LXL04_021998 | RubberDandelionOmics

Gene overview

LXL04_021998

Reference: OH-1004 Chr: Chr04 Coordinates: 142244764-142250607 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1332 bp · LXL04_021998|LXL04_021998|OH1004|cDNA

ATGGATCGGCCGGCGAGTTTACTCGACGAAGCTCTAGGTTTCGAAGACGGCGACTCGAAAAGCCGGCAGCCACGGGAAGGACGCGTTGTTCTACTGGAGGACTGCGTCGAAACTAGCGGCGCGTTTGTGCTACACCACCTTATAAAACGGTTTCTCTCTCCTAATCATTCGTCCTCCGACAGTGTCGTCATTTTTGTAGCATTCGCTCAACCTTTTTCTCACTACGACCGTATCCTGCGTAAGATGGGTTGCAACTTAGC...

CDS

Download CDS FASTA

1332 bp · LXL04_021998|LXL04_021998|OH1004|CDS

ATGGATCGGCCGGCGAGTTTACTCGACGAAGCTCTAGGTTTCGAAGACGGCGACTCGAAAAGCCGGCAGCCACGGGAAGGACGCGTTGTTCTACTGGAGGACTGCGTCGAAACTAGCGGCGCGTTTGTGCTACACCACCTTATAAAACGGTTTCTCTCTCCTAATCATTCGTCCTCCGACAGTGTCGTCATTTTTGTAGCATTCGCTCAACCTTTTTCTCACTACGACCGTATCCTGCGTAAGATGGGTTGCAACTTAGC...

Protein

Download Protein FASTA

443 aa · LXL04_021998|LXL04_021998|OH1004|PROTEIN

MDRPASLLDEALGFEDGDSKSRQPREGRVVLLEDCVETSGAFVLHHLIKRFLSPNHSSSDSVVIFVAFAQPFSHYDRILRKMGCNLAVQRENKRLIFFDMLMLECPDDDGTEGGLLALYGNIHKAVEFNSLNKNITIIIDDISLLEVAANGSTKDVLNFMHYCHTLTTQFGCTIITVIHDDIYSSEDGFTLPTQLEYLSDITIKAEPLVTGLAADIHGQLTVLNKGLGRWKGKIRNFHYRVKENSVPSASNGDLSNYLKT...

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_021998`
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_021998

Location Chr04:142244764-142250607 (-)

Description Similar to ELP6: Elongator complex protein 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g10090`	Component of the elongator complex which is required for multiple tRNA modifications, including mcm5U (5-methoxycarbonylmethyl uridine), mcm5s2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U (5-carbamoylmethyl uridine) (By similarity).	No verified direct reference in this release
`At1g58440`	May catalyze stereospecific oxidation of squalene to (S)-2,3-epoxysqualene in sterol biosynthesis.	Arabidopsis thaliana squalene epoxidase 1 is essential for root and seed development.2007 · DOI: 10.1074/jbc.m611831200 Identification of the Arabidopsis dry2/sqe1-5 mutant reveals a central role for sterols in drought tolerance and regulation of reactive oxygen species.2009 · DOI: 10.1111/j.1365-313x.2009.03849.x Analysis of the arabidopsis dry2/sqe1-5 mutant suggests a role for sterols in signaling.2009 · DOI: 10.4161/psb.4.9.9425
`At2g22830`	Catalyzes the stereospecific oxidation of squalene to (S)-2,3-epoxysqualene, and is considered to be a rate-limiting enzyme in steroid biosynthesis.	Arabidopsis thaliana squalene epoxidase 1 is essential for root and seed development.2007 · DOI: 10.1074/jbc.m611831200

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021998 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002098 tRNA wobble uridine modification Biological Process

GO:0002238 response to molecule of fungal origin Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009725 response to hormone Biological Process

GO:0009751 response to salicylic acid Biological Process

GO:0009753 response to jasmonic acid Biological Process

GO:0009926 auxin polar transport Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0010016 shoot system morphogenesis Biological Process

KEGG gene cross-reference

ath:AT1G58440

ath:AT2G22830

ath:AT4G10090

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.

Peroxisome0.300

Rank 1 · LXL04_021998 · OH-1004

Cytoplasm0.252

Rank 2 · LXL04_021998 · OH-1004

Mitochondrion0.205

Rank 3 · LXL04_021998 · OH-1004

Endoplasmic reticulum0.147

Rank 4 · LXL04_021998 · OH-1004

Nucleus0.145

Rank 5 · LXL04_021998 · 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.

PF09807.16ELP622-242 aa

PF08491.17SE241-428 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021998	`PF09807.16`	ELP6	22	242	9.4e-30	104.6
LXL04_021998	`PF08491.17`	SE	241	428	1.9e-55	188.6

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
`Q8L9Y2`	Arabidopsis thaliana	Elongator complex protein 6	52.140%	Swiss-Prot	moderate database homology
`Q9SM02`	Arabidopsis thaliana	Squalene epoxidase 1	49.590%	Swiss-Prot	weak database homology
`O81000`	Arabidopsis thaliana	Squalene epoxidase 2, mitochondrial	46.694%	Swiss-Prot	weak database homology

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