TkA08G163720 | RubberDandelionOmics

Gene overview

TkA08G163720

Reference: TK1151 Chr: Chr08 Coordinates: 42724474-42727433 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1152 bp · TkA08G163720|TK1151|cDNA

AGAGACTTTTATTCATATATCGGCAAAGCGTTAAACGCCACGCATCAAATCACACCCCCTTTCAGATTTGGGGATGGTTAATTAGGGTTAATAGATAGATCTGGAGGGTGGAGAATAACTGAAACTAGCACTCTCTCTCACTATTTTTTTCTTTCGAGAGTGTCTACTAGGTTCAAGATTTGGGGATAGATTAGGTTTTGTTTATCGTTTTAACAGATCGTGGATTCTATACCATTGTTATGGTTTCTGTTGATATAAAT...

CDS

Download CDS FASTA

387 bp · TkA08G163720|TK1151|CDS

ATGTCTTGGGCGGGTCCTGAAGATATCCATCTATCTACTTCTCTTGCAAGCTATCTCGACAAGAAACTTCTTGTATTGCTAAGAGATGGCAGAAAGCTGTTGGGAATACTTCGCTCTTTTGATCAATTTGCTAATGCTGTTCTAGAAGGTGCTTGTGAACGAGTAATTGTTGGTGATCTGTATTGTGATATCTCGCTAGGTCTTTACGTAATCCGTGGCGAGAATGTTGTTTTGATTGGCGAGCTGGATCTGGAAAAGGA...

Protein

Download Protein FASTA

128 aa · TkA08G163720|TK1151|PROTEIN

MSWAGPEDIHLSTSLASYLDKKLLVLLRDGRKLLGILRSFDQFANAVLEGACERVIVGDLYCDISLGLYVIRGENVVLIGELDLEKEELPPHMTRVSEAEIKRAQKVERDATDLKGSMRKRMEFLDMD

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	`TkA08G163720`
TK1151 ID	TkA08G163720
OH-1004 ID	LXL04_019451
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	41.700
Protein coverage (%)	TK1151 55.469 / OH-1004 73.469 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA08G163720

Location Chr08:42724474-42727433 (-)

Description Similar to LSM8: Sm-like protein LSM8

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g14080`	Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by promoting decapping and leading to accurate 5'-3' mRNA decay.	Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation.2013 · DOI: 10.1093/nar/gkt296
`At1g19120`	Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by promoting decapping and leading to accurate 5'-3' mRNA decay.	Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation.2013 · DOI: 10.1093/nar/gkt296

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_019451 · 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:0000244 spliceosomal tri-snRNP complex assembly Biological Process

GO:0000387 spliceosomal snRNP assembly Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0016070 RNA metabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005688 U6 snRNP Cellular Component

GO:0046540 U4/U6 x U5 tri-snRNP complex Cellular Component

GO:0071005 U2-type precatalytic spliceosome Cellular Component

GO:0071011 precatalytic spliceosome Cellular Component

GO:0120115 Lsm2-8 complex Cellular Component

KEGG gene cross-reference

ath:AT1G65700

bta:613630

hsa:51691

mmu:76522

pon:100172134

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.

Nucleus0.699

Rank 1 · TkA08G163720 · TK1151

Cytoplasm0.584

Rank 2 · TkA08G163720 · TK1151

Endoplasmic reticulum0.026

Rank 3 · TkA08G163720 · TK1151

Cell membrane0.025

Rank 4 · TkA08G163720 · TK1151

Lysosome / Vacuole0.023

Rank 5 · TkA08G163720 · 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.

PF01423LSM14-80 aa

PF17209Hfq22-44 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G163720	`PF01423`	LSM	14	80	1.6e-19	70.0
TkA08G163720	`PF17209`	Hfq	22	44	0.09	13.1

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
`Q8LFL8`	Arabidopsis thaliana	sp\|Q8LFL8\|LSM1B_ARATH Sm-like protein LSM1B	86.700%	Swiss-Prot	High
`Q945P8`	Arabidopsis thaliana	sp\|Q945P8\|LSM1A_ARATH Sm-like protein LSM1A	81.300%	Swiss-Prot	High

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