LXL04_005610 | RubberDandelionOmics

Gene overview

LXL04_005610

Reference: OH-1004 Chr: Chr01 Coordinates: 169191652-169203422 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1005 bp · LXL04_005610|LXL04_005610|OH1004|cDNA

ATGAATGCACGGCTATCTTCTAGTTATAATTGGTATTCTCCTGAAGAGGGCGACGCAAAAATGGAGGAAGAGGAACAACATTTTGGATCAAAAGAGAAAGGATCGATACAAAGTGCATCTAGTGCCTCAGCTGAAGATCATGGAAGAAAGGAACCGGGCACTCTTTGCAACTACAAACCAAAATTCAGCTATATCTTCTCTGATATGGACGGTACACTTCTGAATAGCAAAAGTCTAGTTTCTGCTACAAATGCAGAAGC...

CDS

Download CDS FASTA

1005 bp · LXL04_005610|LXL04_005610|OH1004|CDS

ATGAATGCACGGCTATCTTCTAGTTATAATTGGTATTCTCCTGAAGAGGGCGACGCAAAAATGGAGGAAGAGGAACAACATTTTGGATCAAAAGAGAAAGGATCGATACAAAGTGCATCTAGTGCCTCAGCTGAAGATCATGGAAGAAAGGAACCGGGCACTCTTTGCAACTACAAACCAAAATTCAGCTATATCTTCTCTGATATGGACGGTACACTTCTGAATAGCAAAAGTCTAGTTTCTGCTACAAATGCAGAAGC...

Protein

Download Protein FASTA

334 aa · LXL04_005610|LXL04_005610|OH1004|PROTEIN

MNARLSSSYNWYSPEEGDAKMEEEEQHFGSKEKGSIQSASSASAEDHGRKEPGTLCNYKPKFSYIFSDMDGTLLNSKSLVSATNAEAIKEASSNGVKVVLATGKTRPAAITLLNMVDLSGKDGIVSENSPGVFIQGLLVYGKDGKEIHRTNLDPNVCKEAFQYSIEHNIPLVAFSENRLLTLFSHPLVDSLHTTYHEPKAEIMPSVEDLLGSGDVQKVLFLDTAEGVAGTLRPYWSEATKGRACVVQAQADILEIVPPGT...

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_005610`
TK1151 ID	TkA01G028340
OH-1004 ID	LXL04_005610
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 88.308 / OH-1004 85.928 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_005610

Location Chr01:169191652-169203422 (+)

Description Similar to YBEY: Endoribonuclease YBEY, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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_005610 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009658 chloroplast organization Biological Process

GO:0016311 dephosphorylation Biological Process

GO:1901259 chloroplast rRNA processing Biological Process

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0000287 magnesium ion binding Molecular Function

GO:0004222 metalloendopeptidase activity Molecular Function

GO:0004521 RNA endonuclease activity Molecular Function

GO:0016791 phosphatase activity Molecular Function

GO:0046872 metal ion binding Molecular Function

GO:0050308 sugar-phosphatase activity Molecular Function

KEGG gene cross-reference

ath:AT2G25870

bsu:BSU39550

ecc:c4619

ecj:JW3674

eco:b3697

ecoc:C3026_20040

sfl:SF3767

sfx:S4004

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.

Cytoplasm0.492

Rank 1 · LXL04_005610 · OH-1004

Nucleus0.233

Rank 2 · LXL04_005610 · OH-1004

Mitochondrion0.109

Rank 3 · LXL04_005610 · OH-1004

Endoplasmic reticulum0.102

Rank 4 · LXL04_005610 · OH-1004

Cell membrane0.095

Rank 5 · LXL04_005610 · 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.

PF08282.19Hydrolase_365-329 aa

PF05116.20S6PP243-308 aa

PF00702.33Hydrolase245-296 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005610	`PF08282.19`	Hydrolase_3	65	329	6.2e-54	184.1
LXL04_005610	`PF05116.20`	S6PP	243	308	3.2e-12	47.3
LXL04_005610	`PF00702.33`	Hydrolase	245	296	2.7e-12	48.2

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	66.772%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card