LXL04_010923 | RubberDandelionOmics

Gene overview

LXL04_010923

Reference: OH-1004 Chr: Chr02 Coordinates: 155225016-155225264 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

249 bp · LXL04_010923|LXL04_010923|OH1004|cDNA

ATGTGTTCAAATAAGGTTATGAGGTTGAATGATGTGAAGACGAATGATGATGGCCATAACTGTTGGTTCGATTGCTTCTTTGACAATCGGAGCTTCAATTTGGGCGGAATGGGGTGTAGCGCCGGTGTAATCGTCATCGATCTCGCCAAGGATATGTTACAGGTTTACCGGAGCTTCAACAAGACCCCGCCGGAAAAACCGGCGTCTCTTTATCAAAAGATCTTATGGCAATCGTCGGCGGTGCACTGA

CDS

Download CDS FASTA

249 bp · LXL04_010923|LXL04_010923|OH1004|CDS

ATGTGTTCAAATAAGGTTATGAGGTTGAATGATGTGAAGACGAATGATGATGGCCATAACTGTTGGTTCGATTGCTTCTTTGACAATCGGAGCTTCAATTTGGGCGGAATGGGGTGTAGCGCCGGTGTAATCGTCATCGATCTCGCCAAGGATATGTTACAGGTTTACCGGAGCTTCAACAAGACCCCGCCGGAAAAACCGGCGTCTCTTTATCAAAAGATCTTATGGCAATCGTCGGCGGTGCACTGA

Protein

Download Protein FASTA

82 aa · LXL04_010923|LXL04_010923|OH1004|PROTEIN

MCSNKVMRLNDVKTNDDGHNCWFDCFFDNRSFNLGGMGCSAGVIVIDLAKDMLQVYRSFNKTPPEKPASLYQKILWQSSAVH

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_010923`
TK1151 ID	TkA03G555680
OH-1004 ID	LXL04_010923
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	97.600
Protein coverage (%)	TK1151 65.600 / 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_010923

Location Chr02:155225016-155225264 (+)

Description Similar to KCS9: 3-ketoacyl-CoA synthase 9

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g16280`	Involved in the elongation of C22 to C24 fatty acids, which are precursors for the biosynthesis of cuticular waxes, aliphatic suberins, and membrane lipids, including sphingolipids and phospholipids.	Arabidopsis 3-ketoacyl-coenzyme a synthase9 is involved in the synthesis of tetracosanoic acids as precursors of cuticular waxes, suberins, sphingolipids, and phospholipids.2013 · DOI: 10.1104/pp.112.210450
`At4g34510`	Active on saturated acyl-CoAs up to C22.	Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases.2006 · DOI: 10.1016/j.bbrc.2006.05.162
`At4g34520`	Contributes to fatty acids elongation and stockage in developing seeds.	Engineering and mechanistic studies of the Arabidopsis FAE1 beta-ketoacyl-CoA synthase, FAE1 KCS.2002 · DOI: 10.1046/j.1432-1033.2002.03039.x Specific and differential inhibition of very-long-chain fatty acid elongases from Arabidopsis thaliana by different herbicides.2004 · DOI: 10.1073/pnas.0404600101 Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases.2006 · DOI: 10.1016/j.bbrc.2006.05.162 Natural variation in seed very long chain fatty acid content is controlled by a new isoform of KCS18 in Arabidopsis thaliana.2012 · DOI: 10.1371/journal.pone.0049261 Directed tagging of the Arabidopsis FATTY ACID ELONGATION1 (FAE1) gene with the maize transposon activator.1995 · DOI: 10.1105/tpc.7.3.309 Very-long-chain fatty acid biosynthesis is controlled through the expression and specificity of the condensing enzyme.1997 · DOI: 10.1046/j.1365-313x.1997.12010121.x
`At1g19440`	3-ketoacyl-CoA synthase 4.	No verified direct reference in this release
`At4g34250`	3-ketoacyl-CoA synthase 16.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010923 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000038 very long-chain fatty acid metabolic process Biological Process

GO:0006633 fatty acid biosynthetic process Biological Process

GO:0009409 response to cold Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0030497 fatty acid elongation Biological Process

GO:0160062 cutin-based cuticle development Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005789 endoplasmic reticulum membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016020 membrane Cellular Component

GO:0009922 fatty acid elongase activity Molecular Function

KEGG gene cross-reference

ath:AT1G19440

ath:AT2G16280

ath:AT4G34250

ath:AT4G34510

ath:AT4G34520

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.357

Rank 1 · LXL04_010923 · OH-1004

Nucleus0.218

Rank 2 · LXL04_010923 · OH-1004

Mitochondrion0.200

Rank 3 · LXL04_010923 · OH-1004

Extracellular0.147

Rank 4 · LXL04_010923 · OH-1004

Endoplasmic reticulum0.080

Rank 5 · LXL04_010923 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF08392.19FAE1_CUT1_RppA28-57 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010923	`PF08392.19`	FAE1_CUT1_RppA	28	57	7.8e-10	39.3

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
`Q9SIX1`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 9	86.207%	Swiss-Prot	weak database homology
`O65677`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 17	75.862%	Swiss-Prot	weak database homology
`Q38860`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 18	75.862%	Swiss-Prot	weak database homology
`Q9LN49`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 4	82.143%	Swiss-Prot	weak database homology
`Q9SYZ0`	Arabidopsis thaliana	3-ketoacyl-CoA synthase 16	71.875%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card