LXL04_006780 | RubberDandelionOmics

Gene overview

LXL04_006780

Reference: OH-1004 Chr: Chr02 Coordinates: 25091699-25093848 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1536 bp · LXL04_006780|LXL04_006780|OH1004|cDNA

ATGAAGCTGCAGGCGTTGCAGCAGAGCTATGCCAATCGGGGCCGGAGCAACAGTTTCAGAGGCTCATCGCCGTTAGATTCGTCTGTAGATGGGGGCGGTTCCATTAAATCGCCGGCGGGTATATTTTGGTCGATCCTTCATTGTTTATGCTGTCTGATTAGTCTCGTTCTTGGATTTAGATTCTCTCGTCTCgtcttcttcctcctcttctCAACTTCTTCCGTTAACAACCTCTACACCACAAGCGCCAACGATATAGC...

CDS

Download CDS FASTA

1536 bp · LXL04_006780|LXL04_006780|OH1004|CDS

ATGAAGCTGCAGGCGTTGCAGCAGAGCTATGCCAATCGGGGCCGGAGCAACAGTTTCAGAGGCTCATCGCCGTTAGATTCGTCTGTAGATGGGGGCGGTTCCATTAAATCGCCGGCGGGTATATTTTGGTCGATCCTTCATTGTTTATGCTGTCTGATTAGTCTCGTTCTTGGATTTAGATTCTCTCGTCTCGTCTTCTTCCTCCTCTTCTCAACTTCTTCCGTTAACAACCTCTACACCACAAGCGCCAACGATATAGC...

Protein

Download Protein FASTA

511 aa · LXL04_006780|LXL04_006780|OH1004|PROTEIN

MKLQALQQSYANRGRSNSFRGSSPLDSSVDGGGSIKSPAGIFWSILHCLCCLISLVLGFRFSRLVFFLLFSTSSVNNLYTTSANDIAETLSFTTSLRSFSPLVANTTSAVATSSRVVVGRHGIRIRPWPHPDPEEVMKAHKLIEAVQREQKVQYGIKNPKTLIAITPTYVRTFQALHLTGLMHTLMNLPYDVVWIVVEAGGATNETSALLAKSKLQIKHIGFPKKMPIFWEARHKMESQMRLQALRVVREEQLDGIVMFA...

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_006780`
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_006780

Location Chr02:25091699-25093848 (-)

Description Similar to IRX14: Beta-1,4-xylosyltransferase IRX14

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g36890`	Involved in the synthesis of the hemicellulose glucuronoxylan, a major component of secondary cell walls.	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 IRX14 and IRX14-LIKE, two glycosyl transferases involved in glucuronoxylan biosynthesis and drought tolerance in Arabidopsis.2010 · DOI: 10.1093/mp/ssq028 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 Highly Branched Xylan Made by IRREGULAR XYLEM14 and MUCILAGE-RELATED21 Links Mucilage to Arabidopsis Seeds.2015 · DOI: 10.1104/pp.15.01441 Xylan synthesized by Irregular Xylem 14 (IRX14) maintains the structure of seed coat mucilage in Arabidopsis.2016 · DOI: 10.1093/jxb/erv510
`At5g67230`	Involved in the synthesis of the hemicellulose glucuronoxylan, a major component of secondary cell walls.	No verified direct reference in this release
`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
`Os06g0687900`	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 roles of rice glycosyltransferase family GT43 in xylan biosynthesis.2014 · DOI: 10.4161/psb.27809
`Os04g0650300`	Involved in the synthesis of glucuronoxylan hemicellulose in secondary cell walls.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006780 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0010051 xylem and phloem pattern formation Biological Process

GO:0010154 fruit development Biological Process

GO:0010246 rhamnogalacturonan I biosynthetic process Biological Process

GO:0010417 glucuronoxylan biosynthetic process Biological Process

GO:0010584 pollen exine formation Biological Process

GO:0045491 xylan metabolic process Biological Process

GO:0045492 xylan biosynthetic process Biological Process

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

GO:0048358 mucilage pectin biosynthetic process Biological Process

GO:0048367 shoot system development Biological Process

GO:0071555 cell wall organization Biological Process

KEGG gene cross-reference

ath:AT1G27600

ath:AT4G36890

ath:AT5G67230

dosa:Os04g0650300

dosa:Os06g0687900

osa:4337225

osa:4341895

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 apparatus0.846

Rank 1 · LXL04_006780 · OH-1004

Endoplasmic reticulum0.070

Rank 2 · LXL04_006780 · OH-1004

Cell membrane0.058

Rank 3 · LXL04_006780 · OH-1004

Extracellular0.043

Rank 4 · LXL04_006780 · OH-1004

Cytoplasm0.042

Rank 5 · LXL04_006780 · 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_43181-425 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006780	`PF03360.22`	Glyco_transf_43	181	425	3.5e-48	164.9

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
`Q8L707`	Arabidopsis thaliana	Beta-1,4-xylosyltransferase IRX14	64.333%	Swiss-Prot	strong database homology
`Q9FH90`	Arabidopsis thaliana	Probable beta-1,4-xylosyltransferase IRX14H	58.130%	Swiss-Prot	strong database homology
`Q9SXC4`	Arabidopsis thaliana	Probable beta-1,4-xylosyltransferase IRX9H	30.272%	Swiss-Prot	moderate database homology
`Q653F4`	Oryza sativa subsp. japonica	Probable beta-1,4-xylosyltransferase IRX14	52.183%	Swiss-Prot	strong database homology
`B9FCV3`	Oryza sativa subsp. japonica	Probable glucuronosyltransferase Os04g0650300	34.081%	Swiss-Prot	moderate database homology

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