LXL04_015881 | RubberDandelionOmics

Gene overview

LXL04_015881

Reference: OH-1004 Chr: Chr03 Coordinates: 94589480-94590773 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

660 bp · LXL04_015881|LXL04_015881|OH1004|cDNA

ATGAATCAAGAGTATACCAGTGACTTCATAAAGACCCTGAAGGATAACAACTATGTATACACATGGGGAAATGTTACTGTGAAGCTTGCAGAAACTTATGGCTTTTGCTGGGGTGTTGTGCGTGCAGTTCAGATTGGTTATGAAGCAAGAAAACAATTCTCTGATGAAAAAATATGGATCACAAACGAAATTATTCACAATCCCACCGTTAGTAAGAGGTTAGAGGAGATGGAGGTTAAATACATTCTAATTAAGGATGG...

CDS

Download CDS FASTA

660 bp · LXL04_015881|LXL04_015881|OH1004|CDS

ATGAATCAAGAGTATACCAGTGACTTCATAAAGACCCTGAAGGATAACAACTATGTATACACATGGGGAAATGTTACTGTGAAGCTTGCAGAAACTTATGGCTTTTGCTGGGGTGTTGTGCGTGCAGTTCAGATTGGTTATGAAGCAAGAAAACAATTCTCTGATGAAAAAATATGGATCACAAACGAAATTATTCACAATCCCACCGTTAGTAAGAGGTTAGAGGAGATGGAGGTTAAATACATTCTAATTAAGGATGG...

Protein

Download Protein FASTA

219 aa · LXL04_015881|LXL04_015881|OH1004|PROTEIN

MNQEYTSDFIKTLKDNNYVYTWGNVTVKLAETYGFCWGVVRAVQIGYEARKQFSDEKIWITNEIIHNPTVSKRLEEMEVKYILIKDGEKQFDVIDKGDVVVLPAFGVVVNEMLTLIQIVDTTCPWVFKAISFSSLSVYSSNYYYYLLFCIWDYNVWNSVEKHKKGDYTSIIHGKYAHEETVATTSFAGKYVIVKNMDEAKYVCDYILGGEFNGNTSFKL

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_015881`
TK1151 ID	TkA02G232460
OH-1004 ID	LXL04_015881
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	91.200
Protein coverage (%)	TK1151 100.000 / OH-1004 62.100 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_015881

Location Chr03:94589480-94590773 (-)

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_015881 · 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

ana:all0985

ath:AT4G34350

cyt:cce_1108

dosa:Os03g0731900

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.

Cytoplasm0.570

Rank 1 · LXL04_015881 · OH-1004

Nucleus0.228

Rank 2 · LXL04_015881 · OH-1004

Extracellular0.135

Rank 3 · LXL04_015881 · OH-1004

Mitochondrion0.083

Rank 4 · LXL04_015881 · OH-1004

Lysosome / Vacuole0.080

Rank 5 · LXL04_015881 · 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.

PF02401.24LYTB27-129 aa

PF02401.24LYTB149-202 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015881	`PF02401.24`	LYTB	27	129	1e-31	110.9
LXL04_015881	`PF02401.24`	LYTB	149	202	1e-31	110.9

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
`Q94B35`	Arabidopsis thaliana	4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic	63.063%	Swiss-Prot	strong database homology
`Q6AVG6`	Oryza sativa subsp. japonica	4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic	64.414%	Swiss-Prot	strong database homology

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