LXL04_032971 | RubberDandelionOmics

Gene overview

LXL04_032971

Reference: OH-1004 Chr: Chr07 Coordinates: 32571003-32573189 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1170 bp · LXL04_032971|LXL04_032971|OH1004|cDNA

ATGGCGGAATCGTCGGCGAGGGTAGATCTGGACGGAAATACCATAAATCCGATGACGATTTGCATGATTGGTGCCGGTGGATTCATAGGTTCACACTTGTGCGAGAAATTGCTGTCCGAGACGCCGCACACTATTTTAGCGGTAGACGTGTACAATGACAAGATCAAACACCTTCTCGAGCCGGATTCCCTTCCTTGGGCCGGTCGCATCCAGTTCCACCGCCTCAACATTAAGAATGATTCGCGCCTTGAAGGTCTCAT...

CDS

Download CDS FASTA

1170 bp · LXL04_032971|LXL04_032971|OH1004|CDS

ATGGCGGAATCGTCGGCGAGGGTAGATCTGGACGGAAATACCATAAATCCGATGACGATTTGCATGATTGGTGCCGGTGGATTCATAGGTTCACACTTGTGCGAGAAATTGCTGTCCGAGACGCCGCACACTATTTTAGCGGTAGACGTGTACAATGACAAGATCAAACACCTTCTCGAGCCGGATTCCCTTCCTTGGGCCGGTCGCATCCAGTTCCACCGCCTCAACATTAAGAATGATTCGCGCCTTGAAGGTCTCAT...

Protein

Download Protein FASTA

389 aa · LXL04_032971|LXL04_032971|OH1004|PROTEIN

MAESSARVDLDGNTINPMTICMIGAGGFIGSHLCEKLLSETPHTILAVDVYNDKIKHLLEPDSLPWAGRIQFHRLNIKNDSRLEGLIKCSDLIVNLAAICTPADYNTRPLDTIYSNFIDALPVVKYCSDNNKRLIHFSTCEIYGKTIGSYLPKDSPLRQDPAYYILKEDTSPCIFGPIEKQRWSYACAKQLIERLIFAEGAENGLEFTIVRPFNWIGPRMDFIPGIDGPSEGVPRVLACFSNNLLRREPLKLVDGGESQR...

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_032971`
TK1151 ID	TkA08G217180
OH-1004 ID	LXL04_032971
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
Protein identity (%)	97.600
Protein coverage (%)	TK1151 95.930 / OH-1004 84.833 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_032971

Location Chr07:32571003-32573189 (-)

Description Similar to AXS1: UDP-D-apiose/UDP-D-xylose synthase 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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

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_032971 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009226 nucleotide-sugar biosynthetic process Biological Process

GO:0009245 lipid A biosynthetic process Biological Process

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

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

GO:0046677 response to antibiotic Biological Process

GO:0071555 cell wall organization Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005777 peroxisome Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

KEGG gene cross-reference

ath:AT1G08200

ath:AT2G27860

dosa:Os01g0969100

eca:ECA3144

pct:PC1_2926

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.

Cytoplasm0.671

Rank 1 · LXL04_032971 · OH-1004

Nucleus0.358

Rank 2 · LXL04_032971 · OH-1004

Mitochondrion0.088

Rank 3 · LXL04_032971 · OH-1004

Peroxisome0.064

Rank 4 · LXL04_032971 · OH-1004

Plastid0.058

Rank 5 · LXL04_032971 · 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.

PF01370.28Epimerase20-290 aa

PF03435.25Sacchrp_dh_NADP20-97 aa

PF02719.22Polysacc_synt_221-139 aa

PF01073.263Beta_HSD22-145 aa

PF16363.12GDP_Man_Dehyd24-366 aa

PF07993.19NAD_binding_424-217 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032971	`PF01370.28`	Epimerase	20	290	8.3e-49	166.9
LXL04_032971	`PF03435.25`	Sacchrp_dh_NADP	20	97	1.4e-06	29.4
LXL04_032971	`PF02719.22`	Polysacc_synt_2	21	139	2.2e-08	34.4
LXL04_032971	`PF01073.26`	3Beta_HSD	22	145	6.6e-06	26.1
LXL04_032971	`PF16363.12`	GDP_Man_Dehyd	24	366	1.4e-28	101.1
LXL04_032971	`PF07993.19`	NAD_binding_4	24	217	5.4e-07	29.8

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
`Q9ZUY6`	Arabidopsis thaliana	UDP-D-apiose/UDP-D-xylose synthase 1	87.918%	Swiss-Prot	strong database homology
`Q9SGE0`	Arabidopsis thaliana	UDP-D-apiose/UDP-D-xylose synthase 2	87.661%	Swiss-Prot	strong database homology
`Q8S9Z2`	Oryza sativa subsp. japonica	UDP-D-apiose/UDP-D-xylose synthase	82.507%	Swiss-Prot	strong database homology

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