LXL04_031190 | RubberDandelionOmics

Gene overview

LXL04_031190

Reference: OH-1004 Chr: Chr07 Coordinates: 2009145-2010429 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1086 bp · LXL04_031190|LXL04_031190|OH1004|cDNA

ATGCTCTTTACACGATCGAAACTCCATCAATCGCTAGCTTCCACTCCTCGCAATCTTATAAAACACTTCCTAATTACCACCACAACTACTATGAAagaaatcaaaacaaaaaagCACTCAAATACATCATCGCTATTGAACCCAGATGCAAAATGCTCTTCCAGTGTCAAATCAACCCCAGAAATCGAAAAGAAATACGTCCATCGTGTGTATGATGCGATCGCACCTCATTTTAGTGCAACCCGTTTTGCTAAATGGCC...

CDS

Download CDS FASTA

1086 bp · LXL04_031190|LXL04_031190|OH1004|CDS

ATGCTCTTTACACGATCGAAACTCCATCAATCGCTAGCTTCCACTCCTCGCAATCTTATAAAACACTTCCTAATTACCACCACAACTACTATGAAAGAAATCAAAACAAAAAAGCACTCAAATACATCATCGCTATTGAACCCAGATGCAAAATGCTCTTCCAGTGTCAAATCAACCCCAGAAATCGAAAAGAAATACGTCCATCGTGTGTATGATGCGATCGCACCTCATTTTAGTGCAACCCGTTTTGCTAAATGGCC...

Protein

Download Protein FASTA

361 aa · LXL04_031190|LXL04_031190|OH1004|PROTEIN

MLFTRSKLHQSLASTPRNLIKHFLITTTTTMKEIKTKKHSNTSSLLNPDAKCSSSVKSTPEIEKKYVHRVYDAIAPHFSATRFAKWPKVSAFLNNLPSSSVILDAGCGNGKYLGLNPNCFFIGCDISAPLIQICSERGHEVFVADAVNLPYRTSYADAAISIAVLHHLSTENRRKKAIDELVRVVKKGGHVLITVWAVEQEDKSLLNKWTPLTDKYLEEWIGPGTPRIRSSSSVTLESIPETEVSISQEEVKDFGNLSLV...

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_031190`
TK1151 ID	TkA08G092510
OH-1004 ID	LXL04_031190
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_031190

Location Chr07:2009145-2010429 (-)

Description Similar to TRM9: tRNA (carboxymethyluridine(34)-5-O)-methyltransferase

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g36310`	Catalyzes the methylation of 5-carboxymethyl uridine to 5- methylcarboxymethyl uridine at the wobble position of the anticodon loop in tRNA via its methyltransferase domain.	Roles of Trm9- and ALKBH8-like proteins in the formation of modified wobble uridines in Arabidopsis tRNA.2011 · DOI: 10.1093/nar/gkr406

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031190 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002098 tRNA wobble uridine modification Biological Process

GO:0006974 DNA damage response Biological Process

GO:0030488 tRNA methylation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0043527 tRNA methyltransferase complex Cellular Component

GO:0000049 tRNA binding Molecular Function

GO:0005506 iron ion binding Molecular Function

GO:0008175 tRNA methyltransferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G36310

bta:781788

mmu:67667

xtr:550051

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.

Nucleus0.544

Rank 1 · LXL04_031190 · OH-1004

Cytoplasm0.273

Rank 2 · LXL04_031190 · OH-1004

Plastid0.157

Rank 3 · LXL04_031190 · OH-1004

Mitochondrion0.094

Rank 4 · LXL04_031190 · OH-1004

Cell membrane0.030

Rank 5 · LXL04_031190 · 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.

PF13489.13Methyltransf_2388-210 aa

PF13847.13Methyltransf_3199-206 aa

PF13649.13Methyltransf_25102-189 aa

PF08241.19Methyltransf_11103-193 aa

PF08242.19Methyltransf_12103-191 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_031190	`PF13489.13`	Methyltransf_23	88	210	3.6e-09	37.3
LXL04_031190	`PF13847.13`	Methyltransf_31	99	206	2.5e-08	34.5
LXL04_031190	`PF13649.13`	Methyltransf_25	102	189	3.4e-13	50.8
LXL04_031190	`PF08241.19`	Methyltransf_11	103	193	1.8e-16	61.3
LXL04_031190	`PF08242.19`	Methyltransf_12	103	191	6e-08	34.0

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
`Q94A09`	Arabidopsis thaliana	tRNA (carboxymethyluridine(34)-5-O)-methyltransferase	68.278%	Swiss-Prot	strong database homology

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