LXL04_028318 | RubberDandelionOmics

Gene overview

LXL04_028318

Reference: OH-1004 Chr: Chr06 Coordinates: 37536389-37544518 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2565 bp · LXL04_028318|LXL04_028318|OH1004|cDNA

ATGGCTTCGAATTGTAGTTCTTTAAAGGGCACATTTCTTCCGACAACCATAACGAAAGATGGTTACAGCTCTACTAGTTTGCTTAATCCATCCATCTACCCAATTTTATCGCTAAAAAAGCAAAAGTTCGCGGGAATTGTGGTTGTTGCAAAGTACAATGCGTCTAAGGATAAAGAAGAGCTTATAACAAAGACTATGAGTATGGGAACAACTCTCAAGTACTCTGGCGAGAAACCAAAAACCCCAATTTTGGATACCGT...

CDS

Download CDS FASTA

2565 bp · LXL04_028318|LXL04_028318|OH1004|CDS

ATGGCTTCGAATTGTAGTTCTTTAAAGGGCACATTTCTTCCGACAACCATAACGAAAGATGGTTACAGCTCTACTAGTTTGCTTAATCCATCCATCTACCCAATTTTATCGCTAAAAAAGCAAAAGTTCGCGGGAATTGTGGTTGTTGCAAAGTACAATGCGTCTAAGGATAAAGAAGAGCTTATAACAAAGACTATGAGTATGGGAACAACTCTCAAGTACTCTGGCGAGAAACCAAAAACCCCAATTTTGGATACCGT...

Protein

Download Protein FASTA

854 aa · LXL04_028318|LXL04_028318|OH1004|PROTEIN

MASNCSSLKGTFLPTTITKDGYSSTSLLNPSIYPILSLKKQKFAGIVVVAKYNASKDKEELITKTMSMGTTLKYSGEKPKTPILDTVNNPVHMKNLNVEELENLADELREEIVYTVSKTGGHLSSNLGVVELTISLHFVFDTPDDKIIWDVGHQSYPHKILTGRRSRMGTIRQTCGLASFPKREESPHDAFGVGHSSTSISAGLGMAVGRDLVGKNNHVIAVIGDGAMTAGQAYEAINNAGYMDANFIIVLNDNRQVSLP...

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_028318`
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_028318

Location Chr06:37536389-37544518 (-)

Description Similar to Os07g0190000: Probable 1-deoxy-D-xylulose-5-phosphate synthase 2, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g15560`	Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (DXP).	Analysis of the expression of CLA1, a gene that encodes the 1-deoxyxylulose 5-phosphate synthase of the 2-C-methyl-D-erythritol-4-phosphate pathway in Arabidopsis.2000 · DOI: 10.1104/pp.124.1.95 CLA1, a novel gene required for chloroplast development, is highly conserved in evolution.1996 · DOI: 10.1046/j.1365-313x.1996.9050649.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0190000`	Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP).	No verified direct reference in this release
`Os05g0408900`	Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028318 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009228 thiamine biosynthetic process Biological Process

GO:0015995 chlorophyll biosynthetic process Biological Process

GO:0016114 terpenoid biosynthetic process Biological Process

GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Biological Process

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0008661 1-deoxy-D-xylulose-5-phosphate synthase activity Molecular Function

GO:0016744 transketolase or transaldolase activity Molecular Function

GO:0042802 identical protein binding Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

ath:AT4G15560

dosa:Os07g0190000

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.

Plastid0.893

Rank 1 · LXL04_028318 · OH-1004

Mitochondrion0.095

Rank 2 · LXL04_028318 · OH-1004

Cytoplasm0.048

Rank 3 · LXL04_028318 · OH-1004

Nucleus0.027

Rank 4 · LXL04_028318 · OH-1004

Peroxisome0.025

Rank 5 · LXL04_028318 · 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.

PF13292.12DXP_synthase_N84-369 aa

PF00676.26E1_dh197-255 aa

PF02779.30Transket_pyr405-471 aa

PF02779.30Transket_pyr613-693 aa

PF02780.26Transketolase_C711-834 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028318	`PF13292.12`	DXP_synthase_N	84	369	1.2e-105	353.4
LXL04_028318	`PF00676.26`	E1_dh	197	255	6.1e-06	26.1
LXL04_028318	`PF02779.30`	Transket_pyr	405	471	4.2e-35	121.7
LXL04_028318	`PF02779.30`	Transket_pyr	613	693	4.2e-35	121.7
LXL04_028318	`PF02780.26`	Transketolase_C	711	834	7.3e-30	104.1

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
`Q38854`	Arabidopsis thaliana	1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic	66.337%	Swiss-Prot	weak database homology
`Q6YU51`	Oryza sativa subsp. japonica	Probable 1-deoxy-D-xylulose-5-phosphate synthase 2, chloroplastic	69.690%	Swiss-Prot	weak database homology
`O22567`	Oryza sativa subsp. japonica	1-deoxy-D-xylulose-5-phosphate synthase 1, chloroplastic	66.080%	Swiss-Prot	weak database homology

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