TkA03G417390 | RubberDandelionOmics

Gene overview

TkA03G417390

Reference: TK1151 Chr: Chr03 Coordinates: 103876667-103879611 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1945 bp · TkA03G417390|TK1151|cDNA

AACAAAATCAACCGCAACCAGAGGCTTCAATCGCCACCGGAAATTGGATTTCAGCCGTTCCAGACGCCTCGTCGCCGGCGGTCCATTTCTGCGATTTGCAGTGACTCACATTATTGATAGTGTTCACACGATTTTTATGTTCGTCGTTAGATTGACAAGAACGAGATCGGAGATCCAATCTAGAACATGATTACAATTCCATATTTGACCGCGCTGACCACCTATTTCAGTTACGGATTGCTCTTCGCTTTTGGACAATT...

CDS

Download CDS FASTA

1470 bp · TkA03G417390|TK1151|CDS

ATGATTACAATTCCATATTTGACCGCGCTGACCACCTATTTCAGTTACGGATTGCTCTTCGCTTTTGGACAATTGCGAGATTTCTTCCGCAACTTCATTGATTGGTGGAAAGCCAGCAATCTCCAGGGCTATGCACCGATCTGTTTAGGGCTTGAAGATTTCTATATCCGCCGCCTCTATCTCCGTATTCAGGATTGCTTTGGAAGACCAATATCGAGCCCTCCTGATGCTTGGTTTGATGTGGTGGAGCGTGTTTCGAA...

Protein

Download Protein FASTA

489 aa · TkA03G417390|TK1151|PROTEIN

MITIPYLTALTTYFSYGLLFAFGQLRDFFRNFIDWWKASNLQGYAPICLGLEDFYIRRLYLRIQDCFGRPISSPPDAWFDVVERVSNDNNKTLKRTTKVSRCLNLGSYNYLGFAAADEYCTPRVTETLKRYSASTCSTRVEGGTTALHIELEDVVADFVGKPAAMVTGMGYVTNSAILPVLIRHGGLIISDSLNHNSIVNGARGSGATVRVFQHNTPSHLEKVLREHIADGQPRTHRPWKKIIVIVEGIYSMEGELCKLP...

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	`TkA03G417390`
TK1151 ID	TkA03G417390
OH-1004 ID	LXL04_030831
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	92.600
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA03G417390

Location Chr03:103876667-103879611 (-)

Description Similar to LCB2a: Long chain base biosynthesis protein 2a

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / 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 ID	Possible function	Papers / 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. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

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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 reticulum0.663

Rank 1 · TkA03G417390 · TK1151

Mitochondrion0.137

Rank 2 · TkA03G417390 · TK1151

Cytoplasm0.076

Rank 3 · TkA03G417390 · TK1151

Peroxisome0.061

Rank 4 · TkA03G417390 · TK1151

Cell membrane0.059

Rank 5 · TkA03G417390 · TK1151

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.

PF00155Aminotran_1_2102-460 aa

PF01212Beta_elim_lyase149-333 aa

PF01041DegT_DnrJ_EryC1150-284 aa

PF00266Aminotran_5150-282 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G417390	`PF00155`	Aminotran_1_2	102	460	8.6e-53	180.5
TkA03G417390	`PF01212`	Beta_elim_lyase	149	333	4.5e-09	36.8
TkA03G417390	`PF01041`	DegT_DnrJ_EryC1	150	284	0.0002	21.4
TkA03G417390	`PF00266`	Aminotran_5	150	282	0.014	15.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9LSZ9`	Arabidopsis thaliana	sp\|Q9LSZ9\|LCB2A_ARATH Long chain base biosynthesis protein 2a	83.800%	Swiss-Prot	High
`Q9M304`	Arabidopsis thaliana	sp\|Q9M304\|LCB2B_ARATH Long chain base biosynthesis protein 2b	82.400%	Swiss-Prot	High
`Q2R3K3`	Oryza sativa subsp. japonica	sp\|Q2R3K3\|LCB2A_ORYSJ Long chain base biosynthesis protein 2a	84.700%	Swiss-Prot	High
`Q5JK39`	Oryza sativa subsp. japonica	sp\|Q5JK39\|LCB2D_ORYSJ Long chain base biosynthesis protein 2d	83.200%	Swiss-Prot	High
`Q8RYL0`	Oryza sativa subsp. japonica	sp\|Q8RYL0\|LCB2C_ORYSJ Long chain base biosynthesis protein 2c	78.000%	Swiss-Prot	High

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