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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_030831
Reference: OH-1004 Chr: Chr06 Coordinates: 123712775-123717842 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1470 bp · LXL04_030831|LXL04_030831|OH1004|cDNA

ATGATCACGATTCCGTATATAACCGCCTTGACAACCTACTTCAGCTACGGATTGCTCTTCGCTTTTGGTCAATTGCGTGATTTCTTCCGTAATATCCTTGACTGGTGGAAAGCTAGCAATCTCCAGGGATATGCACCGATCTGCTTAGGGCTAGAAGATTTCTATATTCGCCGCCTCTATCTGCGTATACAGGATTGTTTTGGACGACCTATATCAAGCCCCCCTGATGCATGGTTTGACGTGGTGGAGCGTGTTTCCAA...

CDS

Download CDS FASTA

1470 bp · LXL04_030831|LXL04_030831|OH1004|CDS

ATGATCACGATTCCGTATATAACCGCCTTGACAACCTACTTCAGCTACGGATTGCTCTTCGCTTTTGGTCAATTGCGTGATTTCTTCCGTAATATCCTTGACTGGTGGAAAGCTAGCAATCTCCAGGGATATGCACCGATCTGCTTAGGGCTAGAAGATTTCTATATTCGCCGCCTCTATCTGCGTATACAGGATTGTTTTGGACGACCTATATCAAGCCCCCCTGATGCATGGTTTGACGTGGTGGAGCGTGTTTCCAA...

Protein

Download Protein FASTA

489 aa · LXL04_030831|LXL04_030831|OH1004|PROTEIN

MITIPYITALTTYFSYGLLFAFGQLRDFFRNILDWWKASNLQGYAPICLGLEDFYIRRLYLRIQDCFGRPISSPPDAWFDVVERVSNDNNKTLKRTTKVSRCLNLGSYNYLGFAAADEYCTPRVIETLKKYFASTCSSRVDGGTTALHTELEDVVADFVGKPAALVTGMGYVTNSAILPVLIGKGGLIISDSLNHNSIVNGARGSGATIRVFQHNTPSHLEKVLREYIADGQPRTHRPWKKIIVVVEGIYSMEGEICKLP...

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.

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ID Mapping

Input IDLXL04_030831
Source versionOH-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 IDLXL04_030831
LocationChr06:123712775-123717842 (+)
DescriptionSimilar to LCB2a: Long chain base biosynthesis protein 2a
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g23670 Serine palmitoyltransferase (SPT).
Characterization of an Arabidopsis cDNA encoding a subunit of serine palmitoyltransferase, the initial enzyme in sphingolipid biosynthesis.2001 · DOI: 10.1093/pcp/pce165
Loss-of-function mutations and inducible RNAi suppression of Arabidopsis LCB2 genes reveal the critical role of sphingolipids in gametophytic and sporophytic cell viability.2008 · DOI: 10.1111/j.1365-313x.2008.03420.x
MPK6, sphinganine and the LCB2a gene from serine palmitoyltransferase are required in the signaling pathway that mediates cell death induced by long chain bases in Arabidopsis.2011 · DOI: 10.1111/j.1469-8137.2011.03727.x
At3g48780 Serine palmitoyltransferase (SPT).
Loss-of-function mutations and inducible RNAi suppression of Arabidopsis LCB2 genes reveal the critical role of sphingolipids in gametophytic and sporophytic cell viability.2008 · DOI: 10.1111/j.1365-313x.2008.03420.x

Rice

Reference gene IDPossible functionPapers / DOI
Os11g0516000 Serine palmitoyltransferase (SPT). No verified direct reference in this release
Os01g0928800 Serine palmitoyltransferase (SPT). No verified direct reference in this release
Os01g0928700 Serine palmitoyltransferase (SPT). No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_030831 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009555 pollen development Biological Process
GO:0009640 photomorphogenesis Biological Process
GO:0030148 sphingolipid biosynthetic process Biological Process
GO:0043067 regulation of programmed cell death Biological Process
GO:0046512 sphingosine biosynthetic process Biological Process
GO:0046513 ceramide biosynthetic process Biological Process
GO:0005773 vacuole Cellular Component
GO:0005783 endoplasmic reticulum Cellular Component
GO:0005789 endoplasmic reticulum membrane Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0016020 membrane Cellular Component
GO:0017059 serine palmitoyltransferase complex Cellular Component
KEGG gene cross-reference
ath:AT3G48780
ath:AT5G23670
dosa:Os01g0928700
dosa:Os01g0928800
dosa:Os11g0516000
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.

Endoplasmic reticulum0.684
Rank 1 · LXL04_030831 · OH-1004
Mitochondrion0.124
Rank 2 · LXL04_030831 · OH-1004
Cytoplasm0.081
Rank 3 · LXL04_030831 · OH-1004
Peroxisome0.061
Rank 4 · LXL04_030831 · OH-1004
Cell membrane0.060
Rank 5 · LXL04_030831 · 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.

PF00155.28Aminotran_1_2102-460 aa
PF01212.28Beta_elim_lyase149-333 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_030831PF00155.28Aminotran_1_21024601.3e-51176.6
LXL04_030831PF01212.28Beta_elim_lyase1493338.2e-0935.9

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9LSZ9Arabidopsis thalianaLong chain base biosynthesis protein 2a85.417%Swiss-Protstrong database homology
Q9M304Arabidopsis thalianaLong chain base biosynthesis protein 2b84.232%Swiss-Protstrong database homology
Q2R3K3Oryza sativa subsp. japonicaLong chain base biosynthesis protein 2a83.678%Swiss-Protstrong database homology
Q5JK39Oryza sativa subsp. japonicaLong chain base biosynthesis protein 2d83.745%Swiss-Protstrong database homology
Q8RYL0Oryza sativa subsp. japonicaLong chain base biosynthesis protein 2c77.062%Swiss-Protstrong database homology

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