LXL04_000062 | RubberDandelionOmics

Gene overview

LXL04_000062

Reference: OH-1004 Chr: Chr01 Coordinates: 1415124-1416398 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1034 bp · LXL04_000062|LXL04_000062|OH1004|cDNA

AACATATAAAGGCGAAAACGGGCACAAGCCACACCCTTGCAGCCACTGCATAGTATCCCCAAACAGCCTCCattcacacacacacacacacacagtgCTACGAATCAATGGACGGAACCGGAGTAGTGGCGGTGTACGGCAACGGTGCTCTGACGGAGAGCAAGAAATCACCATACTCCGTCAAGGTCGGCCTCGCTCAGATGCTTCGTGGCGGCGTCATCATGGACGTCGTCAACGCAGAACAAGCCCGCATAGCCGAA...

CDS

Download CDS FASTA

927 bp · LXL04_000062|LXL04_000062|OH1004|CDS

ATGGACGGAACCGGAGTAGTGGCGGTGTACGGCAACGGTGCTCTGACGGAGAGCAAGAAATCACCATACTCCGTCAAGGTCGGCCTCGCTCAGATGCTTCGTGGCGGCGTCATCATGGACGTCGTCAACGCAGAACAAGCCCGCATAGCCGAAGAAGCCGGCGCCTGTGCTGTCATGGCCCTAGAGCGTGTCCCAGCAGACATCCGTGCGCAAGGCGGCGTTGCTCGGATGAGCGACCCACAACTGATAAAGGAAATCAA...

Protein

Download Protein FASTA

308 aa · LXL04_000062|LXL04_000062|OH1004|PROTEIN

MDGTGVVAVYGNGALTESKKSPYSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRAQGGVARMSDPQLIKEIKQAVTIPVMAKARIGHFVEAQILEAIGVDYVDESEVLTLADDMNHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVMGDIRVLANMDDDEVFTFAKKIAAPYDLVMQTKQLGRLPVVQFAAGGVATPADAALMMQLGCDGVFVGSGVFKSGDP...

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_000062`
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_000062

Location Chr01:1415124-1416398 (+)

Description Similar to PDX1: Probable pyridoxal 5'-phosphate synthase subunit PDX1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g01410`	Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia.	No verified direct reference in this release
`At2g38230`	Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0100200`	Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000062 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006520 amino acid metabolic process Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0006982 response to lipid hydroperoxide Biological Process

GO:0008615 pyridoxine biosynthetic process Biological Process

GO:0009651 response to salt stress Biological Process

GO:0010224 response to UV-B Biological Process

GO:0010335 response to non-ionic osmotic stress Biological Process

GO:0015994 chlorophyll metabolic process Biological Process

GO:0042538 hyperosmotic salinity response Biological Process

GO:0042823 pyridoxal phosphate biosynthetic process Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

KEGG gene cross-reference

ath:AT2G38230

ath:AT5G01410

dosa:Os07g0100200

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.715

Rank 1 · LXL04_000062 · OH-1004

Nucleus0.296

Rank 2 · LXL04_000062 · OH-1004

Cell membrane0.101

Rank 3 · LXL04_000062 · OH-1004

Endoplasmic reticulum0.061

Rank 4 · LXL04_000062 · OH-1004

Mitochondrion0.045

Rank 5 · LXL04_000062 · 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.

PF01680.24SOR_SNZ24-228 aa

PF05690.21ThiG208-272 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000062	`PF01680.24`	SOR_SNZ	24	228	4.1e-112	373.7
LXL04_000062	`PF05690.21`	ThiG	208	272	8.6e-11	42.4

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
`Q8L940`	Arabidopsis thaliana	Pyridoxal 5'-phosphate synthase subunit PDX1.3	92.557%	Swiss-Prot	strong database homology
`O80448`	Arabidopsis thaliana	Pyridoxal 5'-phosphate synthase subunit PDX1.1	89.320%	Swiss-Prot	strong database homology
`Q69LA6`	Oryza sativa subsp. japonica	Probable pyridoxal 5'-phosphate synthase subunit PDX1.1	86.667%	Swiss-Prot	strong database homology

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