LXL04_013289 | RubberDandelionOmics

Gene overview

LXL04_013289

Reference: OH-1004 Chr: Chr03 Coordinates: 27168446-27169381 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

936 bp · LXL04_013289|LXL04_013289|OH1004|cDNA

ATGGCTATAAAAAAACCAACACCGGAATCATTACCCGAAGAAATTGATATGGCAGCTTCTGATTCCGACCCCGAGACAGATTCCGGATCAGAATCAGAATCAGAAGGCGATGAAGACATAAAACTATCAGAACCTTCAAAAACCGCAATCTACAACAAAGAAGGCATCCTCGATAAACTCAACGACATTGTCTTTCCCGAAGACATCGAGTGGACCCACAAGCTCTCACTGGACATCCCACAAGAAGATGAAGTAGACGT...

CDS

Download CDS FASTA

936 bp · LXL04_013289|LXL04_013289|OH1004|CDS

ATGGCTATAAAAAAACCAACACCGGAATCATTACCCGAAGAAATTGATATGGCAGCTTCTGATTCCGACCCCGAGACAGATTCCGGATCAGAATCAGAATCAGAAGGCGATGAAGACATAAAACTATCAGAACCTTCAAAAACCGCAATCTACAACAAAGAAGGCATCCTCGATAAACTCAACGACATTGTCTTTCCCGAAGACATCGAGTGGACCCACAAGCTCTCACTGGACATCCCACAAGAAGATGAAGTAGACGT...

Protein

Download Protein FASTA

311 aa · LXL04_013289|LXL04_013289|OH1004|PROTEIN

MAIKKPTPESLPEEIDMAASDSDPETDSGSESESEGDEDIKLSEPSKTAIYNKEGILDKLNDIVFPEDIEWTHKLSLDIPQEDEVDVNDDLARELAFYNQALQGTREAFVKFETMKLPFLRPSDYYAEMVKTDSHMEKIKGRLIAEKRRMEEAEERRKMRGKMRDNKKKAKEVQAVKQRERVKQKKDEIESVKKWRKQRQQSGFAEKDSGDIGFEDGKGSESVKKGNKRQGVSPWDRTGGKGKREEKGGGGSGKRKSREF...

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_013289`
TK1151 ID	TkA02G507460
OH-1004 ID	LXL04_013289
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	92.200
Protein coverage (%)	TK1151 100.000 / OH-1004 94.855 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_013289

Location Chr03:27168446-27169381 (-)

Description Similar to EBP2: Probable rRNA-processing protein EBP2 homolog

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g22660`	Required for the processing of the 27S pre-rRNA (By similarity).	The nucleolar GTPase nucleostemin-like 1 plays a role in plant growth and senescence by modulating ribosome biogenesis.2015 · DOI: 10.1093/jxb/erv337

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013289 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000280 nuclear division Biological Process

GO:0006364 rRNA processing Biological Process

GO:0042273 ribosomal large subunit biogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005694 chromosome Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0030684 preribosome Cellular Component

GO:0030687 preribosome, large subunit precursor Cellular Component

GO:0034399 nuclear periphery Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0003924 GTPase activity Molecular Function

KEGG gene cross-reference

ath:AT3G22660

cel:CELE_C18A3.3

mmu:69072

sce:YKL172W

spo:2542121

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.

Nucleus0.964

Rank 1 · LXL04_013289 · OH-1004

Cytoplasm0.119

Rank 2 · LXL04_013289 · OH-1004

Extracellular0.012

Rank 3 · LXL04_013289 · OH-1004

Mitochondrion0.012

Rank 4 · LXL04_013289 · OH-1004

Cell membrane0.010

Rank 5 · LXL04_013289 · 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.

PF05890.18Ebp250-309 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013289	`PF05890.18`	Ebp2	50	309	6.7e-63	213.3

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
`Q9LUJ5`	Arabidopsis thaliana	Probable rRNA-processing protein EBP2 homolog	59.582%	Swiss-Prot	strong database homology

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