LXL04_008159 | RubberDandelionOmics

Gene overview

LXL04_008159

Reference: OH-1004 Chr: Chr02 Coordinates: 90253894-90256464 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1701 bp · LXL04_008159|LXL04_008159|OH1004|cDNA

ATGGGTTACTCAAACGCTGGAATTTACATGTGGGGGAGTATTATCTTAGTGCCTTCTCCAGAATTGGATGATTACATATGCCCTGTTGCTGAGTCTCTTGTCATAATGGCTTTCAAATCGAGGGAGGATCACAGGAAACAAATGGAACTGGAGGAAGCGCGTAAAGCTGGGCTGGCACCTGCAGAAGTGGATGAAGATGGAAAGGAAATCAATCCCCATATTCCTCAATACATGTCGTCTGCCCCTTGGTATCTGAATGC...

CDS

Download CDS FASTA

1701 bp · LXL04_008159|LXL04_008159|OH1004|CDS

ATGGGTTACTCAAACGCTGGAATTTACATGTGGGGGAGTATTATCTTAGTGCCTTCTCCAGAATTGGATGATTACATATGCCCTGTTGCTGAGTCTCTTGTCATAATGGCTTTCAAATCGAGGGAGGATCACAGGAAACAAATGGAACTGGAGGAAGCGCGTAAAGCTGGGCTGGCACCTGCAGAAGTGGATGAAGATGGAAAGGAAATCAATCCCCATATTCCTCAATACATGTCGTCTGCCCCTTGGTATCTGAATGC...

Protein

Download Protein FASTA

566 aa · LXL04_008159|LXL04_008159|OH1004|PROTEIN

MGYSNAGIYMWGSIILVPSPELDDYICPVAESLVIMAFKSREDHRKQMELEEARKAGLAPAEVDEDGKEINPHIPQYMSSAPWYLNAERPSLKHQRKWKSDPNYTKSWYDRGAKIYQADKYRKGACENCGAMTHTTKTCMERPRKLGAKWTSKNIAPDEKIETFELDYDGKRDRWNGYDAASYAHVIERYEARDEARKKFLKDQQLKKLEEKGGGENADEGVSDDEDNEDALKIDEAKVDESKQMDFAKVEKRVRTTGGG...

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_008159`
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_008159

Location Chr02:90253894-90256464 (-)

Description Similar to Os08g0127700: Pre-mRNA-splicing factor SLU7

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g65660`	Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'-splice site to generate spliced mRNA and the excised lariat intron (By similarity).	The recessive epigenetic swellmap mutation affects the expression of two step II splicing factors required for the transcription of the cell proliferation gene STRUWWELPETER and for the timing of cell cycle arrest in the Arabidopsis leaf.2005 · DOI: 10.1105/tpc.105.032771
`At4g37120`	Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'-splice site to generate spliced mRNA and the excised lariat intron (By similarity).	The recessive epigenetic swellmap mutation affects the expression of two step II splicing factors required for the transcription of the cell proliferation gene STRUWWELPETER and for the timing of cell cycle arrest in the Arabidopsis leaf.2005 · DOI: 10.1105/tpc.105.032771 SWELLMAP 2, a phyB-Interacting Splicing Factor, Negatively Regulates Seedling Photomorphogenesis in Arabidopsis .2022 · DOI: 10.3389/fpls.2022.836519

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0127700`	Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'-splice site to generate spliced mRNA and the excised lariat intron.	No verified direct reference in this release
`UniProt: A2YQU8`	Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'-splice site to generate spliced mRNA and the excised lariat intron.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_008159 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009637 response to blue light Biological Process

GO:0010100 negative regulation of photomorphogenesis Biological Process

GO:0010114 response to red light Biological Process

GO:0010218 response to far red light Biological Process

GO:0010230 alternative respiration Biological Process

GO:0045292 mRNA cis splicing, via spliceosome Biological Process

GO:1900140 regulation of seedling development Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G65660

ath:AT4G37120

dosa:Os08g0127700

gga:416157

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.

Nucleus0.744

Rank 1 · LXL04_008159 · OH-1004

Cytoplasm0.287

Rank 2 · LXL04_008159 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_008159 · OH-1004

Mitochondrion0.027

Rank 4 · LXL04_008159 · OH-1004

Endoplasmic reticulum0.020

Rank 5 · LXL04_008159 · 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.

PF30379.1SLU7_N120-145 aa

PF11708.14Slu7166-435 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008159	`PF30379.1`	SLU7_N	120	145	1.7e-09	37.7
LXL04_008159	`PF11708.14`	Slu7	166	435	1.3e-96	324.1

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
`Q9SHY8`	Arabidopsis thaliana	Pre-mRNA-splicing factor SLU7-A	80.189%	Swiss-Prot	strong database homology
`O23174`	Arabidopsis thaliana	Pre-mRNA-splicing factor SLU7-B	76.560%	Swiss-Prot	strong database homology
`Q6ZK48`	Oryza sativa subsp. japonica	Pre-mRNA-splicing factor SLU7	81.544%	Swiss-Prot	strong database homology
`A2YQU8`	Oryza sativa subsp. indica	Pre-mRNA-splicing factor SLU7	81.544%	Swiss-Prot	strong database homology

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