LXL04_003842 | RubberDandelionOmics

Gene overview

LXL04_003842

Reference: OH-1004 Chr: Chr01 Coordinates: 108772652-108773265 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

453 bp · LXL04_003842|LXL04_003842|OH1004|cDNA

AtgTTAAAGTTACCGTATCATATAGTGTCTATAGTCGTTAATGCCTTAATTGATGCTGCAGCAAAGAAGTATGATTTAGAAGCATGGTTTTCTGCTTCCAAAACTTACAAAGAGTTGGTGTCGTATTCAAATTGCATTGATTACCAGTCAAGAAAGTTGGAGATCAGATATGGCCAGAAGAagAGTAATGATCAAACAAAGCAATATTGTCATTTATTGAATACTACACTCACGGCAACAAAGAGGACTCTGTGTTGTAA...

CDS

Download CDS FASTA

453 bp · LXL04_003842|LXL04_003842|OH1004|CDS

ATGTTAAAGTTACCGTATCATATAGTGTCTATAGTCGTTAATGCCTTAATTGATGCTGCAGCAAAGAAGTATGATTTAGAAGCATGGTTTTCTGCTTCCAAAACTTACAAAGAGTTGGTGTCGTATTCAAATTGCATTGATTACCAGTCAAGAAAGTTGGAGATCAGATATGGCCAGAAGAAGAGTAATGATCAAACAAAGCAATATTGTCATTTATTGAATACTACACTCACGGCAACAAAGAGGACTCTGTGTTGTAA...

Protein

Download Protein FASTA

150 aa · LXL04_003842|LXL04_003842|OH1004|PROTEIN

MLKLPYHIVSIVVNALIDAAAKKYDLEAWFSASKTYKELVSYSNCIDYQSRKLEIRYGQKKSNDQTKQYCHLLNTTLTATKRTLCCNIENYMRQDGVVVHEMLQPFMGGQTLFILMPDLLKNNKWKEIKVVVLYVLDRNKFLINLYGFLR

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	`LXL04_003842`
TK1151 ID	TkA01G253100
OH-1004 ID	LXL04_003842
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
Protein coverage (%)	TK1151 95.745 / OH-1004 90.000 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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_003842

Location Chr01:108772652-108773265 (-)

Description Similar to Serine--tRNA ligase

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g27470`	Catalyzes the attachment of serine to tRNA(Ser) in a two-step reaction: serine is first activated by ATP to form Ser-AMP and then transferred to the acceptor end of tRNA(Ser).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_003842 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002181 cytoplasmic translation Biological Process

GO:0006434 seryl-tRNA aminoacylation Biological Process

GO:0110004 positive regulation of tRNA methylation Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

GO:0000049 tRNA binding Molecular Function

GO:0004828 serine-tRNA ligase activity Molecular Function

GO:0005524 ATP binding Molecular Function

GO:1990825 sequence-specific mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT5G27470

cal:CAALFM_C302780WA

sce:YDR023W

spo:2542163

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.

Mitochondrion0.340

Rank 1 · LXL04_003842 · OH-1004

Cytoplasm0.293

Rank 2 · LXL04_003842 · OH-1004

Nucleus0.252

Rank 3 · LXL04_003842 · OH-1004

Cell membrane0.058

Rank 4 · LXL04_003842 · OH-1004

Peroxisome0.055

Rank 5 · LXL04_003842 · OH-1004

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.

PF00587.31tRNA-synt_2b13-91 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003842	`PF00587.31`	tRNA-synt_2b	13	91	4.5e-09	37.3

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
`Q39230`	Arabidopsis thaliana	Serine--tRNA ligase, cytoplasmic	73.874%	Swiss-Prot	strong database homology

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