TkA01G558120 | RubberDandelionOmics

Gene overview

TkA01G558120

Reference: TK1151 Chr: Chr01 Coordinates: 140385438-140387360 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1195 bp · TkA01G558120|TK1151|cDNA

GACGACGCTAACCTACCGTCTATCCGATTTTTTTCCTTTTCTTTTTATTTTTTTGCATGTTAACCGGAAAAGTACTAATCGAGCCTACAAACATCAAATTTAAATTTTTTTAGGTCTGACTTGTAAATAAAGCTAAATATAAAATACTCTTGTCTTTTTAGAGAGAATTTAAAATTTTGGCTGGACTAGTATTTTTCTCTTAAAAAAACATCAAAGACTATTTAAGGTTGAGATATATTTCTGTCGCTGTTTACAGCAAG...

CDS

Download CDS FASTA

387 bp · TkA01G558120|TK1151|CDS

ATGCTTCCTCTATCTCTACTAAAGACGGCACAAGGCCATCCTATGTTGGTAGAACTGAAGAACGGGGAGACATACAATGGACATTTGGTGAATTGCGATACTTGGATGAACATCCATCTGCGTGAAGTGATATGTACCTCAAAGGATGGAGATAGGTTTTGGCGAATGCCTGAGTGCTACATTCGGGGTAATACGATCAAGTATCTTAGAGTTCCTGATGAGGTTATCGATAAGGTTCAAGAAGAGAGCAAGAGTCGTTC...

Protein

Download Protein FASTA

128 aa · TkA01G558120|TK1151|PROTEIN

MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQEESKSRSDRKPPGVGRGRGRGGGGGGDDKGRGRGGGRTGGARGGGRGR

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	`TkA01G558120`
TK1151 ID	TkA01G558120
OH-1004 ID	LXL04_016125
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	95.800
Protein coverage (%)	TK1151 74.219 / OH-1004 63.333 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 TkA01G558120

Location Chr01:140385438-140387360 (-)

Description Similar to Probable U6 snRNA-associated Sm-like protein LSm4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g27720`	Component of LSM protein complexes, which are involved in RNA processing.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0256900`	Binds specifically to the 3'-terminal U-tract of U6 snRNA.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016125 · 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:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA Biological Process

GO:0000387 spliceosomal snRNP assembly Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0000956 nuclear-transcribed mRNA catabolic process Biological Process

GO:0033962 P-body assembly Biological Process

GO:0000932 P-body Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005688 U6 snRNP Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT5G27720

dosa:Os01g0256900

mmu:50783

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.

Nucleus0.844

Rank 1 · TkA01G558120 · TK1151

Cytoplasm0.345

Rank 2 · TkA01G558120 · TK1151

Endoplasmic reticulum0.034

Rank 3 · TkA01G558120 · TK1151

Cell membrane0.030

Rank 4 · TkA01G558120 · TK1151

Mitochondrion0.020

Rank 5 · TkA01G558120 · 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.

PF01423LSM6-70 aa

PF14438SM-ATX6-48 aa

PF01423LSM75-89 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G558120	`PF01423`	LSM	6	70	4.9e-18	65.3
TkA01G558120	`PF14438`	SM-ATX	6	48	0.015	16.2
TkA01G558120	`PF01423`	LSM	75	89	4.9e-18	65.3

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
`F4K4E3`	Arabidopsis thaliana	sp\|F4K4E3\|LSM4_ARATH Sm-like protein LSM4	96.800%	Swiss-Prot	High
`Q9LGE6`	Oryza sativa subsp. japonica	sp\|Q9LGE6\|LSM4_ORYSJ Probable U6 snRNA-associated Sm-like protein LSm4	96.900%	Swiss-Prot	High

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