LXL04_033396 | RubberDandelionOmics

Gene overview

LXL04_033396

Reference: OH-1004 Chr: Chr07 Coordinates: 42702825-42707426 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2522 bp · LXL04_033396|LXL04_033396|OH1004|cDNA

ATTGTTTCTGGATCATGATACAGTcgatcctcttcttcttcaaaacaaTCCATCATCTCCCTACTCCTTTTCTCCGACTCAGACGCCGTCCACCTACCGCCGCCGTGTTCACCACTCCTCCACCGACAAATAGAAACACTACTCTCTGATTTCCtattttttcttttatattttaTCAAACTATCCGCTTCGATTGGCCGCCAGTTAATACGCGCCTGTTTGACGATCAACTGGCGATCGCATCATTTGCCAAGGTGAAA...

CDS

Download CDS FASTA

2307 bp · LXL04_033396|LXL04_033396|OH1004|CDS

CTGTTTGACGATCAACTGGCGATCGCATCATTTGCCAAGGTGAAATTCCGATTGCCACTGTCCTTTACATTCAGTTCTTTTCGCACTGTAAACGGCATGCAGAACAGTGGCAGTCTTCCGAAGAGCAATTCCTTAAAAAACCCTCAACAATCACTTCGCCGCCTCAACTTTTGCTCTCAAATATCAACTGGTCAACAAACATCTCCTGTTGTGTTCCCTGAAAAACGTACAAAAGGAAAAGTCTCAAAACGAAACGATGC...

Protein

Download Protein FASTA

768 aa · LXL04_033396|LXL04_033396|OH1004|PROTEIN

MFDDQLAIASFAKVKFRLPLSFTFSSFRTVNGMQNSGSLPKSNSLKNPQQSLRRLNFCSQISTGQQTSPVVFPEKRTKGKVSKRNDASVNNNDSKKREEHKIDIGDEQSDLLGYEVISGKLVLDKRKTIKATDLKNSSETSHLDSIDAKLTSRALVWGSHVLTLDDVISVSYNYGLRHFIVHSYPVKKHFLKSGRSRKDYCFLASTPDEAFQWVTGFADQHCFVNCSPHPMVSSKKQDSEILASDFSYRHIKSKSPPRML...

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_033396`
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_033396

Location Chr07:42702825-42707426 (+)

Description Similar to LCBK1: Sphingoid long-chain bases kinase 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g23450`	Involved in the production of sphingolipid metabolites.	Phosphorylation of sphingoid long-chain bases in Arabidopsis: functional characterization and expression of the first sphingoid long-chain base Kinase gene in plants.2005 · DOI: 10.1093/pcp/pci023
`At4g21540`	Involved in the production of sphingolipid metabolites.	Involvement of sphingosine kinase in plant cell signalling.2008 · DOI: 10.1111/j.1365-313x.2008.03579.x Phosphatidic acid binds and stimulates Arabidopsis sphingosine kinases.2011 · DOI: 10.1074/jbc.m110.190892 Connections between sphingosine kinase and phospholipase D in the abscisic acid signaling pathway in Arabidopsis.2012 · DOI: 10.1074/jbc.m111.274274
`At4g21534`	Involved in the production of sphingolipid metabolites.	Phosphatidic acid binds and stimulates Arabidopsis sphingosine kinases.2011 · DOI: 10.1074/jbc.m110.190892 Connections between sphingosine kinase and phospholipase D in the abscisic acid signaling pathway in Arabidopsis.2012 · DOI: 10.1074/jbc.m111.274274

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_033396 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006665 sphingolipid metabolic process Biological Process

GO:0006672 ceramide metabolic process Biological Process

GO:0006688 glycosphingolipid biosynthetic process Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009845 seed germination Biological Process

GO:0030148 sphingolipid biosynthetic process Biological Process

GO:0046512 sphingosine biosynthetic process Biological Process

GO:0071215 cellular response to abscisic acid stimulus Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT4G21534

ath:AT4G21540

ath:AT5G23450

hsa:64781

mmu:223753

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.

Cytoplasm0.307

Rank 1 · LXL04_033396 · OH-1004

Endoplasmic reticulum0.222

Rank 2 · LXL04_033396 · OH-1004

Cell membrane0.221

Rank 3 · LXL04_033396 · OH-1004

Nucleus0.216

Rank 4 · LXL04_033396 · OH-1004

Golgi apparatus0.152

Rank 5 · LXL04_033396 · 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.

PF00781.30DAGK_cat258-388 aa

PF19279.5YegS_C670-755 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_033396	`PF00781.30`	DAGK_cat	258	388	2.8e-29	102.0
LXL04_033396	`PF19279.5`	YegS_C	670	755	5.4e-10	39.9

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
`Q9LRB0`	Arabidopsis thaliana	Sphingoid long-chain bases kinase 1	63.199%	Swiss-Prot	strong database homology
`Q8L7L1`	Arabidopsis thaliana	Sphingosine kinase 1	34.685%	Swiss-Prot	weak database homology
`F2Y4A3`	Arabidopsis thaliana	Sphingosine kinase 2	33.500%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card