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

Gene ID: 66583, updated on 5-Mar-2024

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
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Genomic context

See Exosc1 in Genome Data Viewer
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_000085.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 46644 Neighboring gene STARR-positive B cell enhancer ABC_E7659 Neighboring gene phosphoglycerate mutase 1 Neighboring gene STARR-positive B cell enhancer ABC_E3252 Neighboring gene zinc finger, DHHC domain containing 16 Neighboring gene MMS19 cytosolic iron-sulfur assembly component Neighboring gene predicted gene, 23113

Genomic regions, transcripts, and products

Expression

  • 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

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA 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
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
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

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)

  1. NM_001164561.1NP_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:10145
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    pfam14382
    Location:839
    ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
    cl09927
    Location:74113
    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. ...
  2. NM_001320231.1NP_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:839
    ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
    cl09927
    Location:62120
    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. ...
  3. NM_001320232.1NP_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:10169
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    pfam14382
    Location:839
    ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
    cl09927
    Location:62137
    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. ...
  4. NM_001320233.1NP_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:1059
    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 ...
  5. NM_025644.4NP_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:10186
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    cd05791
    Location:62154
    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:839
    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

  1. NC_000085.7 Reference GRCm39 C57BL/6J

    Range
    41911417..41921836 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (1) summary
    cl09927
    Location:3068
    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 ...
  2. XM_011247313.4XP_011245615.1  exosome complex component CSL4 isoform X2

    Conserved Domains (2) summary
    COG1096
    Location:14186
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    cl09927
    Location:79154
    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 ...
  3. XM_036161652.1XP_036017545.1  exosome complex component CSL4 isoform X3

    Conserved Domains (2) summary
    COG1096
    Location:14162
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    cl09927
    Location:91130
    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 ...
  4. XM_011247312.4XP_011245614.1  exosome complex component CSL4 isoform X1

    Conserved Domains (2) summary
    COG1096
    Location:14203
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    cd05791
    Location:79171
    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 ...
  5. XM_030251027.2XP_030106887.1  exosome complex component CSL4 isoform X4

    Conserved Domains (1) summary
    cl09927
    Location:1059
    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 ...