LXL04_012902 | RubberDandelionOmics

Gene overview

LXL04_012902

Reference: OH-1004 Chr: Chr03 Coordinates: 20667511-20671341 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

714 bp · LXL04_012902|LXL04_012902|OH1004|cDNA

ATGGGTATCGTTTTCTCGAGTGTGTGTCTGTATTTGCATATACGATCGAAAGATAAGGCCCAATTGCGTTTTCATTTTTGTAAAGCGTCGACGATAAATTATCAGACTGTACCAGTTAATCCCAAACCTTTCTTGAACAACTTGACTGGAAAGCCTGTGTTTGTGAAACTCAAGTGGGGAATGGAGTACAAAGGTTATCTTGTCTCTGTCGATTCATACATGAACTTGCAGTTGGCCAACTCTGAAGAATACATTGATGG...

CDS

Download CDS FASTA

714 bp · LXL04_012902|LXL04_012902|OH1004|CDS

ATGGGTATCGTTTTCTCGAGTGTGTGTCTGTATTTGCATATACGATCGAAAGATAAGGCCCAATTGCGTTTTCATTTTTGTAAAGCGTCGACGATAAATTATCAGACTGTACCAGTTAATCCCAAACCTTTCTTGAACAACTTGACTGGAAAGCCTGTGTTTGTGAAACTCAAGTGGGGAATGGAGTACAAAGGTTATCTTGTCTCTGTCGATTCATACATGAACTTGCAGTTGGCCAACTCTGAAGAATACATTGATGG...

Protein

Download Protein FASTA

237 aa · LXL04_012902|LXL04_012902|OH1004|PROTEIN

MGIVFSSVCLYLHIRSKDKAQLRFHFCKASTINYQTVPVNPKPFLNNLTGKPVFVKLKWGMEYKGYLVSVDSYMNLQLANSEEYIDGQFTGNLGEILIRCNNVLYLRGVPEDEEIEEADRLNLWLNGGGVIVFSSVCLYLHIRSKHKAQLRTVPVNPKPFLNNLTGKPVFVKLKWGMEYKGYLVSVDSYMNLQLANSEEYIDGQFTGNLGEILIRCNNVLYLRGVPEDEEIEEADRD

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_012902`
TK1151 ID	TkA02G531280
OH-1004 ID	LXL04_012902
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 99.174 / OH-1004 50.633 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_012902

Location Chr03:20667511-20671341 (+)

Description Similar to At4g30220: Probable small nuclear ribonucleoprotein F

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g30220`	Probable common Sm protein, is found in U1 and U2 snRNPs and may be part of the spliceosome.	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_012902 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000387 spliceosomal snRNP assembly Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0008380 RNA splicing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005683 U7 snRNP Cellular Component

GO:0005684 U2-type spliceosomal complex Cellular Component

GO:0005685 U1 snRNP Cellular Component

GO:0005687 U4 snRNP Cellular Component

GO:0005689 U12-type spliceosomal complex Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT4G30220

mmu:69878

xla:108711072

xla:380595

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.

Cytoplasm0.579

Rank 1 · LXL04_012902 · OH-1004

Nucleus0.287

Rank 2 · LXL04_012902 · OH-1004

Mitochondrion0.185

Rank 3 · LXL04_012902 · OH-1004

Peroxisome0.075

Rank 4 · LXL04_012902 · OH-1004

Endoplasmic reticulum0.072

Rank 5 · LXL04_012902 · 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.

PF01423.29LSM44-106 aa

PF01423.29LSM160-222 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012902	`PF01423.29`	LSM	44	106	1.4e-46	156.8
LXL04_012902	`PF01423.29`	LSM	160	222	1.4e-46	156.8

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
`Q9SUM2`	Arabidopsis thaliana	Probable small nuclear ribonucleoprotein F	84.091%	Swiss-Prot	weak database homology

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