LXL04_002706 | RubberDandelionOmics

Gene overview

LXL04_002706

Reference: OH-1004 Chr: Chr01 Coordinates: 55483651-55490742 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2628 bp · LXL04_002706|LXL04_002706|OH1004|cDNA

ATGATCATGAAAGAATTACCGGTAAGTATTGTTGAATACTCTACATTTTCTATTGCCCACCATGTGTTCGACGATATGCTTATGTTAATATCAACCTGGTATAAAGCTACAGATGAATTGAGCACCACGGGAGAGGGTTTTGAACTCAGCATCACAGCCAGTCAGTCACCCCCAGATCTGCATATAATCATTGGATCGATTCGACTCACAGTTAGTCAGATCAGTTATCTTCTATGTCCTGTCATTATCAATAATCCGAT...

CDS

Download CDS FASTA

2628 bp · LXL04_002706|LXL04_002706|OH1004|CDS

ATGATCATGAAAGAATTACCGGTAAGTATTGTTGAATACTCTACATTTTCTATTGCCCACCATGTGTTCGACGATATGCTTATGTTAATATCAACCTGGTATAAAGCTACAGATGAATTGAGCACCACGGGAGAGGGTTTTGAACTCAGCATCACAGCCAGTCAGTCACCCCCAGATCTGCATATAATCATTGGATCGATTCGACTCACAGTTAGTCAGATCAGTTATCTTCTATGTCCTGTCATTATCAATAATCCGAT...

Protein

Download Protein FASTA

875 aa · LXL04_002706|LXL04_002706|OH1004|PROTEIN

MIMKELPVSIVEYSTFSIAHHVFDDMLMLISTWYKATDELSTTGEGFELSITASQSPPDLHIIIGSIRLTVSQISYLLCPVIINNPIDFTVLMVKLASIFIDISRFEMELSNNIATALMNSMKNASDWVTFAFDAPFARAVVFGVPIGGHLFVEGLLLVVILFLLSQKSYKPPKRPLTNKEIDELCAEWVPESLIPPIKGEMAKEPPVLESAAGPHTVINGKEVVNFASANYLGLMGDEKLLESCTSALEKYGVGSCGPR...

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_002706`
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_002706

Location Chr01:55483651-55490742 (+)

Description Similar to LCB1: Long chain base biosynthesis protein 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g36480`	Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine.	The essential nature of sphingolipids in plants as revealed by the functional identification and characterization of the Arabidopsis LCB1 subunit of serine palmitoyltransferase.2006 · DOI: 10.1105/tpc.105.040774 Involvement of sphingoid bases in mediating reactive oxygen intermediate production and programmed cell death in Arabidopsis.2007 · DOI: 10.1038/cr.2007.100 Serine palmitoyltransferase, a key enzyme for de novo synthesis of sphingolipids, is essential for male gametophyte development in Arabidopsis.2008 · DOI: 10.1104/pp.107.113506

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0252800`	Serine palmitoyltransferase (SPT).	No verified direct reference in this release
`Os02g0806900`	Serine palmitoyltransferase (SPT).	No verified direct reference in this release
`Os10g0189600`	Serine palmitoyltransferase (SPT).	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_002706 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006665 sphingolipid metabolic process Biological Process

GO:0006686 sphingomyelin biosynthetic process Biological Process

GO:0006688 glycosphingolipid biosynthetic process Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009825 multidimensional cell growth Biological Process

GO:0030148 sphingolipid biosynthetic process Biological Process

GO:0043067 regulation of programmed cell death Biological Process

GO:0046511 sphinganine biosynthetic process Biological Process

GO:0046512 sphingosine biosynthetic process Biological Process

GO:0046513 ceramide biosynthetic process Biological Process

GO:1904504 positive regulation of lipophagy Biological Process

GO:0005783 endoplasmic reticulum Cellular Component

KEGG gene cross-reference

ath:AT4G36480

dosa:Os02g0806900

dosa:Os03g0252800

dosa:Os10g0189600

mmu:268656

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.

Endoplasmic reticulum0.208

Rank 1 · LXL04_002706 · OH-1004

Cytoplasm0.195

Rank 2 · LXL04_002706 · OH-1004

Mitochondrion0.187

Rank 3 · LXL04_002706 · OH-1004

Plastid0.178

Rank 4 · LXL04_002706 · OH-1004

Cell membrane0.137

Rank 5 · LXL04_002706 · 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.

PF00155.28Aminotran_1_2223-584 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002706	`PF00155.28`	Aminotran_1_2	223	584	1.2e-35	124.1

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
`Q94IB8`	Arabidopsis thaliana	Long chain base biosynthesis protein 1	73.849%	Swiss-Prot	moderate database homology
`Q10P01`	Oryza sativa subsp. japonica	Long chain base biosynthesis protein 1a	70.860%	Swiss-Prot	moderate database homology
`Q6K8E7`	Oryza sativa subsp. japonica	Long chain base biosynthesis protein 1b	72.451%	Swiss-Prot	moderate database homology
`Q7G4P2`	Oryza sativa subsp. japonica	Long chain base biosynthesis protein 1c	70.282%	Swiss-Prot	moderate database homology

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