LXL04_014799 | RubberDandelionOmics

Gene overview

LXL04_014799

Reference: OH-1004 Chr: Chr03 Coordinates: 57176221-57176717 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

420 bp · LXL04_014799|LXL04_014799|OH1004|cDNA

ATGGCGACGATGAGCTTGCGAAAAGGCAACACGAGGCTACCACCAGAGGTCAACAGGGTTCTCTACGTACGCAACTTACCTTTTAACATAACGAGCGAGGAGATGTACGATATCTTTGGCAAGTACGGCGCCATACGGCAGATTCGTATCGGCAACAACAAGGACACTCGGGGCACCGCCTTCGTCGTTTACGAAGACATCTACGACGCCAAGACCGCCGTCGATCACTTATCTGGCTTCAACGTTGCCAATCGATACCT...

CDS

Download CDS FASTA

420 bp · LXL04_014799|LXL04_014799|OH1004|CDS

ATGGCGACGATGAGCTTGCGAAAAGGCAACACGAGGCTACCACCAGAGGTCAACAGGGTTCTCTACGTACGCAACTTACCTTTTAACATAACGAGCGAGGAGATGTACGATATCTTTGGCAAGTACGGCGCCATACGGCAGATTCGTATCGGCAACAACAAGGACACTCGGGGCACCGCCTTCGTCGTTTACGAAGACATCTACGACGCCAAGACCGCCGTCGATCACTTATCTGGCTTCAACGTTGCCAATCGATACCT...

Protein

Download Protein FASTA

139 aa · LXL04_014799|LXL04_014799|OH1004|PROTEIN

MATMSLRKGNTRLPPEVNRVLYVRNLPFNITSEEMYDIFGKYGAIRQIRIGNNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQAKMSKKFDQKKKEEELTKLQEKYGVTAKDLKVFCMELWNSFTGWL

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_014799`
TK1151 ID	TkA02G396460
OH-1004 ID	LXL04_014799
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 89.928 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_014799

Location Chr03:57176221-57176717 (-)

Description Similar to At5g12190: Splicing factor 3B subunit 6-like protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g12190`	May be necessary for the splicing of pre-mRNA.	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_014799 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:1903241 U2-type prespliceosome assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005684 U2-type spliceosomal complex Cellular Component

GO:0005689 U12-type spliceosomal complex Cellular Component

GO:0034693 U11/U12 snRNP Cellular Component

KEGG gene cross-reference

ath:AT5G12190

cel:CELE_C50D2.5

dme:Dmel_CG13298

hsa:51639

mmu:66055

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.

Nucleus0.820

Rank 1 · LXL04_014799 · OH-1004

Cytoplasm0.269

Rank 2 · LXL04_014799 · OH-1004

Mitochondrion0.031

Rank 3 · LXL04_014799 · OH-1004

Cell membrane0.024

Rank 4 · LXL04_014799 · OH-1004

Endoplasmic reticulum0.015

Rank 5 · LXL04_014799 · 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.

PF13893.13RRM_517-108 aa

PF00076.29RRM_121-87 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014799	`PF13893.13`	RRM_5	17	108	4.2e-08	33.7
LXL04_014799	`PF00076.29`	RRM_1	21	87	8.9e-19	67.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FMP4`	Arabidopsis thaliana	Splicing factor 3B subunit 6-like protein	88.618%	Swiss-Prot	strong database homology

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