TkA08G187720 | RubberDandelionOmics

Gene overview

TkA08G187720

Reference: TK1151 Chr: Chr08 Coordinates: 49028262-49033734 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2007 bp · TkA08G187720|TK1151|cDNA

GCACACAGTATTTGATTATTCTATCTATATAATAAACCCGTGGGCACTTTCTACAGTGCACGGGATTCACAACCAAACTAGAGATCTGACCCAGCAGCCTTATCGATTTTTTGCATGCACCGCCTGTTCTTCACTTCATCAACTCACGTTGCTCTGCTCCTTCTCAACTCCACTTACCGGCGATCAACTACTCCGATCTGCATCCCTCCGCCAGCGACGCCGTCGCCTCGATCCTCGCCAGCGACGCTGCCTCCACCAGT...

CDS

Download CDS FASTA

828 bp · TkA08G187720|TK1151|CDS

ATGGAGTTATCAAACAACATCGCTACAGCATTAATGAATTCCATGAAGAATGCGTCTGATTGGGTGACATTTGCATTTGATGCGCCTTTTGCTCGAGCTGTTGTATTTGGAGTGCCAATTGGAGGACATTTGTTTGTGGAGGGTCTACTTCTTGTAGTTATTCTCTTCTTACTATCTCAGAAGAGTTACAAGCCACCTAAGCGCCCCTTAACAAATAAGGAAATAGACGAATTATGTGCTGAATGGGTACCTGAGTCTCT...

Protein

Download Protein FASTA

275 aa · TkA08G187720|TK1151|PROTEIN

MELSNNIATALMNSMKNASDWVTFAFDAPFARAVVFGVPIGGHLFVEGLLLVVILFLLSQKSYKPPKRPLTNKEIDELCAEWVPESLIPPIKGEMAKEPPVLESAAGPHTVINGKEVVNFASANYLGLMGDEKLLESCTSALEKYGVGSCGPRGFYGTIDVHLDCEARIARFLGTPDSILYSYGLSTMFSAIPAFCKKGDIVIVDEGCSWGIQNGLYLSRSTIVYFKHNNMDSLQTTLEKVTQDNKRAKKLRRYIVVESV...

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	`TkA08G187720`
TK1151 ID	TkA08G187720
OH-1004 ID	LXL04_002706
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.300
Protein coverage (%)	TK1151 99.273 / OH-1004 31.200 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA08G187720

Location Chr08:49028262-49033734 (+)

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

View annotation sources

Functional annotation source: OH1004 · LXL04_002706 · 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: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.

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 reticulum0.777

Rank 1 · TkA08G187720 · TK1151

Golgi apparatus0.090

Rank 2 · TkA08G187720 · TK1151

Nucleus0.084

Rank 3 · TkA08G187720 · TK1151

Cytoplasm0.075

Rank 4 · TkA08G187720 · TK1151

Mitochondrion0.056

Rank 5 · TkA08G187720 · TK1151

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.

PF00155Aminotran_1_2116-274 aa

PF01276OKR_DC_1163-245 aa

PF01053Cys_Met_Meta_PP166-233 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G187720	`PF00155`	Aminotran_1_2	116	274	3.3e-16	60.1
TkA08G187720	`PF01276`	OKR_DC_1	163	245	0.11	11.9
TkA08G187720	`PF01053`	Cys_Met_Meta_PP	166	233	0.14	11.4

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	sp\|Q94IB8\|SPTC1_ARATH Long chain base biosynthesis protein 1	75.700%	Swiss-Prot	High
`Q10P01`	Oryza sativa subsp. japonica	sp\|Q10P01\|LCB1A_ORYSJ Long chain base biosynthesis protein 1a	71.600%	Swiss-Prot	High
`Q6K8E7`	Oryza sativa subsp. japonica	sp\|Q6K8E7\|LCB1B_ORYSJ Long chain base biosynthesis protein 1b	73.000%	Swiss-Prot	High
`Q7G4P2`	Oryza sativa subsp. japonica	sp\|Q7G4P2\|LCB1C_ORYSJ Long chain base biosynthesis protein 1c	70.600%	Swiss-Prot	High

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