Exosc1 exosome component 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Exosc1provided by MGI
Official Full Name: exosome component 1provided by MGI
Primary source: MGI:MGI:1913833
See related: Ensembl:ENSMUSG00000034321 AllianceGenome:MGI:1913833
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: 2610035C18Rik; 2610104C07Rik; 2610312F07Rik
Summary: Predicted to enable RNA binding activity. Predicted to act upstream of or within RNA processing. Predicted to be located in nucleolus. Predicted to be part of nuclear exosome (RNase complex). Predicted to be active in cytoplasm. Is expressed in embryo and submandibular gland primordium. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia. Orthologous to human EXOSC1 (exosome component 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 8.9), liver E14.5 (RPKM 7.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 19 C3; 19 35.46 cM

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	19	NC_000085.7 (41911417..41921836, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	19	NC_000085.6 (41922978..41933423, complement)

Chromosome 19 - NC_000085.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Exosome component 1 cleaves single-stranded DNA and sensitizes human kidney renal clear cell carcinoma cells to poly(ADP-ribose) polymerase inhibitor.
Title: Exosome component 1 cleaves single-stranded DNA and sensitizes human kidney renal clear cell carcinoma cells to poly(ADP-ribose) polymerase inhibitor.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI447561 (e-PCR)
- UniSTS:166150

MARC_23511-23512:1027359213:1 (e-PCR)
- UniSTS:268715

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within RNA processing	ISO Inferred from Sequence Orthology more info
involved_in RNA processing	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within rRNA processing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
part_of cytoplasmic exosome (RNase complex)	NAS Non-traceable Author Statement more info	PubMed
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of exosome (RNase complex)	ISO Inferred from Sequence Orthology more info
part_of exosome (RNase complex)	NAS Non-traceable Author Statement more info	PubMed
part_of nuclear exosome (RNase complex)	IBA Inferred from Biological aspect of Ancestor more info
part_of nuclear exosome (RNase complex)	NAS Non-traceable Author Statement more info	PubMed
part_of nucleolar exosome (RNase complex)	NAS Non-traceable Author Statement more info	PubMed
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: exosome complex component CSL4

Names: 3'-5' exoribonuclease CSL4 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001164561.1 → NP_001158033.1 exosome complex component CSL4 isoform 2

See identical proteins and their annotated locations for NP_001158033.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two in-frame exons in the mid-coding region compared to variant 1. The resulting isoform (2) is shorter, missing an internal protein segment compared to isoform 1. Like variant 1, this variant also uses the downstream AUG.

Source sequence(s)

AK002930, BY361617

Consensus CDS

CCDS50436.1

UniProtKB/Swiss-Prot

Q9DAA6

Related

ENSMUSP00000107751.3, ENSMUST00000112123.4

Conserved Domains (3) summary

COG1096
Location:10 → 145

Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]

pfam14382
Location:8 → 39

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

cl09927
Location:74 → 113

S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
NM_001320231.1 → NP_001307160.1 exosome complex component CSL4 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks two consecutive exons in the 3' coding region, which causes a frame-shift compared to variant 1. The resulting isoform (3) is shorter, with a distinct C-terminus compared to isoform 1. Like variant 1, this variant also uses the downstream AUG.

Source sequence(s)

AK002930, AK006018, BY361617

UniProtKB/Swiss-Prot

Q9DAA6

Conserved Domains (2) summary

pfam14382
Location:8 → 39

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

cl09927
Location:62 → 120

S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
NM_001320232.1 → NP_001307161.1 exosome complex component CSL4 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an in-frame exon in the 3' coding region compared to variant 1. The resulting isoform (4) is shorter, missing an internal protein segment compared to isoform 1. Like variant 1, this variant also uses the downstream AUG.

Source sequence(s)

AK002930, AK006018, BY361617

UniProtKB/Swiss-Prot

Q9DAA6

Conserved Domains (3) summary

COG1096
Location:10 → 169

Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]

pfam14382
Location:8 → 39

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

cl09927
Location:62 → 137

S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
NM_001320233.1 → NP_001307162.1 exosome complex component CSL4 isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks an exon in the mid-coding region, which results in translation initiation from an alternate downstream start codon compared to variant 1. The resulting isoform (5) is shorter, with a distinct N-terminus compared to isoform 1.

Source sequence(s)

AK002930, AK006018, BY361617

UniProtKB/Swiss-Prot

Q9DAA6

Conserved Domains (1) summary

cl09927
Location:10 → 59

S1_like; Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains ...
NM_025644.4 → NP_079920.1 exosome complex component CSL4 isoform 1

See identical proteins and their annotated locations for NP_079920.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes the longest isoform (1). It contains an in-frame AUG four codons upstream from the currently annotated translation start site; however, Kozak signal strength and conservation data support the use of the annotated downstream AUG.

Source sequence(s)

AK002930, AK006018, BY361617

Consensus CDS

CCDS29816.1

UniProtKB/Swiss-Prot

Q9DAA6, Q9DCB9

Related

ENSMUSP00000074756.5, ENSMUST00000075280.12

Conserved Domains (3) summary

COG1096
Location:10 → 186

Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]

cd05791
Location:62 → 154

S1_CSL4; S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation ...

pfam14382
Location:8 → 39

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000085.7 Reference GRCm39 C57BL/6J

Range

41911417..41921836 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017318274.1 → XP_017173763.1 exosome complex component CSL4 isoform X5

Conserved Domains (1) summary

cl09927
Location:30 → 68

S1_like; Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains ...
XM_011247313.4 → XP_011245615.1 exosome complex component CSL4 isoform X2

Conserved Domains (2) summary

COG1096
Location:14 → 186

Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]

cl09927
Location:79 → 154

S1_like; Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains ...
XM_036161652.1 → XP_036017545.1 exosome complex component CSL4 isoform X3

Conserved Domains (2) summary

COG1096
Location:14 → 162

Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]

cl09927
Location:91 → 130

S1_like; Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains ...
XM_011247312.4 → XP_011245614.1 exosome complex component CSL4 isoform X1

Conserved Domains (2) summary

COG1096
Location:14 → 203

Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]

cd05791
Location:79 → 171

S1_CSL4; CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in ...
XM_030251027.2 → XP_030106887.1 exosome complex component CSL4 isoform X4

Conserved Domains (1) summary

cl09927
Location:10 → 59

S1_like; Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains ...