LXL04_001903 | RubberDandelionOmics

Gene overview

LXL04_001903

Reference: OH-1004 Chr: Chr01 Coordinates: 36531195-36533379 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1272 bp · LXL04_001903|LXL04_001903|OH1004|cDNA

ATGATGCCGGCGACATGCCATAATCTTGAGTTTGGTCGAACTGCGTTTGTTGATTTCGTTCCTTGTGGGTGTTCTTTCAGTTCTTCATTCGACCGCTTTCCTTCAAGAAATTACGCACGAAAGGTGATCAGAAGTGTGAATAGGGGCTTCTatggcggtggcggtggccggAATTCGATATTTTGCCGCCGTGATGGTAATATCGCAAAGTGTCGAGTTTTTTCAACTGAAGCTCCCGGGACTTTACTAAATGGCGATGC...

CDS

Download CDS FASTA

1272 bp · LXL04_001903|LXL04_001903|OH1004|CDS

ATGATGCCGGCGACATGCCATAATCTTGAGTTTGGTCGAACTGCGTTTGTTGATTTCGTTCCTTGTGGGTGTTCTTTCAGTTCTTCATTCGACCGCTTTCCTTCAAGAAATTACGCACGAAAGGTGATCAGAAGTGTGAATAGGGGCTTCTATGGCGGTGGCGGTGGCCGGAATTCGATATTTTGCCGCCGTGATGGTAATATCGCAAAGTGTCGAGTTTTTTCAACTGAAGCTCCCGGGACTTTACTAAATGGCGATGC...

Protein

Download Protein FASTA

423 aa · LXL04_001903|LXL04_001903|OH1004|PROTEIN

MMPATCHNLEFGRTAFVDFVPCGCSFSSSFDRFPSRNYARKVIRSVNRGFYGGGGGRNSIFCRRDGNIAKCRVFSTEAPGTLLNGDAPGPPPVINEKKESTTDLFEAVSDDLLTLNKNLQSIVGAENPVLMAAAEQIFSAGGKRMRPALVFLVSRATSALAGLEELTREHRRLAEIIEMIHTASLIHDDVLDESDMRRGQETVHQMYGTRVAVLAGDFMFAQSSWYLANLENLEVIKLISQVIKDFASGEIKQASSLFDC...

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_001903`
TK1151 ID	TkA01G499770
OH-1004 ID	LXL04_001903
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_001903

Location Chr01:36531195-36533379 (-)

Description Similar to SPS2: Solanesyl diphosphate synthase 2, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g17050`	Involved in providing solanesyl diphosphate for plastoquinone-9 (PQ-9) formation in plastids (Probable).	Functional modeling identifies paralogous solanesyl-diphosphate synthases that assemble the side chain of plastoquinone-9 in plastids.2013 · DOI: 10.1074/jbc.m113.492769
`At1g78510`	Involved in providing solanesyl diphosphate for plastoquinone-9 (PQ-9) formation in plastids.	Functional modeling identifies paralogous solanesyl-diphosphate synthases that assemble the side chain of plastoquinone-9 in plastids.2013 · DOI: 10.1074/jbc.m113.492769

Rice

Reference gene ID	Possible function	Papers / DOI
`Os12g0271700`	Involved in providing solanesyl diphosphate for plastoquinone-9 (PQ-9) formation.	No verified direct reference in this release
`Os05g0582300`	Involved in providing solanesyl diphosphate for plastoquinone-9 (PQ-9) formation.	Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa.2010 · DOI: 10.1093/jxb/erq103

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001903 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0008299 isoprenoid biosynthetic process Biological Process

GO:0010236 plastoquinone biosynthetic process Biological Process

GO:0015979 photosynthesis Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009536 plastid Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0004311 geranylgeranyl diphosphate synthase activity Molecular Function

GO:0004337 (2E,6E)-farnesyl diphosphate synthase activity Molecular Function

GO:0004659 prenyltransferase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

GO:0052923 all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity Molecular Function

KEGG gene cross-reference

ath:AT1G17050

ath:AT1G78510

dosa:Os12g0271700

osa:4351957

syn:slr0611

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.

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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.

Plastid0.960

Rank 1 · LXL04_001903 · OH-1004

Mitochondrion0.060

Rank 2 · LXL04_001903 · OH-1004

Cytoplasm0.042

Rank 3 · LXL04_001903 · OH-1004

Peroxisome0.030

Rank 4 · LXL04_001903 · OH-1004

Nucleus0.022

Rank 5 · LXL04_001903 · 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.

PF00348.23polyprenyl_synt128-374 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001903	`PF00348.23`	polyprenyl_synt	128	374	6.3e-77	258.9

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q76FS5`	Arabidopsis thaliana	Solanesyl diphosphate synthase 2, chloroplastic	68.458%	Swiss-Prot	strong database homology
`Q8S948`	Arabidopsis thaliana	Solanesyl diphosphate synthase 1, chloroplastic	67.290%	Swiss-Prot	strong database homology
`Q0INZ4`	Oryza sativa subsp. japonica	Probable solanesyl-diphosphate synthase 3, chloroplastic	70.000%	Swiss-Prot	strong database homology
`Q75HZ9`	Oryza sativa subsp. japonica	Solanesyl-diphosphate synthase 2, chloroplastic	71.866%	Swiss-Prot	strong database homology

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