LXL04_004283 | RubberDandelionOmics

Gene overview

LXL04_004283

Reference: OH-1004 Chr: Chr01 Coordinates: 131709252-131723269 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6324 bp · LXL04_004283|LXL04_004283|OH1004|cDNA

ATGGAGGCCTTGAAGGTTTGGTCGTCACGGCCTCTGAGGCACCTCTTTCATTTAGCTTCCTCTTCACCTCCTCCTACCTCTAAATCATATCTCCCTGTTACTTTTATTCGCTGTTGTTCTTCCTCCACTTCCTCCGCCGCCACCTCTGCCGTCGTGCCAAAACAAGGCGGCAGAGGCAGGAGATCATCCGCCGCATCCACTACCACCTCAACCTCCGATAGAGACGCCATTCGCGCAATCCGTCTCAAAAAGGTTGAAGA...

CDS

Download CDS FASTA

6324 bp · LXL04_004283|LXL04_004283|OH1004|CDS

ATGGAGGCCTTGAAGGTTTGGTCGTCACGGCCTCTGAGGCACCTCTTTCATTTAGCTTCCTCTTCACCTCCTCCTACCTCTAAATCATATCTCCCTGTTACTTTTATTCGCTGTTGTTCTTCCTCCACTTCCTCCGCCGCCACCTCTGCCGTCGTGCCAAAACAAGGCGGCAGAGGCAGGAGATCATCCGCCGCATCCACTACCACCTCAACCTCCGATAGAGACGCCATTCGCGCAATCCGTCTCAAAAAGGTTGAAGA...

Protein

Download Protein FASTA

2107 aa · LXL04_004283|LXL04_004283|OH1004|PROTEIN

MEALKVWSSRPLRHLFHLASSSPPPTSKSYLPVTFIRCCSSSTSSAATSAVVPKQGGRGRRSSAASTTTSTSDRDAIRAIRLKKVEELRSKGFEPYAYKWDRTHTANQLQEIYKHLGNGEESNSENDQVSISGRIVARRAFGKLAFLTLRDDSGIIQLYCEKERLENDQFEQLKSLVDIGDILGANGSIKRTEKGELSVCVNSFMILTKSLLPLPDKFHGLTDVDKRYRQRYVDMIANPEVADVFRKRAKIVSIIRQTVE...

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_004283`
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_004283

Location Chr01:131709252-131723269 (+)

Description Similar to Retrovirus-related Pol polyprotein from transposon TNT 1-94

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g13490`	Catalyzes the specific attachment of an amino acid to its cognate tRNA in a 2 step reaction: the amino acid (AA) is first activated by ATP to form AA-AMP and then transferred to the acceptor end of the tRNA.	No verified direct reference in this release
`UniProt: Q94HW2`	Retrovirus-related Pol polyprotein from transposon RE1.	No verified direct reference in this release
`At4g02960`	Retrovirus-related Pol polyprotein from transposon RE2.	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_004283 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006310 DNA recombination Biological Process

GO:0006430 lysyl-tRNA aminoacylation Biological Process

GO:0006508 proteolysis Biological Process

GO:0015074 DNA integration Biological Process

GO:0048481 plant ovule development Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0000049 tRNA binding Molecular Function

GO:0003676 nucleic acid binding Molecular Function

GO:0003677 DNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G13490

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.

Plastid0.341

Rank 1 · LXL04_004283 · OH-1004

Mitochondrion0.332

Rank 2 · LXL04_004283 · OH-1004

Cytoplasm0.159

Rank 3 · LXL04_004283 · OH-1004

Nucleus0.107

Rank 4 · LXL04_004283 · OH-1004

Peroxisome0.082

Rank 5 · LXL04_004283 · 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-codon129-207 aa

PF00152.26tRNA-synt_2224-308 aa

PF00152.26tRNA-synt_2442-720 aa

PF13961.13DUF4219842-867 aa

PF14223.15Retrotran_gag_2855-1016 aa

PF22936.2Pol_BBD1123-1159 aa

PF13976.12gag_pre-integrs1191-1258 aa

PF00665.33rve1272-1373 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004283	`PF01336.32`	tRNA_anti-codon	129	207	4.2e-18	65.8
LXL04_004283	`PF00152.26`	tRNA-synt_2	224	308	8.6e-75	252.4
LXL04_004283	`PF00152.26`	tRNA-synt_2	442	720	8.6e-75	252.4
LXL04_004283	`PF13961.13`	DUF4219	842	867	3e-09	37.1
LXL04_004283	`PF14223.15`	Retrotran_gag_2	855	1016	2.5e-16	60.6
LXL04_004283	`PF22936.2`	Pol_BBD	1123	1159	8.5e-07	29.9
LXL04_004283	`PF13976.12`	gag_pre-integrs	1191	1258	1e-18	67.6
LXL04_004283	`PF00665.33`	rve	1272	1373	2.7e-15	57.2
LXL04_004283	`PF29688.1`	TnsB_C	1339	1392	2.6e-07	31.2
LXL04_004283	`PF25597.2`	SH3_retrovirus	1447	1509	1.1e-21	77.1
LXL04_004283	`PF07727.20`	RVT_2	1634	1876	6.5e-90	301.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9LJE2`	Arabidopsis thaliana	Lysine--tRNA ligase, chloroplastic/mitochondrial	76.761%	Swiss-Prot	weak database homology
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	36.952%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	36.047%	Swiss-Prot	weak database homology

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