LXL04_032697 | RubberDandelionOmics

Gene overview

LXL04_032697

Reference: OH-1004 Chr: Chr07 Coordinates: 27954709-27956403 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1233 bp · LXL04_032697|LXL04_032697|OH1004|cDNA

CAAATCAACTGCCCCATCAAAATCCTTGAGATAAATTTACTATTATATCCCTGTCAGCCCCAGAAACATATAAATCCACCATACTTATTTCCATTTTTATCATCCTCCACCTTTTACCCCTCTCCATCTCACCTCAACTCCCAATTCTGTCTTGTTTTCCGATTATTTACAGTCATGGGATCATCAGAAAGACCGAAGAAGAAAGTCCAGTTATGGAAGAAAGCCACAGTCCATTTCTTGTTATGTTTCATTCTCGGTTT...

CDS

Download CDS FASTA

1059 bp · LXL04_032697|LXL04_032697|OH1004|CDS

ATGGGATCATCAGAAAGACCGAAGAAGAAAGTCCAGTTATGGAAGAAAGCCACAGTCCATTTCTTGTTATGTTTCATTCTCGGTTTCTTCACTGGTTTTTCCCCTACAAACAAGTCGTCTTTCCCTCCTAATGATAATGTTATTGCATCCAAAGATTCGCAGGAGATTTCCCCACCACCAAAGGTAATCCCTAACGAAATATCCAAACAGGAAAATGGGAATTTTGATAGGAGCATGATGGATGAATCTTTATCAATGAA...

Protein

Download Protein FASTA

352 aa · LXL04_032697|LXL04_032697|OH1004|PROTEIN

MGSSERPKKKVQLWKKATVHFLLCFILGFFTGFSPTNKSSFPPNDNVIASKDSQEISPPPKVIPNEISKQENGNFDRSMMDESLSMKVQERPNLGPIEEEGKNAILTQEKGETETLTPRRLVIIVTPTSDKDELRGVLLRKMANTLALVPPPLLWVVVESQSESDEVSDILRKTNVMYRHLVFKENFTDVEVEMDHQRNVALKHIEYHRLSGIVHFASLYNVYDLSFFEEIRAIEVFGTWPMAFLSTNRQRVRIEGPVCD...

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_032697`
TK1151 ID	TkA08G198500
OH-1004 ID	LXL04_032697
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 85.854 / 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_032697

Location Chr07:27954709-27956403 (+)

Description Similar to IRX9: Beta-1,4-xylosyltransferase IRX9

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g37090`	Involved in the synthesis of the hemicellulose glucuronoxylan, a major component of secondary cell walls.	Development and application of a suite of polysaccharide-degrading enzymes for analyzing plant cell walls.2006 · DOI: 10.1073/pnas.0604632103 Arabidopsis irregular xylem8 and irregular xylem9: implications for the complexity of glucuronoxylan biosynthesis.2007 · DOI: 10.1105/tpc.106.049320 The irregular xylem9 mutant is deficient in xylan xylosyltransferase activity.2007 · DOI: 10.1093/pcp/pcm135 Comparison of five xylan synthesis mutants reveals new insight into the mechanisms of xylan synthesis.2007 · DOI: 10.1111/j.1365-313x.2007.03307.x The Arabidopsis family GT43 glycosyltransferases form two functionally nonredundant groups essential for the elongation of glucuronoxylan backbone.2010 · DOI: 10.1104/pp.110.155309 Analysis of the Arabidopsis IRX9/IRX9-L and IRX14/IRX14-L pairs of glycosyltransferase genes reveals critical contributions to biosynthesis of the hemicellulose glucuronoxylan.2010 · DOI: 10.1104/pp.110.154971 Arabidopsis family GT43 members are xylan xylosyltransferases required for the elongation of the xylan backbone.2012 · DOI: 10.1093/pcp/pcr158 Site-directed mutagenesis of IRX9, IRX9L and IRX14 proteins involved in xylan biosynthesis: glycosyltransferase activity is not required for IRX9 function in Arabidopsis.2014 · DOI: 10.1371/journal.pone.0105014
`At1g27600`	Involved in the synthesis of the hemicellulose glucuronoxylan, a major component of secondary cell walls.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0287800`	Involved in the synthesis of glucuronoxylan hemicellulose in secondary cell walls.	No verified direct reference in this release
`Os05g0123100`	Probable beta-1,4-xylosyltransferase involved in xylan biosynthesis in cell walls.	Functional roles of rice glycosyltransferase family GT43 in xylan biosynthesis.2014 · DOI: 10.4161/psb.27809
`Os01g0675500`	Probable beta-1,4-xylosyltransferase involved in xylan biosynthesis in cell walls.	Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis.2013 · DOI: 10.3389/fpls.2013.00083

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032697 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0010413 glucuronoxylan metabolic process Biological Process

GO:0010417 glucuronoxylan biosynthetic process Biological Process

GO:0010584 pollen exine formation Biological Process

GO:0045492 xylan biosynthetic process Biological Process

GO:0071555 cell wall organization Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0015018 galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity Molecular Function

GO:0042285 xylosyltransferase activity Molecular Function

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

KEGG gene cross-reference

ath:AT1G27600

ath:AT2G37090

dosa:Os01g0675500

dosa:Os03g0287800

dosa:Os05g0123100

osa:4325514

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 apparatus0.822

Rank 1 · LXL04_032697 · OH-1004

Endoplasmic reticulum0.064

Rank 2 · LXL04_032697 · OH-1004

Cell membrane0.061

Rank 3 · LXL04_032697 · OH-1004

Extracellular0.050

Rank 4 · LXL04_032697 · OH-1004

Cytoplasm0.043

Rank 5 · LXL04_032697 · 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.

PF03360.22Glyco_transf_43142-347 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032697	`PF03360.22`	Glyco_transf_43	142	347	5.3e-55	187.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9ZQC6`	Arabidopsis thaliana	Beta-1,4-xylosyltransferase IRX9	54.342%	Swiss-Prot	strong database homology
`Q9SXC4`	Arabidopsis thaliana	Probable beta-1,4-xylosyltransferase IRX9H	37.026%	Swiss-Prot	moderate database homology
`Q10N05`	Oryza sativa subsp. japonica	Probable glucuronosyltransferase Os03g0287800	39.031%	Swiss-Prot	moderate database homology
`Q75L84`	Oryza sativa subsp. japonica	Probable beta-1,4-xylosyltransferase GT43A	40.431%	Swiss-Prot	moderate database homology
`Q5QM25`	Oryza sativa subsp. japonica	Probable beta-1,4-xylosyltransferase IRX9L	33.690%	Swiss-Prot	moderate database homology

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