 glycosyltransferase activity Molecular Function

GO:0035252 UDP-xylosyltransferase activity Molecular Function

GO:0047517 1,4-beta-D-xylan synthase activity Molecular Function

GO:0052636 arabinosyltransferase activity Molecular Function

KEGG gene cross-reference

ath:AT3G10320

dosa:Os02g0329800

dosa:Os02g0330200

dosa:Os03g0567600

dosa:Os06g0707000

osa:4329203

osa:4329205

osa:4333275

osa:4342010

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.

Golgi apparatus0.506

Rank 1 · LXL04_016239 · OH-1004

Lysosome / Vacuole0.134

Rank 2 · LXL04_016239 · OH-1004

Endoplasmic reticulum0.132

Rank 3 · LXL04_016239 · OH-1004

Cell membrane0.081

Rank 4 · LXL04_016239 · OH-1004

Cytoplasm0.076

Rank 5 · LXL04_016239 · 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.

PF04577.20Glyco_transf_61273-374 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016239	`PF04577.20`	Glyco_transf_61	273	374	1.8e-14	54.9

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
`Q9SS43`	Arabidopsis thaliana	Xylan glycosyltransferase MUCI21	30.498%	Swiss-Prot	moderate database homology
`Q6ZFR0`	Oryza sativa subsp. japonica	Alpha-1,3-arabinosyltransferase XAT2	40.173%	Swiss-Prot	moderate database homology
`Q10I20`	Oryza sativa subsp. japonica	Alpha-1,3-arabinosyltransferase XAT3	39.589%	Swiss-Prot	moderate database homology
`Q6Z7I3`	Oryza sativa subsp. japonica	Beta-1,2-xylosyltransferease XAX1	35.171%	Swiss-Prot	moderate database homology
`Q5Z8T8`	Oryza sativa subsp. japonica	Beta-1,2-xylosyltransferase XYXT1	39.542%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card