LXL04_020278 | RubberDandelionOmics

Gene overview

LXL04_020278

Reference: OH-1004 Chr: Chr04 Coordinates: 63080406-63085384 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1743 bp · LXL04_020278|LXL04_020278|OH1004|cDNA

ATGGGGAAGCAGTTTTACGTTTCACCATCCGTTTTAGTTGTACTACTGCTTGCCACAGTTGTACCTTCTTGTTCATCTTCCAGCAACTCTAGACGCTTTCACTTCGAtGTCCAATGGAAGAACATAAGTCGTTTATGCAGTAGAAAAGCCATACTGACAGTGAATGGGGAGTTTCCAGGGCCAACAATCGCTGTAAATGAAGGAGAGAATGTGGAGATTAAGGTTACTAATGGAGTTTCTTTAAACACCACTATCCATTG...

CDS

Download CDS FASTA

1743 bp · LXL04_020278|LXL04_020278|OH1004|CDS

ATGGGGAAGCAGTTTTACGTTTCACCATCCGTTTTAGTTGTACTACTGCTTGCCACAGTTGTACCTTCTTGTTCATCTTCCAGCAACTCTAGACGCTTTCACTTCGATGTCCAATGGAAGAACATAAGTCGTTTATGCAGTAGAAAAGCCATACTGACAGTGAATGGGGAGTTTCCAGGGCCAACAATCGCTGTAAATGAAGGAGAGAATGTGGAGATTAAGGTTACTAATGGAGTTTCTTTAAACACCACTATCCATTG...

Protein

Download Protein FASTA

580 aa · LXL04_020278|LXL04_020278|OH1004|PROTEIN

MGKQFYVSPSVLVVLLLATVVPSCSSSSNSRRFHFDVQWKNISRLCSRKAILTVNGEFPGPTIAVNEGENVEIKVTNGVSLNTTIHWHGIKQLRSGWADGPAYVTQCPIKPGQSYTYKFTVIGQRGTLWWHAHIAWQRATIYGAIIIYPRMPYPFSTPIAEEIPIIFGEWWNLPVEGIETEMNKYGNGPNSSDAYTINGLPGLLYPCAYKDTFIQTVERGKTYMLRIINAALNDELFFSIANHTLTVVEIDASYTKPFDT...

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_020278`
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_020278

Location Chr04:63080406-63085384 (-)

Description Similar to LAC1: Laccase-1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g18140`	Lignin degradation and detoxification of lignin-derived products.	No verified direct reference in this release
`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
`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_020278 · 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:0048226 Casparian strip Cellular Component

GO:0005507 copper ion binding Molecular Function

GO:0016491 oxidoreductase activity Molecular Function

KEGG gene cross-reference

ath:AT1G18140

ath:AT2G29130

ath:AT5G60020

dosa:Os01g0842400

dosa:Os05g0458600

osa:4339003

osa:4339004

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.

Extracellular0.835

Rank 1 · LXL04_020278 · OH-1004

Cell membrane0.060

Rank 2 · LXL04_020278 · OH-1004

Cytoplasm0.054

Rank 3 · LXL04_020278 · OH-1004

Endoplasmic reticulum0.045

Rank 4 · LXL04_020278 · OH-1004

Lysosome / Vacuole0.026

Rank 5 · LXL04_020278 · 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.

PF07732.22Cu-oxidase_337-150 aa

PF00394.29Cu-oxidase161-315 aa

PF07731.21Cu-oxidase_2428-563 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_020278	`PF07732.22`	Cu-oxidase_3	37	150	7.3e-45	152.6
LXL04_020278	`PF00394.29`	Cu-oxidase	161	315	4.3e-43	147.8
LXL04_020278	`PF07731.21`	Cu-oxidase_2	428	563	8.1e-45	152.7

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
`Q9LMS3`	Arabidopsis thaliana	Laccase-1	65.480%	Swiss-Prot	strong database homology
`Q9FJD5`	Arabidopsis thaliana	Laccase-17	53.887%	Swiss-Prot	strong database homology
`O81081`	Arabidopsis thaliana	Laccase-2	52.398%	Swiss-Prot	strong database homology
`Q5N9X2`	Oryza sativa subsp. japonica	Laccase-4	53.641%	Swiss-Prot	strong database homology
`P0DKK6`	Oryza sativa subsp. japonica	Laccase-13	52.289%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card