LXL04_012833 | RubberDandelionOmics

Gene overview

LXL04_012833

Reference: OH-1004 Chr: Chr03 Coordinates: 19521245-19522967 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1026 bp · LXL04_012833|LXL04_012833|OH1004|cDNA

ATGAGCGTCCTTCACGGCGCGTGCGCATCGACATTCCTTACCTCCACATTCACGCGCCAATTAAGACTCTTCAGCGGAAGTAAACGGCAGCCGTCGCAGCGACTTAAAAGAGGAGCTATTAGTGCCATGGGTTCTATGTCAGTTACGACAGCGGATGACCAGCGGTTGAAGAAAGGAATAGCAGAGTTCTACGACGAATCATCGGGAGTTTGGGAGAATATATGGGGAGAACACATGCATCACGGATTTTACGACCCTGA...

CDS

Download CDS FASTA

1026 bp · LXL04_012833|LXL04_012833|OH1004|CDS

ATGAGCGTCCTTCACGGCGCGTGCGCATCGACATTCCTTACCTCCACATTCACGCGCCAATTAAGACTCTTCAGCGGAAGTAAACGGCAGCCGTCGCAGCGACTTAAAAGAGGAGCTATTAGTGCCATGGGTTCTATGTCAGTTACGACAGCGGATGACCAGCGGTTGAAGAAAGGAATAGCAGAGTTCTACGACGAATCATCGGGAGTTTGGGAGAATATATGGGGAGAACACATGCATCACGGATTTTACGACCCTGA...

Protein

Download Protein FASTA

341 aa · LXL04_012833|LXL04_012833|OH1004|PROTEIN

MSVLHGACASTFLTSTFTRQLRLFSGSKRQPSQRLKRGAISAMGSMSVTTADDQRLKKGIAEFYDESSGVWENIWGEHMHHGFYDPDAVVQISDHRSAQIRMIEQALVFASVPEESEKKPRSIVDVGCGIGGSSRYLSRKYGAVCVGITLSPVQAQRANALAAAQGLANKVSFEVADALNQPFPDGKFDLVWSMESGEHMPDKLKFVSELDRVASPGGTIIIVTWCHRDLSPGEESLLPEEKKLLDKICDAFYLPAWCST...

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_012833`
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_012833

Location Chr03:19521245-19522967 (+)

Description Similar to VTE4: Probable tocopherol O-methyltransferase, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g64970`	Involved in the synthesis of tocopherol (vitamin E).	Characterization of an Arabidopsis mutant deficient in gamma-tocopherol methyltransferase.2003 · DOI: 10.1023/b:plan.0000004307.62398.91

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0701600`	Involved in the synthesis of tocopherol (vitamin E).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012833 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009820 alkaloid metabolic process Biological Process

GO:0009821 alkaloid biosynthetic process Biological Process

GO:0010189 vitamin E biosynthetic process Biological Process

GO:0032259 methylation Biological Process

GO:1900985 vindoline biosynthetic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009705 plant-type vacuole membrane Cellular Component

GO:0009706 chloroplast inner membrane Cellular Component

GO:0008168 methyltransferase activity Molecular Function

GO:0008170 N-methyltransferase activity Molecular Function

GO:0008757 S-adenosylmethionine-dependent methyltransferase activity Molecular Function

KEGG gene cross-reference

ath:AT1G64970

dosa:Os02g0701600

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.

Plastid0.722

Rank 1 · LXL04_012833 · OH-1004

Mitochondrion0.286

Rank 2 · LXL04_012833 · OH-1004

Cytoplasm0.071

Rank 3 · LXL04_012833 · OH-1004

Peroxisome0.035

Rank 4 · LXL04_012833 · OH-1004

Nucleus0.032

Rank 5 · LXL04_012833 · 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.

PF13489.13Methyltransf_23115-239 aa

PF01209.25Ubie_methyltran116-227 aa

PF02353.27CMAS120-225 aa

PF13847.13Methyltransf_31121-251 aa

PF13649.13Methyltransf_25123-218 aa

PF08241.19Methyltransf_11124-222 aa

PF08242.19Methyltransf_12124-220 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012833	`PF13489.13`	Methyltransf_23	115	239	4.2e-14	53.3
LXL04_012833	`PF01209.25`	Ubie_methyltran	116	227	4.2e-06	27.0
LXL04_012833	`PF02353.27`	CMAS	120	225	4e-11	43.5
LXL04_012833	`PF13847.13`	Methyltransf_31	121	251	8.9e-15	55.5
LXL04_012833	`PF13649.13`	Methyltransf_25	123	218	2.5e-19	70.4
LXL04_012833	`PF08241.19`	Methyltransf_11	124	222	1.7e-21	77.4
LXL04_012833	`PF08242.19`	Methyltransf_12	124	220	4.1e-11	44.2

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
`Q9ZSK1`	Arabidopsis thaliana	Tocopherol O-methyltransferase, chloroplastic	74.483%	Swiss-Prot	strong database homology
`Q6ZIK0`	Oryza sativa subsp. japonica	Probable tocopherol O-methyltransferase, chloroplastic	77.273%	Swiss-Prot	strong database homology

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