LXL04_005609 | RubberDandelionOmics

Gene overview

LXL04_005609

Reference: OH-1004 Chr: Chr01 Coordinates: 169183750-169188194 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2307 bp · LXL04_005609|LXL04_005609|OH1004|cDNA

ATGTCTTTCGAAATAGGAGAAAGCGTGGAGGTCATCGGCAATGAAGATGGAATGGAGGGGTCCTACTTTAGGGGCCAGGTGATTGACCGCTCACCTGGGAGGAGAACAATCAGGTATCAGTCTCTGCTTGCTGATGATGGATCACCTCTGGAAGAGGTCATCAGCGTTAGGAGACTTCGACCCCCTCCTCCCACTGTCCTGGCGCGATTTCATCTTGGTGACATGGTGGATGCTTGGCACAATGAAGACTGGTGGGTAGG...

CDS

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2307 bp · LXL04_005609|LXL04_005609|OH1004|CDS

ATGTCTTTCGAAATAGGAGAAAGCGTGGAGGTCATCGGCAATGAAGATGGAATGGAGGGGTCCTACTTTAGGGGCCAGGTGATTGACCGCTCACCTGGGAGGAGAACAATCAGGTATCAGTCTCTGCTTGCTGATGATGGATCACCTCTGGAAGAGGTCATCAGCGTTAGGAGACTTCGACCCCCTCCTCCCACTGTCCTGGCGCGATTTCATCTTGGTGACATGGTGGATGCTTGGCACAATGAAGACTGGTGGGTAGG...

Protein

Download Protein FASTA

768 aa · LXL04_005609|LXL04_005609|OH1004|PROTEIN

MSFEIGESVEVIGNEDGMEGSYFRGQVIDRSPGRRTIRYQSLLADDGSPLEEVISVRRLRPPPPTVLARFHLGDMVDAWHNEDWWVGRHLQINMFPIQKHKIVFIKSGRNWRKEESGSMSRDRVEGIKRNEGCWMNVGGCYSGEEKRLPEKKIELSGNNNQRFLSPSPVRMSSRLPPILLRNLHSSLDVSSMAAAGFIFRTLSTHSLSASSKLSSLPSLVSHCRSNLSYSTTSSSPLLGGLFSAHRSIDGDWMHSRRLGG...

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_005609`
TK1151 ID	TkA01G028270
OH-1004 ID	LXL04_005609
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 48.958 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_005609

Location Chr01:169183750-169188194 (+)

Description Similar to YBEY: Endoribonuclease YBEY, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g25870`	Endoribonuclease required for chloroplast ribosomal RNA (rRNA) processing and essential for normal growth and development.	The conserved endoribonuclease YbeY is required for chloroplast ribosomal RNA processing in Arabidopsis.2015 · DOI: 10.1104/pp.114.255000

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005609 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006364 rRNA processing Biological Process

GO:0009658 chloroplast organization Biological Process

GO:1901259 chloroplast rRNA processing Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0004222 metalloendopeptidase activity Molecular Function

GO:0004521 RNA endonuclease activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0046872 metal ion binding Molecular Function

KEGG gene cross-reference

aae:aq_1354

ade:Adeh_2719

ath:AT2G25870

hmo:HM1_2448

sul:SYO3AOP1_0254

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.

Plastid0.859

Rank 1 · LXL04_005609 · OH-1004

Mitochondrion0.122

Rank 2 · LXL04_005609 · OH-1004

Cytoplasm0.073

Rank 3 · LXL04_005609 · OH-1004

Nucleus0.068

Rank 4 · LXL04_005609 · OH-1004

Peroxisome0.027

Rank 5 · LXL04_005609 · 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.

PF05641.19Agenet6-64 aa

PF02130.25YbeY346-455 aa

PF08282.19Hydrolase_3499-763 aa

PF05116.20S6PP677-742 aa

PF00702.33Hydrolase689-730 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005609	`PF05641.19`	Agenet	6	64	2.2e-12	47.9
LXL04_005609	`PF02130.25`	YbeY	346	455	3.1e-35	121.9
LXL04_005609	`PF08282.19`	Hydrolase_3	499	763	8.6e-54	183.7
LXL04_005609	`PF05116.20`	S6PP	677	742	4.6e-12	46.8
LXL04_005609	`PF00702.33`	Hydrolase	689	730	1.9e-11	45.5

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
`Q8L5Z4`	Arabidopsis thaliana	Endoribonuclease YBEY, chloroplastic	68.266%	Swiss-Prot	strong database homology

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