LXL04_015199 | RubberDandelionOmics

Gene overview

LXL04_015199

Reference: OH-1004 Chr: Chr03 Coordinates: 65760925-65762797 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

387 bp · LXL04_015199|LXL04_015199|OH1004|cDNA

ATGAGTCGGAGCTTAGGTATACCGGTGAAGCTGCTCCACGAGGCCGCCGGTCACATTGTGACCGTAGAACTTAAAAGCGGAGAAGTGTACAGAGGAAGCTTGGTGGAATGCGAAGACAACTGGAACTGCCAAGTGGAAAACGTTACTTTCACCGCTAAGGATGGAAAGGTCTCACAACTTGAGCATGTCTTTATTCGAGGCAGCAAAGTTAGGTTTTTGATCATACCAGACATGCTTAAAAACGCTCCTATGTTCAAAAG...

CDS

Download CDS FASTA

387 bp · LXL04_015199|LXL04_015199|OH1004|CDS

ATGAGTCGGAGCTTAGGTATACCGGTGAAGCTGCTCCACGAGGCCGCCGGTCACATTGTGACCGTAGAACTTAAAAGCGGAGAAGTGTACAGAGGAAGCTTGGTGGAATGCGAAGACAACTGGAACTGCCAAGTGGAAAACGTTACTTTCACCGCTAAGGATGGAAAGGTCTCACAACTTGAGCATGTCTTTATTCGAGGCAGCAAAGTTAGGTTTTTGATCATACCAGACATGCTTAAAAACGCTCCTATGTTCAAAAG...

Protein

Download Protein FASTA

128 aa · LXL04_015199|LXL04_015199|OH1004|PROTEIN

MSRSLGIPVKLLHEAAGHIVTVELKSGEVYRGSLVECEDNWNCQVENVTFTAKDGKVSQLEHVFIRGSKVRFLIIPDMLKNAPMFKRLEARIKGKSSALGVGRGRAVAMRARAQAAGRGGAAGPGRGR

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_015199`
TK1151 ID	TkA02G356850
OH-1004 ID	LXL04_015199
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 78.906 / OH-1004 78.906 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_015199

Location Chr03:65760925-65762797 (+)

Description Similar to SMD3B: Small nuclear ribonucleoprotein SmD3b

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g20580`	Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (By similarity).	No verified direct reference in this release
`At1g76300`	Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (By similarity).	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_015199 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000244 spliceosomal tri-snRNP complex assembly Biological Process

GO:0000245 spliceosomal complex assembly Biological Process

GO:0000387 spliceosomal snRNP assembly Biological Process

GO:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006479 protein methylation Biological Process

GO:0008380 RNA splicing Biological Process

GO:0036261 7-methylguanosine cap hypermethylation Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0045087 innate immune response Biological Process

GO:0048025 negative regulation of mRNA splicing, via spliceosome Biological Process

GO:0048589 developmental growth Biological Process

KEGG gene cross-reference

ath:AT1G20580

ath:AT1G76300

hsa:6634

mmu:67332

xla:431993

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.

Nucleus0.795

Rank 1 · LXL04_015199 · OH-1004

Cytoplasm0.369

Rank 2 · LXL04_015199 · OH-1004

Cell membrane0.034

Rank 3 · LXL04_015199 · OH-1004

Endoplasmic reticulum0.026

Rank 4 · LXL04_015199 · OH-1004

Mitochondrion0.025

Rank 5 · LXL04_015199 · 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.

PF01423.29LSM10-74 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015199	`PF01423.29`	LSM	10	74	2.3e-18	66.4

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
`Q9LM92`	Arabidopsis thaliana	Small nuclear ribonucleoprotein SmD3b	83.929%	Swiss-Prot	strong database homology
`Q9S7E6`	Arabidopsis thaliana	Small nuclear ribonucleoprotein SmD3a	80.357%	Swiss-Prot	strong database homology

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