LXL04_013909 | RubberDandelionOmics

Gene overview

LXL04_013909

Reference: OH-1004 Chr: Chr03 Coordinates: 37807839-37812645 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2802 bp · LXL04_013909|LXL04_013909|OH1004|cDNA

ATGTTACAAAACAAGTCATTCGTGCGGAAAACTAAACAAGGCAAAGTTATCAAGGTGGTCAGAGAACATTATCTCAGAGATGATATATACTGTGGAGCTTCGTTTTGCCAACATTGTGATACAAAAAGTGCTCGTTTCAGCTCCCCTGACTCCACAATCCTTGTTCTCGACACTAATGTTGTTCTGAATCAGATTGATTTGCTCGAgaatccagcaattgatgatgtTGTGGTGCTGTCTGTGGTGTTGGATGAGGTCAA...

CDS

Download CDS FASTA

2802 bp · LXL04_013909|LXL04_013909|OH1004|CDS

ATGTTACAAAACAAGTCATTCGTGCGGAAAACTAAACAAGGCAAAGTTATCAAGGTGGTCAGAGAACATTATCTCAGAGATGATATATACTGTGGAGCTTCGTTTTGCCAACATTGTGATACAAAAAGTGCTCGTTTCAGCTCCCCTGACTCCACAATCCTTGTTCTCGACACTAATGTTGTTCTGAATCAGATTGATTTGCTCGAGAATCCAGCAATTGATGATGTTGTGGTGCTGTCTGTGGTGTTGGATGAGGTCAA...

Protein

Download Protein FASTA

933 aa · LXL04_013909|LXL04_013909|OH1004|PROTEIN

MLQNKSFVRKTKQGKVIKVVREHYLRDDIYCGASFCQHCDTKSARFSSPDSTILVLDTNVVLNQIDLLENPAIDDVVVLSVVLDEVKNKNLAVYNRLRALCSNTLRRFFVFSNEHHKDTYVKAMAGESPNDRNDRAIRVAAQWYKNHLGGPTKVLMITNDRENKRKATEEGIIADTVESYVKSLGQPALLDLLVQPHSSEDMEIEDMRPSKKKVIYTEHKPMSEITSGIRCGIYHQGKLRVNRYNPFEAYVGSESIGDEI...

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_013909`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_013909

Location Chr03:37807839-37812645 (+)

Description Similar to RRP44A: Exosome complex exonuclease RRP44 homolog A

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g17510`	Catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events.	Arabidopsis AtRRP44A is the functional homolog of Rrp44/Dis3, an exosome component, is essential for viability and is required for RNA processing and degradation.2013 · DOI: 10.1371/journal.pone.0079219

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013909 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Biological Process

GO:0000465 exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006396 RNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006401 RNA catabolic process Biological Process

GO:0016075 rRNA catabolic process Biological Process

GO:0030847 termination of RNA polymerase II transcription, exosome-dependent Biological Process

GO:0033621 nuclear mRNA surveillance of meiosis-specific transcripts Biological Process

GO:0043628 regulatory ncRNA 3'-end processing Biological Process

GO:0070478 nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Biological Process

KEGG gene cross-reference

ath:AT2G17510

hsa:22894

mmu:72662

sce:YOL021C

spo:2540398

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.

Nucleus0.652

Rank 1 · LXL04_013909 · OH-1004

Cytoplasm0.459

Rank 2 · LXL04_013909 · OH-1004

Mitochondrion0.060

Rank 3 · LXL04_013909 · OH-1004

Cell membrane0.031

Rank 4 · LXL04_013909 · OH-1004

Endoplasmic reticulum0.022

Rank 5 · LXL04_013909 · 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.

PF13638.13PIN_454-176 aa

PF17216.10Rrp44_CSD1217-305 aa

PF25049.2OB_HELZ2233-290 aa

PF17849.8OB_Dis3371-438 aa

PF00773.26RNB469-798 aa

PF17215.10Rrp44_S1850-920 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013909	`PF13638.13`	PIN_4	54	176	1.6e-19	71.2
LXL04_013909	`PF17216.10`	Rrp44_CSD1	217	305	1.3e-12	48.4
LXL04_013909	`PF25049.2`	OB_HELZ2	233	290	1.7e-07	31.7
LXL04_013909	`PF17849.8`	OB_Dis3	371	438	8.8e-21	74.4
LXL04_013909	`PF00773.26`	RNB	469	798	4.7e-99	332.4
LXL04_013909	`PF17215.10`	Rrp44_S1	850	920	5.9e-08	33.3

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
`Q9SHL7`	Arabidopsis thaliana	Exosome complex exonuclease RRP44 homolog A	79.060%	Swiss-Prot	strong database homology

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