LXL04_017298 | RubberDandelionOmics

Gene overview

LXL04_017298

Reference: OH-1004 Chr: Chr03 Coordinates: 145536801-145538229 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

648 bp · LXL04_017298|LXL04_017298|OH1004|cDNA

ATGGGTGCAGCTAGGTCGAAACGCGAGAAAGCTTTAGGCAACCAATTTCCAGAAGGCAAACGATACTTCGGTCTCGAAATTTTTGGCAATACATGTTCACACTTGTGCGAGAAATTGCTGTCGGAGACGCCGCACACTATTTTAGCCGTCGACGTGTACAATGACAAGATCAAACACCTTCTCGAGCCGGATTCCCTTCCTTGGGCCGGTCGCATCCAGTTCCACCGCCTCAACATTAAGAATGATTCGCGCCTTGAAGG...

CDS

Download CDS FASTA

648 bp · LXL04_017298|LXL04_017298|OH1004|CDS

ATGGGTGCAGCTAGGTCGAAACGCGAGAAAGCTTTAGGCAACCAATTTCCAGAAGGCAAACGATACTTCGGTCTCGAAATTTTTGGCAATACATGTTCACACTTGTGCGAGAAATTGCTGTCGGAGACGCCGCACACTATTTTAGCCGTCGACGTGTACAATGACAAGATCAAACACCTTCTCGAGCCGGATTCCCTTCCTTGGGCCGGTCGCATCCAGTTCCACCGCCTCAACATTAAGAATGATTCGCGCCTTGAAGG...

Protein

Download Protein FASTA

215 aa · LXL04_017298|LXL04_017298|OH1004|PROTEIN

MGAARSKREKALGNQFPEGKRYFGLEIFGNTCSHLCEKLLSETPHTILAVDVYNDKIKHLLEPDSLPWAGRIQFHRLNIKNDSRLEGLIKCSDLSEEVIQLSCYVVQLLNTPLNCASFTSRLVKYMGKPSAAIFPKTAPYDRIPLTKSLKKIHPLAFSGQLRNRDEGAENGLEFTIVRPFNWIGPRMDFIPGIDGPSEGVPRVQKDVSGNRVFSK

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_017298`
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_017298

Location Chr03:145536801-145538229 (+)

Description Similar to AXS2: UDP-D-apiose/UDP-D-xylose synthase 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g08200`	Together with AXS1, catalyzes the conversion of UDP-D- glucuronate into a mixture of UDP-D-apiose (UDP-Api) as the main product and UDP-D-xylose to a lesser extent, via a cycle of oxidation and reduction.	UDP-Api/UDP-Xyl synthases affect plant development by controlling the content of UDP-Api to regulate the RG-II-borate complex.2020 · DOI: 10.1111/tpj.14921
`At2g27860`	Together with AXS2, catalyzes the conversion of UDP-D- glucuronate into a mixture of UDP-D-apiose (UDP-Api) as the main product and UDP-D-xylose to a lesser extent, via a cycle of oxidation and reduction.	The biosynthesis of the branched-chain sugar d-apiose in plants: functional cloning and characterization of a UDP-d-apiose/UDP-d-xylose synthase from Arabidopsis.2003 · DOI: 10.1046/j.1365-313x.2003.01841.x Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis.2019 · DOI: 10.1038/s41929-019-0382-8 UDP-Api/UDP-Xyl synthases affect plant development by controlling the content of UDP-Api to regulate the RG-II-borate complex.2020 · DOI: 10.1111/tpj.14921
`At2g22310`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	Ubiquitin-specific proteases from Arabidopsis thaliana: cloning of AtUBP5 and analysis of substrate specificity of AtUBP3, AtUBP4, and AtUBP5 using Escherichia coli in vivo and in vitro assays.2000 · DOI: 10.1006/abbi.2000.1874 The ubiquitin-specific protease subfamily UBP3/UBP4 is essential for pollen development and transmission in Arabidopsis.2007 · DOI: 10.1104/pp.106.095323
`At4g39910`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	Ubiquitin-specific proteases from Arabidopsis thaliana: cloning of AtUBP5 and analysis of substrate specificity of AtUBP3, AtUBP4, and AtUBP5 using Escherichia coli in vivo and in vitro assays.2000 · DOI: 10.1006/abbi.2000.1874 The ubiquitin-specific protease subfamily UBP3/UBP4 is essential for pollen development and transmission in Arabidopsis.2007 · DOI: 10.1104/pp.106.095323

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0969100`	Catalyzes the conversion of UDP-D-glucuronate to a mixture of UDP-D-apiose and UDP-D-xylose.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017298 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006508 proteolysis Biological Process

GO:0009226 nucleotide-sugar biosynthetic process Biological Process

GO:0016579 protein deubiquitination Biological Process

GO:0031647 regulation of protein stability Biological Process

GO:0033320 UDP-D-xylose biosynthetic process Biological Process

GO:0033352 UDP-D-apiose biosynthetic process Biological Process

GO:0071555 cell wall organization Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005777 peroxisome Cellular Component

GO:0005794 Golgi apparatus Cellular Component

KEGG gene cross-reference

ath:AT1G08200

ath:AT2G22310

ath:AT2G27860

ath:AT4G39910

dosa:Os01g0969100

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.

Cytoplasm0.393

Rank 1 · LXL04_017298 · OH-1004

Nucleus0.276

Rank 2 · LXL04_017298 · OH-1004

Mitochondrion0.175

Rank 3 · LXL04_017298 · OH-1004

Extracellular0.097

Rank 4 · LXL04_017298 · OH-1004

Cell membrane0.066

Rank 5 · LXL04_017298 · 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.

PF01370.28Epimerase33-186 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017298	`PF01370.28`	Epimerase	33	186	3e-06	27.6

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
`Q9SGE0`	Arabidopsis thaliana	UDP-D-apiose/UDP-D-xylose synthase 2	50.467%	Swiss-Prot	strong database homology
`Q9ZUY6`	Arabidopsis thaliana	UDP-D-apiose/UDP-D-xylose synthase 1	50.463%	Swiss-Prot	strong database homology
`Q8LAM0`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 4	81.250%	Swiss-Prot	weak database homology
`O24454`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 3	81.250%	Swiss-Prot	weak database homology
`Q8S9Z2`	Oryza sativa subsp. japonica	UDP-D-apiose/UDP-D-xylose synthase	45.794%	Swiss-Prot	moderate database homology

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