LXL04_018370 | RubberDandelionOmics

Gene overview

LXL04_018370

Reference: OH-1004 Chr: Chr04 Coordinates: 12242698-12243674 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

387 bp · LXL04_018370|LXL04_018370|OH1004|cDNA

ATGCAGATATTCGTGAAAACCCTAACCGGGAAAACCATAACCCTCGAGGTTGAGAGCAGCGACACCATCGACAATGTCAAGGCCAAGATTCAGGACAAGGAAGGAATCCCACCGGATCAGCAGAGGTTGATCTTTGCCGGAAAGCAACTCGAAGATGGCCGTACTCTTGCCGATTACAACATCCAGAAAGAATCTACCCTTCATTTGGTGTTGAGGCTAAGGGGAGGAATCATTGAACCTTCTTTGATGGCATTGGCTAG...

CDS

Download CDS FASTA

387 bp · LXL04_018370|LXL04_018370|OH1004|CDS

ATGCAGATATTCGTGAAAACCCTAACCGGGAAAACCATAACCCTCGAGGTTGAGAGCAGCGACACCATCGACAATGTCAAGGCCAAGATTCAGGACAAGGAAGGAATCCCACCGGATCAGCAGAGGTTGATCTTTGCCGGAAAGCAACTCGAAGATGGCCGTACTCTTGCCGATTACAACATCCAGAAAGAATCTACCCTTCATTTGGTGTTGAGGCTAAGGGGAGGAATCATTGAACCTTCTTTGATGGCATTGGCTAG...

Protein

Download Protein FASTA

128 aa · LXL04_018370|LXL04_018370|OH1004|PROTEIN

MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGIIEPSLMALARKYNQDKTICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIK

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_018370`
TK1151 ID	TkA04G038880
OH-1004 ID	LXL04_018370
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_018370

Location Chr04:12242698-12243674 (-)

Description Similar to UBICEP52-7: Ubiquitin-60S ribosomal protein L40

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g52590`	Exists either covalently attached to another protein, or free (unanchored).	No verified direct reference in this release
`At2g36170`	Exists either covalently attached to another protein, or free (unanchored).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0568400`	Exists either covalently attached to another protein, or free (unanchored).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018370 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006412 translation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0019941 modification-dependent protein catabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005840 ribosome Cellular Component

GO:0022625 cytosolic large ribosomal subunit Cellular Component

GO:0022626 cytosolic ribosome Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

KEGG gene cross-reference

ath:AT2G36170

ath:AT3G52590

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.575

Rank 1 · LXL04_018370 · OH-1004

Nucleus0.397

Rank 2 · LXL04_018370 · OH-1004

Cell membrane0.121

Rank 3 · LXL04_018370 · OH-1004

Mitochondrion0.092

Rank 4 · LXL04_018370 · OH-1004

Endoplasmic reticulum0.081

Rank 5 · LXL04_018370 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF11976.15Rad60-SLD1-71 aa

PF00240.30ubiquitin3-74 aa

PF01020.24Ribosomal_L40e78-127 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018370	`PF11976.15`	Rad60-SLD	1	71	1.1e-17	64.3
LXL04_018370	`PF00240.30`	ubiquitin	3	74	9.8e-33	112.5
LXL04_018370	`PF01020.24`	Ribosomal_L40e	78	127	1.5e-30	105.6

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q42202`	Arabidopsis thaliana	Ubiquitin-ribosomal protein eL40y fusion protein	98.438%	Swiss-Prot	strong database homology
`B9DHA6`	Arabidopsis thaliana	Ubiquitin-ribosomal protein eL40z fusion protein	98.438%	Swiss-Prot	strong database homology
`P0CH35`	Oryza sativa subsp. japonica	Ubiquitin-ribosomal protein eL40y fusion protein	98.438%	Swiss-Prot	strong database homology

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