LXL04_018531 | RubberDandelionOmics

Gene overview

LXL04_018531

Reference: OH-1004 Chr: Chr04 Coordinates: 14305284-14309562 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2532 bp · LXL04_018531|LXL04_018531|OH1004|cDNA

CATTTTCGGACATTGCTAAAAGATCCGATTCACACTTTCGGTTCTACCCGGTTTGCCCCATCAAAGCTTTATCATCAACAAGACGAAAAACCGGAGCCAACACTCCAGGCTCTGATGCTCGTTGTCACCCTTCCATGCTCAACCATGGTGGTTCGAACGGTAAATTCAATATCACTCCTCAGGTCCTCTTCTCCGCCACATCCCCTGCCATTTCCAGCGTTCCGGTACCACCAAATTCGAGCTTATCAGTATTTGCAGCT...

CDS

Download CDS FASTA

2520 bp · LXL04_018531|LXL04_018531|OH1004|CDS

TTGCTAAAAGATCCGATTCACACTTTCGGTTCTACCCGGTTTGCCCCATCAAAGCTTTATCATCAACAAGACGAAAAACCGGAGCCAACACTCCAGGCTCTGATGCTCGTTGTCACCCTTCCATGCTCAACCATGGTGGTTCGAACGGTAAATTCAATATCACTCCTCAGGTCCTCTTCTCCGCCACATCCCCTGCCATTTCCAGCGTTCCGGTACCACCAAATTCGAGCTTATCAGTATTTGCAGCTCTCTCGTGTTTC...

Protein

Download Protein FASTA

839 aa · LXL04_018531|LXL04_018531|OH1004|PROTEIN

MLKDPIHTFGSTRFAPSKLYHQQDEKPEPTLQALMLVVTLPCSTMVVRTVNSISLLRSSSPPHPLPFPAFRYHQIRAYQYLQLSRVSIRNPMVFGYHNIKSGRSRSYSIQSFVDTVLEEFEALRRRRTVRASNKSVLTSSKELVEDKLRKQVLQKGLLLEFKKDTDRILLAVVQKPDGRKNWIVSDQNGVSTSIKPQQITYIVPGVDNFNTTEISDFNQRAQNNLDPALLEFAWMELLETNKSVTVEELAEMIFGSAAPV...

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_018531`
TK1151 ID	TkA08G066610
OH-1004 ID	LXL04_018531
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.900
Protein coverage (%)	TK1151 99.526 / 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_018531

Location Chr04:14305284-14309562 (+)

Description Similar to RNR1: Ribonuclease II, chloroplastic/mitochondrial

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g02250`	3'-5' exoribonuclease that catalyzes 3' maturation of chloroplast and mitochondrion ribosomal RNAs; degrades short nucleotidic extensions to generate the mature 3'-ends.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018531 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006364 rRNA processing Biological Process

GO:0006402 mRNA catabolic process Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0000932 P-body Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0000175 3'-5'-RNA exonuclease activity Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0004540 RNA nuclease activity Molecular Function

GO:0008859 exoribonuclease II activity Molecular Function

KEGG gene cross-reference

ath:AT5G02250

bsu:BSU33610

cmu:TC_0676

ctr:CT_397

syn:sll1290

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.

Plastid0.797

Rank 1 · LXL04_018531 · OH-1004

Mitochondrion0.250

Rank 2 · LXL04_018531 · OH-1004

Cytoplasm0.027

Rank 3 · LXL04_018531 · OH-1004

Nucleus0.026

Rank 4 · LXL04_018531 · OH-1004

Peroxisome0.010

Rank 5 · LXL04_018531 · 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.

PF23163.2CSD_RNase_II153-214 aa

PF25255.2WHD_RNase_II217-295 aa

PF23161.2HTH_RNase_II296-399 aa

PF00773.26RNB433-728 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018531	`PF23163.2`	CSD_RNase_II	153	214	3.6e-27	94.8
LXL04_018531	`PF25255.2`	WHD_RNase_II	217	295	5.1e-30	104.1
LXL04_018531	`PF23161.2`	HTH_RNase_II	296	399	4.3e-28	98.7
LXL04_018531	`PF00773.26`	RNB	433	728	2.8e-76	257.6

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
`Q6NQJ6`	Arabidopsis thaliana	Ribonuclease II, chloroplastic/mitochondrial	65.711%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card