LXL04_009418 | RubberDandelionOmics

Gene overview

LXL04_009418

Reference: OH-1004 Chr: Chr02 Coordinates: 125665159-125668152 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1668 bp · LXL04_009418|LXL04_009418|OH1004|cDNA

ATGGCGGATGCGAGCTGTGTGAATCCCCAAAATGGGTTTTGTTCAAAGATAAAGGTCTTTCACAGCCTCCGGTCACCGGCACCTCTGCCTCCTCCTTCACAGCCCCTCTCAATCACCGACCACACTCTCTCCCTCCTCCGATCTGACCCCGCATTTTCCCCATTTACAACTCATTTCCTAATCGACTCCGCCACCGGCCGCCGACTCTCATACTCCGACTTCATCCGTCAATTCCAGTCCCTCTCCGCCGCGCTCGTAAA...

CDS

Download CDS FASTA

1668 bp · LXL04_009418|LXL04_009418|OH1004|CDS

ATGGCGGATGCGAGCTGTGTGAATCCCCAAAATGGGTTTTGTTCAAAGATAAAGGTCTTTCACAGCCTCCGGTCACCGGCACCTCTGCCTCCTCCTTCACAGCCCCTCTCAATCACCGACCACACTCTCTCCCTCCTCCGATCTGACCCCGCATTTTCCCCATTTACAACTCATTTCCTAATCGACTCCGCCACCGGCCGCCGACTCTCATACTCCGACTTCATCCGTCAATTCCAGTCCCTCTCCGCCGCGCTCGTAAA...

Protein

Download Protein FASTA

555 aa · LXL04_009418|LXL04_009418|OH1004|PROTEIN

MADASCVNPQNGFCSKIKVFHSLRSPAPLPPPSQPLSITDHTLSLLRSDPAFSPFTTHFLIDSATGRRLSYSDFIRQFQSLSAALVNKFPTLAKNQVALILSPTSIHIPVLYFALLSIGVTVSPVNPLSTKSELTDLVGLSNPVIAFATSSVASKLPSSFPLGTIIIDSPQFLPMLQNHHSNFSSQQVKQSDTAGILYSSGTTGRIKGVELTHRNFIAITSTSYHNRFVKDENSPREHPVSLFPLPLFHVFGFYMLIRAA...

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_009418`
TK1151 ID	TkA03G435870
OH-1004 ID	LXL04_009418
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
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

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_009418

Location Chr02:125665159-125668152 (+)

Description Similar to 4CLL9: 4-coumarate--CoA ligase-like 9

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g63380`	Contributes to jasmonic acid biosynthesis by initiating the beta-oxidative chain shortening of its precursors.	A new type of peroxisomal acyl-coenzyme A synthetase from Arabidopsis thaliana has the catalytic capacity to activate biosynthetic precursors of jasmonic acid.2005 · DOI: 10.1074/jbc.m413578200
`At1g20510`	Contributes to jasmonic acid biosynthesis by initiating the beta-oxidative chain shortening of its precursors.	Identification of a peroxisomal acyl-activating enzyme involved in the biosynthesis of jasmonic acid in Arabidopsis.2006 · DOI: 10.1074/jbc.m607854200 Jasmonates meet fatty acids: functional analysis of a new acyl-coenzyme A synthetase family from Arabidopsis thaliana.2008 · DOI: 10.1093/jxb/erm325

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0901600`	Carboxylate--CoA ligase that may use 4-coumarate as substrate.	No verified direct reference in this release
`Os01g0901500`	Carboxylate--CoA ligase that may use 4-coumarate as substrate.	No verified direct reference in this release
`Os07g0280200`	Carboxylate--CoA ligase that may use 4-coumarate as substrate.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009418 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009611 response to wounding Biological Process

GO:0009617 response to bacterium Biological Process

GO:0009695 jasmonic acid biosynthetic process Biological Process

GO:0009698 phenylpropanoid metabolic process Biological Process

GO:0009753 response to jasmonic acid Biological Process

GO:0031408 oxylipin biosynthetic process Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0005777 peroxisome Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0004321 fatty-acyl-CoA synthase activity Molecular Function

GO:0005524 ATP binding Molecular Function

GO:0016207 4-coumarate-CoA ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G20510

ath:AT5G63380

dosa:Os01g0901500

dosa:Os07g0280200

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.

Peroxisome0.539

Rank 1 · LXL04_009418 · OH-1004

Cytoplasm0.269

Rank 2 · LXL04_009418 · OH-1004

Mitochondrion0.096

Rank 3 · LXL04_009418 · OH-1004

Nucleus0.083

Rank 4 · LXL04_009418 · OH-1004

Plastid0.082

Rank 5 · LXL04_009418 · 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.

PF00501.35AMP-binding60-407 aa

PF13193.13AMP-binding_C459-537 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009418	`PF00501.35`	AMP-binding	60	407	2.4e-77	261.1
LXL04_009418	`PF13193.13`	AMP-binding_C	459	537	1.4e-14	55.5

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
`Q84P23`	Arabidopsis thaliana	4-coumarate--CoA ligase-like 9	58.970%	Swiss-Prot	strong database homology
`Q84P21`	Arabidopsis thaliana	Peroxisomal OPC-8:0-CoA ligase 1	44.583%	Swiss-Prot	moderate database homology
`Q8RU95`	Oryza sativa subsp. japonica	4-coumarate--CoA ligase-like 6	50.615%	Swiss-Prot	strong database homology
`Q7F1X5`	Oryza sativa subsp. japonica	4-coumarate--CoA ligase-like 5	50.622%	Swiss-Prot	strong database homology
`Q69RG7`	Oryza sativa subsp. japonica	4-coumarate--CoA ligase-like 7	47.585%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card