LXL04_005939 | RubberDandelionOmics

Gene overview

LXL04_005939

Reference: OH-1004 Chr: Chr01 Coordinates: 175985206-175989436 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2742 bp · LXL04_005939|LXL04_005939|OH1004|cDNA

ATGGGTGGCTTAGGAATTCTCTTCTCGTTGGTCGCGATAACTTCATTCCTTCCGGTTTACATTGTTGGTGGCACCACCAGGAGTTATGAGTTTAACATCCAACTGCAAAATGTTACACGGCTGTGTCACACAAGGAGCATGGTGACCGTGAACGGGAAATTTCCAGGTCCTCGAATCGTTGCTAGAGAGGGTGACCGTTTGCTTATCAAAGTCACAAACCATGTCTCCAATAACATAACAATCCATTGGCATGGTATCCG...

CDS

Download CDS FASTA

2742 bp · LXL04_005939|LXL04_005939|OH1004|CDS

ATGGGTGGCTTAGGAATTCTCTTCTCGTTGGTCGCGATAACTTCATTCCTTCCGGTTTACATTGTTGGTGGCACCACCAGGAGTTATGAGTTTAACATCCAACTGCAAAATGTTACACGGCTGTGTCACACAAGGAGCATGGTGACCGTGAACGGGAAATTTCCAGGTCCTCGAATCGTTGCTAGAGAGGGTGACCGTTTGCTTATCAAAGTCACAAACCATGTCTCCAATAACATAACAATCCATTGGCATGGTATCCG...

Protein

Download Protein FASTA

913 aa · LXL04_005939|LXL04_005939|OH1004|PROTEIN

MGGLGILFSLVAITSFLPVYIVGGTTRSYEFNIQLQNVTRLCHTRSMVTVNGKFPGPRIVAREGDRLLIKVTNHVSNNITIHWHGIRQLRSGWADGPAYITQCPIQTGQSYVYNYTVVGQRGTLFWHAHISWLRASVYGPLIILPKLNVPYPFTKPYKEVPIIFGEWFNTDPEAIIAQATQTGGGPNVSDAYTFNGLPGPLYNCSAKDTFKLKVKNGKTYLLRLINAALNDELFFSIANHSLTVVEADAIYVKPFNTKTI...

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_005939`
TK1151 ID	TkA04G099590
OH-1004 ID	LXL04_005939
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	59.800
Protein coverage (%)	TK1151 69.714 / OH-1004 26.725 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_005939

Location Chr01:175985206-175989436 (-)

Description Similar to LAC17: Laccase-17

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g60020`	Lignin degradation and detoxification of lignin-derived products.	No verified direct reference in this release
`At2g29130`	Lignin degradation and detoxification of lignin-derived products (By similarity).	Mutant identification and characterization of the laccase gene family in Arabidopsis.2006 · DOI: 10.1093/jxb/erl022

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0842400`	Lignin degradation and detoxification of lignin-derived products.	No verified direct reference in this release
`Os03g0273200`	Lignin degradation and detoxification of lignin-derived products.	No verified direct reference in this release
`Os05g0458600`	Lignin degradation and detoxification of lignin-derived products.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005939 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009414 response to water deprivation Biological Process

GO:0009698 phenylpropanoid metabolic process Biological Process

GO:0009809 lignin biosynthetic process Biological Process

GO:0046274 lignin catabolic process Biological Process

GO:0080022 primary root development Biological Process

GO:0080112 seed growth Biological Process

GO:0005576 extracellular region Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0048046 apoplast Cellular Component

GO:0005507 copper ion binding Molecular Function

GO:0016491 oxidoreductase activity Molecular Function

GO:0052716 hydroquinone:oxygen oxidoreductase activity Molecular Function

KEGG gene cross-reference

ath:AT2G29130

ath:AT5G60020

dosa:Os01g0842400

dosa:Os03g0273200

dosa:Os05g0458600

osa:4339003

osa:4339004

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.

Cell membrane0.241

Rank 1 · LXL04_005939 · OH-1004

Lysosome / Vacuole0.221

Rank 2 · LXL04_005939 · OH-1004

Extracellular0.191

Rank 3 · LXL04_005939 · OH-1004

Endoplasmic reticulum0.156

Rank 4 · LXL04_005939 · OH-1004

Cytoplasm0.135

Rank 5 · LXL04_005939 · 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.

PF07732.22Cu-oxidase_333-146 aa

PF00394.29Cu-oxidase159-310 aa

PF07731.21Cu-oxidase_2426-549 aa

PF13966.12zf-RVT747-813 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005939	`PF07732.22`	Cu-oxidase_3	33	146	9.5e-43	145.8
LXL04_005939	`PF00394.29`	Cu-oxidase	159	310	3.7e-43	148.1
LXL04_005939	`PF07731.21`	Cu-oxidase_2	426	549	4.7e-42	143.7
LXL04_005939	`PF13966.12`	zf-RVT	747	813	1.5e-14	55.2

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
`Q9FJD5`	Arabidopsis thaliana	Laccase-17	75.347%	Swiss-Prot	moderate database homology
`O81081`	Arabidopsis thaliana	Laccase-2	71.481%	Swiss-Prot	moderate database homology
`Q5N9X2`	Oryza sativa subsp. japonica	Laccase-4	73.140%	Swiss-Prot	moderate database homology
`Q10ND7`	Oryza sativa subsp. japonica	Laccase-10	69.818%	Swiss-Prot	moderate database homology
`P0DKK6`	Oryza sativa subsp. japonica	Laccase-13	69.510%	Swiss-Prot	moderate database homology

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