LXL04_038305 | RubberDandelionOmics

Gene overview

LXL04_038305

Reference: OH-1004 Chr: Chr09 Coordinates: 36941482-36944078 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1377 bp · LXL04_038305|LXL04_038305|OH1004|cDNA

ATGCTCTGTTCGACTTGCTCGGCTGCTCTTGGGTCCTCCTCACTGGCCGACGCCGACCAGTTTGTATCATTTGATTTTAACAGGTTTGATTTTAACAGGAAGCCTCATCAGAAAATGGATTTGAAATTCGGGGGCGGGGGAacgggggcgggggcggggggAATTCTGGaattcgggggcgggggcgggggcggggatTCCAAAAaattcgggggcgggggcgggggcgggggtaCCGGGGAAtttcgggggcgggggcg...

CDS

Download CDS FASTA

1377 bp · LXL04_038305|LXL04_038305|OH1004|CDS

ATGCTCTGTTCGACTTGCTCGGCTGCTCTTGGGTCCTCCTCACTGGCCGACGCCGACCAGTTTGTATCATTTGATTTTAACAGGTTTGATTTTAACAGGAAGCCTCATCAGAAAATGGATTTGAAATTCGGGGGCGGGGGAACGGGGGCGGGGGCGGGGGGAATTCTGGAATTCGGGGGCGGGGGCGGGGGCGGGGATTCCAAAAAATTCGGGGGCGGGGGCGGGGGCGGGGGTACCGGGGAATTTCGGGGGCGGGGGCG...

Protein

Download Protein FASTA

458 aa · LXL04_038305|LXL04_038305|OH1004|PROTEIN

MLCSTCSAALGSSSLADADQFVSFDFNRFDFNRKPHQKMDLKFGGGGTGAGAGGILEFGGGGGGGDSKKFGGGGGGGGTGEFRGRGRGQLPPSRLPPLPSLYQTLSTARQILPVPKPLFLRCSTGDTSPPLSGGSDFDAKVFRHNLTRSDNYNRKGFGHKKETLELMNQEYTSDIIETLKENNYVYTWGNVTVKLAEAYGFCWGVEHAVRIAYEARKQYPDEKIWITNEIIHNPTVNKRLAEMGFKGFPIKNGEKQFDAI...

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_038305`
TK1151 ID	TkA04G415850
OH-1004 ID	LXL04_038305
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
Protein identity (%)	92.200
Protein coverage (%)	TK1151 99.405 / OH-1004 67.467 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_038305

Location Chr09:36941482-36944078 (-)

Description Similar to ISPH: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34350`	Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that converts 1-hydroxy-2-methyl-2-(E)-butenyl 4- diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP).	Characterization of the Arabidopsis clb6 mutant illustrates the importance of posttranscriptional regulation of the methyl-D-erythritol 4-phosphate pathway.2005 · DOI: 10.1105/tpc.104.028860 The Arabidopsis IspH homolog is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis.2005 · DOI: 10.1104/pp.104.058735

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0731900`	Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038305 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016114 terpenoid biosynthetic process Biological Process

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

GO:0050992 dimethylallyl diphosphate biosynthetic process Biological Process

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin) Molecular Function

GO:0046872 metal ion binding Molecular Function

GO:0051539 4 iron, 4 sulfur cluster binding Molecular Function

GO:0051745 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity Molecular Function

KEGG gene cross-reference

ath:AT4G34350

cyt:cce_1108

dosa:Os03g0731900

mar:MAE_16190

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.

Plastid0.708

Rank 1 · LXL04_038305 · OH-1004

Mitochondrion0.232

Rank 2 · LXL04_038305 · OH-1004

Cytoplasm0.071

Rank 3 · LXL04_038305 · OH-1004

Nucleus0.044

Rank 4 · LXL04_038305 · OH-1004

Endoplasmic reticulum0.029

Rank 5 · LXL04_038305 · 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.

PF02401.24LYTB193-418 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038305	`PF02401.24`	LYTB	193	418	1.9e-46	159.2

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q94B35`	Arabidopsis thaliana	4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic	67.173%	Swiss-Prot	moderate database homology
`Q6AVG6`	Oryza sativa subsp. japonica	4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic	69.836%	Swiss-Prot	moderate database homology

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