LXL04_002935 | RubberDandelionOmics

Gene overview

LXL04_002935

Reference: OH-1004 Chr: Chr01 Coordinates: 61713167-61717444 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1362 bp · LXL04_002935|LXL04_002935|OH1004|cDNA

ATGGTTCATCAATCTGTTTGCTCTGAAAATCTGATCAAATTTGTTGATTTCTCCTTATGGGTTTGTTTCGAGGAACTAAAACAGCATCGACGTTCTTTTCATGTATCATTAAGAGCATCAAAGGGTAACAGTAACAGAGTCATTCGATCATGTGAATCAAGTATTGTGAGACACAATTTTAGCAGTTTTAATAAAAGTTTTCTACTTTCAAATAAACGGAACACAAAACCTGTCGCAAGTGCAGTTTCTGAACAACCTAT...

CDS

Download CDS FASTA

1362 bp · LXL04_002935|LXL04_002935|OH1004|CDS

ATGGTTCATCAATCTGTTTGCTCTGAAAATCTGATCAAATTTGTTGATTTCTCCTTATGGGTTTGTTTCGAGGAACTAAAACAGCATCGACGTTCTTTTCATGTATCATTAAGAGCATCAAAGGGTAACAGTAACAGAGTCATTCGATCATGTGAATCAAGTATTGTGAGACACAATTTTAGCAGTTTTAATAAAAGTTTTCTACTTTCAAATAAACGGAACACAAAACCTGTCGCAAGTGCAGTTTCTGAACAACCTAT...

Protein

Download Protein FASTA

453 aa · LXL04_002935|LXL04_002935|OH1004|PROTEIN

MVHQSVCSENLIKFVDFSLWVCFEELKQHRRSFHVSLRASKGNSNRVIRSCESSIVRHNFSSFNKSFLLSNKRNTKPVASAVSEQPIEPESASPKKLLPSAFDAFYRFSRPHTVIGTALSIVSVSLLAVQNLSDFSPLFFAGVLQAIVAAFFMNIYIVGLNQLSDIEIDKVNKPYLPLASGEYSVKTGVMIVSSFAIMSFVLGWMVGSWPLFWALFISFLLGTAYSINVPMLRWKRFALVAAMCILAVRAVIVQIAFYLH...

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_002935`
TK1151 ID	TkA01G408920
OH-1004 ID	LXL04_002935
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	47.600
Protein coverage (%)	TK1151 85.794 / OH-1004 68.874 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_002935

Location Chr01:61713167-61717444 (+)

Description Similar to HPT1: Homogentisate phytyltransferase 1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g18950`	Involved in the synthesis of tocopherol (vitamin E).	Isolation and characterization of homogentisate phytyltransferase genes from Synechocystis sp. PCC 6803 and Arabidopsis.2002 · DOI: 10.1104/pp.010747 Homogentisate phytyltransferase activity is limiting for tocopherol biosynthesis in Arabidopsis.2003 · DOI: 10.1104/pp.015222 Seed-specific overexpression of antioxidant genes in Arabidopsis enhances oxidative stress tolerance during germination and early seedling growth.2010 · DOI: 10.1111/j.1467-7652.2010.00509.x Vitamin E biosynthesis: functional characterization of the monocot homogentisate geranylgeranyl transferase.2011 · DOI: 10.1111/j.1365-313x.2010.04417.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0658900`	Involved in the synthesis of tocopherol (vitamin E).	No verified direct reference in this release
`Os06g0646900`	Involved in the synthesis of tocotrienol (vitamin E).	Antioxidant activity and inhibition of lipid peroxidation in germinating seeds of transgenic soybean expressing OsHGGT.2011 · DOI: 10.1021/jf104012z

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002935 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006636 unsaturated fatty acid biosynthetic process Biological Process

GO:0009266 response to temperature stimulus Biological Process

GO:0009915 phloem sucrose loading Biological Process

GO:0010189 vitamin E biosynthetic process Biological Process

GO:0031347 regulation of defense response Biological Process

GO:0042362 fat-soluble vitamin biosynthetic process Biological Process

GO:0071555 cell wall organization Biological Process

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0031969 chloroplast membrane Cellular Component

GO:0004659 prenyltransferase activity Molecular Function

GO:0010176 homogentisate phytyltransferase activity Molecular Function

KEGG gene cross-reference

ath:AT2G18950

dosa:Os06g0646900

dosa:Os06g0658900

osa:4341727

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.

Plastid0.971

Rank 1 · LXL04_002935 · OH-1004

Mitochondrion0.027

Rank 2 · LXL04_002935 · OH-1004

Cytoplasm0.025

Rank 3 · LXL04_002935 · OH-1004

Endoplasmic reticulum0.024

Rank 4 · LXL04_002935 · OH-1004

Peroxisome0.022

Rank 5 · LXL04_002935 · 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.

PF01040.24UbiA125-385 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002935	`PF01040.24`	UbiA	125	385	1.1e-38	133.7

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
`Q8VWJ1`	Arabidopsis thaliana	Homogentisate phytyltransferase 1, chloroplastic	65.517%	Swiss-Prot	strong database homology
`B7FA90`	Oryza sativa subsp. japonica	Probable homogentisate phytyltransferase 1, chloroplastic	73.030%	Swiss-Prot	strong database homology
`Q0DAK7`	Oryza sativa subsp. japonica	Homogentisate geranylgeranyltransferase, chloroplastic	52.874%	Swiss-Prot	strong database homology

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