LXL04_010520 | RubberDandelionOmics

Gene overview

LXL04_010520

Reference: OH-1004 Chr: Chr02 Coordinates: 148214025-148216130 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1724 bp · LXL04_010520|LXL04_010520|OH1004|cDNA

TAAAACCCCAAGCACGGCTAATACCTTTGCTTTGACATCACCACCATCATCGGCAAATGGAGATCGACGAGAACGAAAACCCTAACGCTAACCCTAATGCCACCACTTCACCTCCAGACTCCATTGCTCAAATTGCACCAGTCGAGCCTCCAATTCCAGTAGCCCCAACTGCAATCTTACCCCCAATCGCTCCAATCCCACGTCCACTCGCCCATCTTCCCCCCGTTCGTCCACCAAATGGCGACGCAGCGAAGGCAACA...

CDS

Download CDS FASTA

1668 bp · LXL04_010520|LXL04_010520|OH1004|CDS

ATGGAGATCGACGAGAACGAAAACCCTAACGCTAACCCTAATGCCACCACTTCACCTCCAGACTCCATTGCTCAAATTGCACCAGTCGAGCCTCCAATTCCAGTAGCCCCAACTGCAATCTTACCCCCAATCGCTCCAATCCCACGTCCACTCGCCCATCTTCCCCCCGTTCGTCCACCAAATGGCGACGCAGCGAAGGCAACAAACAAAGACGCCGATTCTGACGAAGAAGGCGATGATTCGGGTCCCGAATACGAAAT...

Protein

Download Protein FASTA

555 aa · LXL04_010520|LXL04_010520|OH1004|PROTEIN

MEIDENENPNANPNATTSPPDSIAQIAPVEPPIPVAPTAILPPIAPIPRPLAHLPPVRPPNGDAAKATNKDADSDEEGDDSGPEYEISEESRLFREKQEKAKQEFLMKQRAAALAVPTNDNSVRSRLRRLEEPVTLFGEKEMERRDRLRMLMARLDSDGQSDKLLKVLEEEEAAAANAAGIDDGSYEVEGEAVQYPFYTEGSMALLKARYEIAKDSVVKSAKRLARARRKRNDPDEDEDSEINWVLENAKTFSLDCSEIG...

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_010520`
TK1151 ID	TkA03G532520
OH-1004 ID	LXL04_010520
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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_010520

Location Chr02:148214025-148216130 (-)

Description Similar to LIS: U4/U6 small nuclear ribonucleoprotein PRP4-like protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g41500`	Participates in pre-mRNA splicing.	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_010520 · 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:0000375 RNA splicing, via transesterification reactions 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:0001709 cell fate determination Biological Process

GO:0006396 RNA processing Biological Process

GO:0007267 cell-cell signaling Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009553 embryo sac development Biological Process

GO:0009560 embryo sac egg cell differentiation Biological Process

KEGG gene cross-reference

ath:AT2G41500

bta:508735

hsa:9128

mmu:70052

pon:100174168

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.

Nucleus0.711

Rank 1 · LXL04_010520 · OH-1004

Cytoplasm0.314

Rank 2 · LXL04_010520 · OH-1004

Cell membrane0.035

Rank 3 · LXL04_010520 · OH-1004

Mitochondrion0.034

Rank 4 · LXL04_010520 · OH-1004

Lysosome / Vacuole0.023

Rank 5 · LXL04_010520 · 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.

PF08799.18PRP4123-149 aa

PF24805.2EIF3I260-334 aa

PF25173.2Beta-prop_WDR3_1st261-415 aa

PF25175.2Beta-prop_WDR5262-443 aa

PF23414.2Beta-prop_EML_2263-379 aa

PF25391.2WD40_Gbeta265-371 aa

PF25168.2Beta-prop_WDR36-Utp21_2nd265-327 aa

PF25174.2Beta-prop_THOC3266-353 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010520	`PF08799.18`	PRP4	123	149	4.4e-10	39.6
LXL04_010520	`PF24805.2`	EIF3I	260	334	2.2e-35	123.0
LXL04_010520	`PF25173.2`	Beta-prop_WDR3_1st	261	415	9.6e-57	192.4
LXL04_010520	`PF25175.2`	Beta-prop_WDR5	262	443	8e-72	242.7
LXL04_010520	`PF23414.2`	Beta-prop_EML_2	263	379	3.8e-34	119.0
LXL04_010520	`PF25391.2`	WD40_Gbeta	265	371	1.6e-39	136.6
LXL04_010520	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	265	327	5.7e-27	95.6
LXL04_010520	`PF25174.2`	Beta-prop_THOC3	266	353	5.8e-58	196.8
LXL04_010520	`PF23381.2`	Beta-prop_IFT122_1st	267	378	6.4e-65	219.9
LXL04_010520	`PF25172.2`	Beta-prop_WDR3_2nd	267	415	2.3e-41	142.7
LXL04_010520	`PF24105.2`	Beta-prop_CAF1B_HIR1	268	334	2.7e-31	109.6
LXL04_010520	`PF23869.2`	Beta-prop_WDR75_1st	270	341	1.4e-18	68.0
LXL04_010520	`PF24814.2`	WD40_Prp19	272	490	1.8e-66	224.8
LXL04_010520	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	274	456	5e-19	69.5
LXL04_010520	`PF24807.2`	WD40_CDC20-Fz	286	331	2.3e-39	136.2
LXL04_010520	`PF25047.1`	Beta-prop_TEP1_2nd	293	417	3.5e-26	92.6

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
`O22212`	Arabidopsis thaliana	U4/U6 small nuclear ribonucleoprotein PRP4-like protein	64.632%	Swiss-Prot	strong database homology

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