LXL04_013571 | RubberDandelionOmics

Gene overview

LXL04_013571

Reference: OH-1004 Chr: Chr03 Coordinates: 31772501-31774690 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1741 bp · LXL04_013571|LXL04_013571|OH1004|cDNA

GACACAAGCAGAGCACTCGTTTCCTGTTCAAGCTACCAAAATGGCAGACAATGGAGTGCTGCCGGTCGACAAGTTAACAATTTCCGACACTGTCGAAGAAGCCGAGTTCTCACAGCGTGTACTGATTCGATCAATTCTGGGCCGTCCGGACGGCGGCGCTGGCCTTGCTGGGAAGACCTTGAGGGTAGGCGGCTGGGTGAAGAAAGGTCGAGAACAAGGCAAAGGTTCATTTGCCTTTCTTGAACTTAACGACGGATCTT...

CDS

Download CDS FASTA

1701 bp · LXL04_013571|LXL04_013571|OH1004|CDS

ATGGCAGACAATGGAGTGCTGCCGGTCGACAAGTTAACAATTTCCGACACTGTCGAAGAAGCCGAGTTCTCACAGCGTGTACTGATTCGATCAATTCTGGGCCGTCCGGACGGCGGCGCTGGCCTTGCTGGGAAGACCTTGAGGGTAGGCGGCTGGGTGAAGAAAGGTCGAGAACAAGGCAAAGGTTCATTTGCCTTTCTTGAACTTAACGACGGATCTTGTCCGGCGAACCTCCAGCTTATAATATACTCGGATGTAGC...

Protein

Download Protein FASTA

566 aa · LXL04_013571|LXL04_013571|OH1004|PROTEIN

MADNGVLPVDKLTISDTVEEAEFSQRVLIRSILGRPDGGAGLAGKTLRVGGWVKKGREQGKGSFAFLELNDGSCPANLQLIIYSDVAPLGQFTPTGTCLHVEGVLQMPPADKQGKQSIELKVSKVLDIGAADPAKYPLPKTRLTLEFLRDYVHLRPRTNTISSIARIRNALAYATHTFFQKHGFLYVHTPIITTSDCEGAGEMFQVTTLINDSEKLEKELIKNPPPSQQDVDTARAAVKEKGEIVAKLKSDKAGKPAITA...

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_013571`
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_013571

Location Chr03:31772501-31774690 (+)

Description Similar to SYNC1: Asparagine--tRNA ligase, cytoplasmic 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g56680`	Asparagine--tRNA ligase, cytoplasmic 1.	No verified direct reference in this release
`At1g70980`	Asparagine--tRNA ligase, cytoplasmic 3.	No verified direct reference in this release
`At4g17300`	Asparagine--tRNA ligase, chloroplastic/mitochondrial.	No verified direct reference in this release
`At3g07420`	Asparagine--tRNA ligase, cytoplasmic 2.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013571 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006421 asparaginyl-tRNA aminoacylation Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0048481 plant ovule development Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009536 plastid Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0003676 nucleic acid binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0004816 asparagine-tRNA ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G70980

ath:AT3G07420

ath:AT4G17300

ath:AT5G56680

sfu:Sfum_2475

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.

Cytoplasm0.613

Rank 1 · LXL04_013571 · OH-1004

Mitochondrion0.236

Rank 2 · LXL04_013571 · OH-1004

Nucleus0.214

Rank 3 · LXL04_013571 · OH-1004

Peroxisome0.080

Rank 4 · LXL04_013571 · OH-1004

Cell membrane0.044

Rank 5 · LXL04_013571 · OH-1004

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.

PF01336.32tRNA_anti-codon48-125 aa

PF00152.26tRNA-synt_2148-211 aa

PF00458.26WHEP-TRS236-276 aa

PF00152.26tRNA-synt_2297-559 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013571	`PF01336.32`	tRNA_anti-codon	48	125	4.1e-07	30.6
LXL04_013571	`PF00152.26`	tRNA-synt_2	148	211	9.1e-59	199.7
LXL04_013571	`PF00458.26`	WHEP-TRS	236	276	8.2e-06	26.5
LXL04_013571	`PF00152.26`	tRNA-synt_2	297	559	9.1e-59	199.7

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
`Q9SW96`	Arabidopsis thaliana	Asparagine--tRNA ligase, cytoplasmic 1	69.755%	Swiss-Prot	strong database homology
`Q9SSK1`	Arabidopsis thaliana	Asparagine--tRNA ligase, cytoplasmic 3	69.164%	Swiss-Prot	strong database homology
`O48593`	Arabidopsis thaliana	Asparagine--tRNA ligase, chloroplastic/mitochondrial	50.000%	Swiss-Prot	strong database homology
`Q9SW95`	Arabidopsis thaliana	Asparagine--tRNA ligase, cytoplasmic 2	45.957%	Swiss-Prot	moderate database homology

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