LXL04_004616 | RubberDandelionOmics

Gene overview

LXL04_004616

Reference: OH-1004 Chr: Chr01 Coordinates: 141645677-141647931 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1170 bp · LXL04_004616|LXL04_004616|OH1004|cDNA

ATGGCATCTACGACGGCGAGGTTAGATCTGGATGGAAATACGATAAATCCGATGACGATATGCATGATTGGCGCTGGAGGATTCATAGGTTCGCACTTGTGCGACAAATTGATGAATGAGACGCCACACACGGTGTTAGCTGTTGATGTTTACAATGACAAGATCAAGCACCTACTCGAACCGGACTCTCTTCCTTGGGCCGGGCGCATTCAGTTCCACCGTCTTAATATCAAGAATGATTCTCGTCTCGAAGGGCTCAT...

CDS

Download CDS FASTA

1170 bp · LXL04_004616|LXL04_004616|OH1004|CDS

ATGGCATCTACGACGGCGAGGTTAGATCTGGATGGAAATACGATAAATCCGATGACGATATGCATGATTGGCGCTGGAGGATTCATAGGTTCGCACTTGTGCGACAAATTGATGAATGAGACGCCACACACGGTGTTAGCTGTTGATGTTTACAATGACAAGATCAAGCACCTACTCGAACCGGACTCTCTTCCTTGGGCCGGGCGCATTCAGTTCCACCGTCTTAATATCAAGAATGATTCTCGTCTCGAAGGGCTCAT...

Protein

Download Protein FASTA

389 aa · LXL04_004616|LXL04_004616|OH1004|PROTEIN

MASTTARLDLDGNTINPMTICMIGAGGFIGSHLCDKLMNETPHTVLAVDVYNDKIKHLLEPDSLPWAGRIQFHRLNIKNDSRLEGLIKCSDLTINLAAICTPADYNTRPLDTIYSNFIDALPVVKYCSENSKRLIHFSTCEVYGKTIGSYLPKDSPLRQDPAYYILKEDTSPCIFGSVEKQRWSYACAKQLIERLIYAEGAENGLEFTIVRPFNWIGPRMDFIPGIDGPSEGVPRVLACFSNNLLRREPLKLVDGGESQR...

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_004616`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_004616

Location Chr01:141645677-141647931 (+)

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

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_004616 · 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

sse:Ssed_0924

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.

Cytoplasm0.663

Rank 1 · LXL04_004616 · OH-1004

Nucleus0.342

Rank 2 · LXL04_004616 · OH-1004

Mitochondrion0.100

Rank 3 · LXL04_004616 · OH-1004

Peroxisome0.062

Rank 4 · LXL04_004616 · OH-1004

Plastid0.058

Rank 5 · LXL04_004616 · 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

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004616	`PF01370.28`	Epimerase	20	290	5.2e-48	164.3
LXL04_004616	`PF03435.25`	Sacchrp_dh_NADP	20	97	9.7e-06	26.7
LXL04_004616	`PF02719.22`	Polysacc_synt_2	21	139	4.4e-07	30.1
LXL04_004616	`PF01073.26`	3Beta_HSD	22	145	3.7e-06	26.9
LXL04_004616	`PF16363.12`	GDP_Man_Dehyd	24	366	7.4e-28	98.7

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	89.460%	Swiss-Prot	strong database homology
`Q9ZUY6`	Arabidopsis thaliana	UDP-D-apiose/UDP-D-xylose synthase 1	87.404%	Swiss-Prot	strong database homology
`Q8S9Z2`	Oryza sativa subsp. japonica	UDP-D-apiose/UDP-D-xylose synthase	83.551%	Swiss-Prot	strong database homology

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