LXL04_014364 | RubberDandelionOmics

Gene overview

LXL04_014364

Reference: OH-1004 Chr: Chr03 Coordinates: 47508358-47517459 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5670 bp · LXL04_014364|LXL04_014364|OH1004|cDNA

ATGCTAATTACAGAAGATATGGGTAAACCTTCAAAGAAACCCTTCAACAAGAAATCAGAAGACAGGCTTAAGACATTTCAAAAACCATCTAAAAAGCCATTTAAACCGCCTCAAAAATCAAATAGCACTGTGTCTAAAGATGCTGTACCAATTCATATTGAAGACGATGTTCCTGACTTCCCCAGAGGCGGGCAGAGTTCACTCAGCAGGGCAGAGGTAAATGAAGTTCGGGCAGAGGTTGATAAAGAGTTTGGAACAGA...

CDS

Download CDS FASTA

5670 bp · LXL04_014364|LXL04_014364|OH1004|CDS

ATGCTAATTACAGAAGATATGGGTAAACCTTCAAAGAAACCCTTCAACAAGAAATCAGAAGACAGGCTTAAGACATTTCAAAAACCATCTAAAAAGCCATTTAAACCGCCTCAAAAATCAAATAGCACTGTGTCTAAAGATGCTGTACCAATTCATATTGAAGACGATGTTCCTGACTTCCCCAGAGGCGGGCAGAGTTCACTCAGCAGGGCAGAGGTAAATGAAGTTCGGGCAGAGGTTGATAAAGAGTTTGGAACAGA...

Protein

Download Protein FASTA

1889 aa · LXL04_014364|LXL04_014364|OH1004|PROTEIN

MLITEDMGKPSKKPFNKKSEDRLKTFQKPSKKPFKPPQKSNSTVSKDAVPIHIEDDVPDFPRGGQSSLSRAEVNEVRAEVDKEFGTETMVLKKKKKEKPRNLNRSNEDELGSLFGDSQGGKLPRFANKITLKNVTPGMKLWGVISEVNEKDLEVSLPGGLRGLVRASEAIDPLLHDGMEGDTEDEVLSAIFTVGQLVSCIVLKLDDDKKEKEKGKHKIWLSMRLSLLHSSFTLDTIQEGMVVSAYVKSIEDHGYMLHFGV...

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_014364`
TK1151 ID	TkA02G433610
OH-1004 ID	LXL04_014364
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.900
Protein coverage (%)	TK1151 98.528 / OH-1004 81.472 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_014364

Location Chr03:47508358-47517459 (+)

Description Similar to RRP5: rRNA biogenesis protein RRP5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g11964`	Involved in the biogenesis of ribosomal RNA (rRNA).	40S ribosome biogenesis co-factors are essential for gametophyte and embryo development.2013 · DOI: 10.1371/journal.pone.0054084

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_014364 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006364 rRNA processing Biological Process

GO:0009553 embryo sac development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0032040 small-subunit processome Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0051059 NF-kappaB binding Molecular Function

KEGG gene cross-reference

ath:AT3G11964

hsa:22984

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.

Nucleus0.907

Rank 1 · LXL04_014364 · OH-1004

Cytoplasm0.124

Rank 2 · LXL04_014364 · OH-1004

Cell membrane0.025

Rank 3 · LXL04_014364 · OH-1004

Mitochondrion0.018

Rank 4 · LXL04_014364 · OH-1004

Endoplasmic reticulum0.015

Rank 5 · LXL04_014364 · 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.

PF23459.2S1_RRP5134-209 aa

PF23459.2S1_RRP5322-392 aa

PF24685.2OB_RRP5_4th402-493 aa

PF23459.2S1_RRP5498-558 aa

PF00575.30S1499-562 aa

PF00575.30S1593-644 aa

PF00575.30S1765-834 aa

PF24682.2OB_RRP5959-1045 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014364	`PF23459.2`	S1_RRP5	134	209	3.6e-77	255.6
LXL04_014364	`PF23459.2`	S1_RRP5	322	392	3.6e-77	255.6
LXL04_014364	`PF24685.2`	OB_RRP5_4th	402	493	9.7e-58	192.9
LXL04_014364	`PF23459.2`	S1_RRP5	498	558	3.6e-77	255.6
LXL04_014364	`PF00575.30`	S1	499	562	1.1e-68	228.3
LXL04_014364	`PF00575.30`	S1	593	644	1.1e-68	228.3
LXL04_014364	`PF00575.30`	S1	765	834	1.1e-68	228.3
LXL04_014364	`PF24682.2`	OB_RRP5	959	1045	1.5e-42	143.9
LXL04_014364	`PF29086.1`	OB_PDCD11	1056	1124	8e-32	110.1
LXL04_014364	`PF23459.2`	S1_RRP5	1336	1407	3.6e-77	255.6
LXL04_014364	`PF00575.30`	S1	1339	1408	1.1e-68	228.3
LXL04_014364	`PF00575.30`	S1	1427	1499	1.1e-68	228.3
LXL04_014364	`PF23233.2`	HAT_Syf1_CNRKL1_N	1603	1710	3e-15	57.1
LXL04_014364	`PF23240.2`	HAT_PRP39_N	1624	1710	1.4e-10	42.2
LXL04_014364	`PF23231.2`	HAT_Syf1_CNRKL1_C	1638	1885	1.9e-08	34.2
LXL04_014364	`PF05843.21`	Suf	1643	1713	5.6e-13	49.0

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
`F4J8K6`	Arabidopsis thaliana	rRNA biogenesis protein RRP5	58.765%	Swiss-Prot	strong database homology

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