LXL04_011773 | RubberDandelionOmics

Gene overview

LXL04_011773

Reference: OH-1004 Chr: Chr03 Coordinates: 14149-19121 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1752 bp · LXL04_011773|LXL04_011773|OH1004|cDNA

ATGTTGTCTGTCAAAGCTCAAAAACCAGAAACCCCTCCTCCTCCGCCCCTTGTTTCTTCTTCCTCATCACCATCAACTTCAACTTCTAATAATACTAATACAAATAATATTCATAATGTCGATGATAATTCCAGTAGAAATGTTGTGTTCAGATCAAAACTACCAGACTTACCCAACATCCCAAACCATATCCCTCTGCATACCTACTGTTTCGAGAATCTTCCCCTCTTCTCCGAAAAACCTTGCCTTGTTGTCGGTTC...

CDS

Download CDS FASTA

1752 bp · LXL04_011773|LXL04_011773|OH1004|CDS

ATGTTGTCTGTCAAAGCTCAAAAACCAGAAACCCCTCCTCCTCCGCCCCTTGTTTCTTCTTCCTCATCACCATCAACTTCAACTTCTAATAATACTAATACAAATAATATTCATAATGTCGATGATAATTCCAGTAGAAATGTTGTGTTCAGATCAAAACTACCAGACTTACCCAACATCCCAAACCATATCCCTCTGCATACCTACTGTTTCGAGAATCTTCCCCTCTTCTCCGAAAAACCTTGCCTTGTTGTCGGTTC...

Protein

Download Protein FASTA

583 aa · LXL04_011773|LXL04_011773|OH1004|PROTEIN

MLSVKAQKPETPPPPPLVSSSSSPSTSTSNNTNTNNIHNVDDNSSRNVVFRSKLPDLPNIPNHIPLHTYCFENLPLFSEKPCLVVGSNGTTYTFSQTYLLSRKIAVGLSTLGISKGDVIMLLLQNCAEFALTFMAASMIGAVTTAANPFYTAGEIFKQFNSSNSKMIITQSQYVDKLRDHGVHNPKMGQDFPVITIDDPPEECLHFSMLFRTNEHKIPSVRIDPDDAVALPFSSGTTGLPKGVILTHKSLITSVAQQVDG...

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_011773`
TK1151 ID	TkA02G616570
OH-1004 ID	LXL04_011773
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_011773

Location Chr03:14149-19121 (+)

Description Similar to 4-coumarate--CoA ligase 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g65060`	Produces CoA thioesters of a variety of hydroxy- and methoxy-substituted cinnamic acids, which are used to synthesize several phenylpropanoid-derived compounds, including anthocyanins, flavonoids, isoflavonoids, coumarins, lignin, suberin and wall-bound phenolics.	Three 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms.1999 · DOI: 10.1046/j.1365-313x.1999.00491.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0697400`	Involved in the phenylpropanoid metabolism by mediating the activation of a number of hydroxycinnamates for the biosynthesis of monolignols and other phenolic secondary metabolites.	Functional characterization of evolutionarily divergent 4-coumarate:coenzyme a ligases in rice.2011 · DOI: 10.1104/pp.111.178301 Analysis of five rice 4-coumarate:coenzyme A ligase enzyme activity and stress response for potential roles in lignin and flavonoid biosynthesis in rice.2013 · DOI: 10.1016/j.bbrc.2012.12.019

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011773 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009411 response to UV Biological Process

GO:0009698 phenylpropanoid metabolic process Biological Process

GO:0010584 pollen exine formation Biological Process

GO:0009507 chloroplast Cellular Component

GO:0005524 ATP binding Molecular Function

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

GO:0016405 CoA-ligase activity Molecular Function

GO:0050563 trans-feruloyl-CoA synthase activity Molecular Function

GO:0106286 (E)-caffeate-CoA ligase activity Molecular Function

GO:0106290 trans-cinnamate-CoA ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G65060

dosa:Os02g0697400

gmx:547930

nta:107803673

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.

Cytoplasm0.356

Rank 1 · LXL04_011773 · OH-1004

Peroxisome0.356

Rank 2 · LXL04_011773 · OH-1004

Nucleus0.114

Rank 3 · LXL04_011773 · OH-1004

Mitochondrion0.107

Rank 4 · LXL04_011773 · OH-1004

Endoplasmic reticulum0.075

Rank 5 · LXL04_011773 · 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.

PF00501.35AMP-binding78-444 aa

PF13193.13AMP-binding_C495-570 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011773	`PF00501.35`	AMP-binding	78	444	3.5e-92	309.9
LXL04_011773	`PF13193.13`	AMP-binding_C	495	570	2.8e-17	64.1

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
`Q9S777`	Arabidopsis thaliana	4-coumarate--CoA ligase 3	71.963%	Swiss-Prot	strong database homology
`Q42982`	Oryza sativa subsp. japonica	4-coumarate--CoA ligase 2	68.392%	Swiss-Prot	strong database homology

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