LXL04_038879 | RubberDandelionOmics

Gene overview

LXL04_038879

Reference: OH-1004 Chr: Chr09 Coordinates: 52383134-52385018 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1071 bp · LXL04_038879|LXL04_038879|OH1004|cDNA

ATGGCGAATCGTACGGACCCGTCGGCGAAAAGCATACATGGAACAAACCCCCAAAACCTTATTGAGAAGATATTGAGGTCTAAGATTTACCAAAACGTCTTCTGGAAGGAGCAGTGTTTCGGTTTGACAGCTGAGACGCTTGTGGACAAGGCCATGGAGCTCGATCACATCGGCGGTACCCACGGCGGAAACCGAAGACCCACGCCATTCATCTGCCTCGTCATGAAGATGCTCCAGATCCAGCCTGATAAAGAAATTGT...

CDS

Download CDS FASTA

1071 bp · LXL04_038879|LXL04_038879|OH1004|CDS

ATGGCGAATCGTACGGACCCGTCGGCGAAAAGCATACATGGAACAAACCCCCAAAACCTTATTGAGAAGATATTGAGGTCTAAGATTTACCAAAACGTCTTCTGGAAGGAGCAGTGTTTCGGTTTGACAGCTGAGACGCTTGTGGACAAGGCCATGGAGCTCGATCACATCGGCGGTACCCACGGCGGAAACCGAAGACCCACGCCATTCATCTGCCTCGTCATGAAGATGCTCCAGATCCAGCCTGATAAAGAAATTGT...

Protein

Download Protein FASTA

356 aa · LXL04_038879|LXL04_038879|OH1004|PROTEIN

MANRTDPSAKSIHGTNPQNLIEKILRSKIYQNVFWKEQCFGLTAETLVDKAMELDHIGGTHGGNRRPTPFICLVMKMLQIQPDKEIVVEFIKNEDYKYVRVLGAFYLRLTGTDIDVYRYLEPLYNDYRKLRRKLGDGQYSLTHMDEVIDELLTKDYSCDIALPRIKKRLTIEAIGALEPRKSALEDDFEEEEEKEDEEQPMDTDVGGHDKDYYRAQSPTKERGRDRKRDSHRHRDRDYDREYERDYDRDRGRGRDRDRDR...

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_038879`
TK1151 ID	TkA04G473380
OH-1004 ID	LXL04_038879
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.500
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_038879

Location Chr09:52383134-52385018 (-)

Description Similar to PRP38: Pre-mRNA-splicing factor 38

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g40650`	Probably required for the first pre-mRNA cleavage reaction catalyzed by the spliceosome.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_038879 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0010389 regulation of G2/M transition of mitotic cell cycle Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0032991 protein-containing complex Cellular Component

GO:0071005 U2-type precatalytic spliceosome Cellular Component

GO:0071011 precatalytic spliceosome Cellular Component

GO:0071013 catalytic step 2 spliceosome Cellular Component

GO:0003723 RNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G40650

dme:Dmel_CG30342

hsa:84950

mcf:102116944

pon:100171974

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.

Nucleus0.964

Rank 1 · LXL04_038879 · OH-1004

Cytoplasm0.113

Rank 2 · LXL04_038879 · OH-1004

Cell membrane0.017

Rank 3 · LXL04_038879 · OH-1004

Mitochondrion0.013

Rank 4 · LXL04_038879 · OH-1004

Endoplasmic reticulum0.009

Rank 5 · LXL04_038879 · 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.

PF03371.21PRP3810-172 aa

PF12871.13PRP38_assoc179-270 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038879	`PF03371.21`	PRP38	10	172	8.7e-67	225.0
LXL04_038879	`PF12871.13`	PRP38_assoc	179	270	5.8e-09	37.1

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
`Q8LB54`	Arabidopsis thaliana	Pre-mRNA-splicing factor 38	81.522%	Swiss-Prot	moderate database homology

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