LXL04_019451 | RubberDandelionOmics

Gene overview

LXL04_019451

Reference: OH-1004 Chr: Chr04 Coordinates: 31502163-31502835 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

297 bp · LXL04_019451|LXL04_019451|OH1004|cDNA

ATGCTGGGTGGGCCTGGACTTGAAACGGTTGTTGATCAAATCATATCGGTCATTACAAATGATGGTCGCAACATAGTGGGAGTATTGAAAGGGTTCGATCAAGCTACAAATATAATTCTTGATGAATCTCATGAAAGAGTTTATTCCACCAAGGAAGGTGTTCAGCAACTCGTATTAGGTCTCTACATCATAAGGGGTGATAacatAAGTGTTATTGGGGAGTTAGATGAAGAGCTTGATGCCAGCTTGGATTTGTCACA...

CDS

Download CDS FASTA

297 bp · LXL04_019451|LXL04_019451|OH1004|CDS

ATGCTGGGTGGGCCTGGACTTGAAACGGTTGTTGATCAAATCATATCGGTCATTACAAATGATGGTCGCAACATAGTGGGAGTATTGAAAGGGTTCGATCAAGCTACAAATATAATTCTTGATGAATCTCATGAAAGAGTTTATTCCACCAAGGAAGGTGTTCAGCAACTCGTATTAGGTCTCTACATCATAAGGGGTGATAACATAAGTGTTATTGGGGAGTTAGATGAAGAGCTTGATGCCAGCTTGGATTTGTCACA...

Protein

Download Protein FASTA

98 aa · LXL04_019451|LXL04_019451|OH1004|PROTEIN

MLGGPGLETVVDQIISVITNDGRNIVGVLKGFDQATNIILDESHERVYSTKEGVQQLVLGLYIIRGDNISVIGELDEELDASLDLSQLKAHPLKPVIH

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_019451`
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_019451

Location Chr04:31502163-31502835 (+)

Description Similar to LSM8: Sm-like protein LSM8

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g65700`	Component of the nuclear LSM2-LSM8 complex which is involved splicing nuclear mRNAs.	Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation.2013 · DOI: 10.1093/nar/gkt296 Prefoldins contribute to maintaining the levels of the spliceosome LSM2-8 complex through Hsp90 in Arabidopsis.2020 · DOI: 10.1093/nar/gkaa354

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_019451 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000244 spliceosomal tri-snRNP complex assembly Biological Process

GO:0000387 spliceosomal snRNP assembly Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0016070 RNA metabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005688 U6 snRNP Cellular Component

GO:0046540 U4/U6 x U5 tri-snRNP complex Cellular Component

GO:0071005 U2-type precatalytic spliceosome Cellular Component

GO:0071011 precatalytic spliceosome Cellular Component

GO:0120115 Lsm2-8 complex Cellular Component

KEGG gene cross-reference

ath:AT1G65700

bta:613630

hsa:51691

mmu:76522

pon:100172134

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.

Nucleus0.858

Rank 1 · LXL04_019451 · OH-1004

Cytoplasm0.539

Rank 2 · LXL04_019451 · OH-1004

Mitochondrion0.017

Rank 3 · LXL04_019451 · OH-1004

Cell membrane0.014

Rank 4 · LXL04_019451 · OH-1004

Lysosome / Vacuole0.013

Rank 5 · LXL04_019451 · 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.

PF01423.29LSM7-73 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019451	`PF01423.29`	LSM	7	73	3.2e-18	65.9

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
`Q8VYI0`	Arabidopsis thaliana	Sm-like protein LSM8	87.755%	Swiss-Prot	strong database homology

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