EXOSC1 exosome component 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EXOSC1provided by HGNC
Official Full Name: exosome component 1provided by HGNC
Primary source: HGNC:HGNC:17286
See related: Ensembl:ENSG00000171311 MIM:606493; AllianceGenome:HGNC:17286
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: p13; CSL4; SKI4; Csl4p; PCH1F; Ski4p; CGI-108
Summary: This gene encodes a core component of the exosome. The mammalian exosome is required for rapid degradation of AU rich element-containing RNAs but not for poly(A) shortening. The association of this protein with the exosome is mediated by protein-protein interactions with ribosomal RNA-processing protein 42 and ribosomal RNA-processing protein 46. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression: Ubiquitous expression in lymph node (RPKM 9.3), urinary bladder (RPKM 7.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q24.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (97435909..97446006, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (98316090..98326186, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (99195666..99205763, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Bi-allelic missense variant, p.Ser35Leu in EXOSC1 is associated with pontocerebellar hypoplasia.
Title: Bi-allelic missense variant, p.Ser35Leu in EXOSC1 is associated with pontocerebellar hypoplasia.
Post-transcriptional control of cellular differentiation by the RNA exosome complex.
Title: Post-transcriptional control of cellular differentiation by the RNA exosome complex.
The combined p16- and p53-expression status in cervical metastases of CUP may represent a simple method for risk stratification. Further validation of these biomarkers in large prospective trials is essential to design rational trials for CUP treatment optimization.
Title: Combined p16 and p53 expression in cervical cancer of unknown primary and other prognostic parameters : A single-center analysis.
Human exosome hCsl4p participates in RNA degradation.
Title: Yeast RNA viruses as indicators of exosome activity: human exosome hCsl4p participates in RNA degradation in Saccharomyces cerevisiae'.
association of hCsl4p with the exosome is mediated by protein-protein interactions with hRrp42p and hRrp46p
Title: Protein-protein interactions of hCsl4p with other human exosome subunits.
Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring.
Title: Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Pontocerebellar hypoplasia, type 1F MedGen: C5543331 OMIM: 619304 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	HIV-1 Rev interacting protein, exosome component 1 (EXOSC1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with EXOSC1 is increased by RRE	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-11032 (e-PCR)
- UniSTS:14608

D8S2279 (e-PCR)
- UniSTS:473907

D15S1477 (e-PCR)
- UniSTS:474482

D1S3697 (e-PCR)
- UniSTS:474275

EXOSC1 (e-PCR)
- UniSTS:502975

SHGC-132201 (e-PCR)
- UniSTS:170708

D10S2396 (e-PCR)
- UniSTS:78298

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	NAS Non-traceable Author Statement more info	PubMed
NOT enables RNA exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in 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	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
part_of exosome (RNase complex)	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: exosome complex component CSL4

Names: 3'-5' exoribonuclease CSL4 homolog; exosomal core protein CSL4; homolog of yeast exosomal core protein CSL4

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_001318362.2 → NP_001305291.1 exosome complex component CSL4 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.

Source sequence(s)

AF151866, AW954858, BI550688

Consensus CDS

CCDS81492.1

UniProtKB/TrEMBL

B1AMU3, B1AMU4

Related

ENSP00000359922.4, ENST00000370885.8

Conserved Domains (2) summary

cd05791
Location:48 → 129

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
NM_001318363.2 → NP_001305292.1 exosome complex component CSL4 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site and lacks two alternate in-frame exons in the 3' coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform a.

Source sequence(s)

AF151866, BC022067, BI550688, N34159

UniProtKB/TrEMBL

R4GMQ7

Related

ENSP00000473660.1, ENST00000485122.6

Conserved Domains (2) summary

pfam14382
Location:8 → 39

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

cl09927
Location:62 → 116

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_001318364.2 → NP_001305293.1 exosome complex component CSL4 isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks three alternate exons, resulting in the loss of an in-frame segment in the central coding region, compared to variant 1. The encoded isoform (d) is shorter than isoform a.

Source sequence(s)

AF151866, BI550688, W39427

UniProtKB/Swiss-Prot

Q9Y3B2

Conserved Domains (2) summary

cl09927
Location:44 → 88

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. ...

cl26026
Location:10 → 120

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
NM_001318365.2 → NP_001305294.1 exosome complex component CSL4 isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (5) includes an additional exon and uses an alternate splice site, and it thus differs in its 5' UTR and initiates translation from an alternate start codon, compared to variant 1. The encoded isoform (e) has a distinct and shorter N-terminus, compared to isoform a. Both variants 5 and 6 encode isoform e.

Source sequence(s)

AF151866, BG331954, BI550688

UniProtKB/Swiss-Prot

Q9Y3B2

Conserved Domains (1) summary

cl09927
Location:29 → 68

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_001318366.2 → NP_001305295.1 exosome complex component CSL4 isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate splice site, and it thus differs in its 5' UTR and initiates translation from an alternate start codon, compared to variant 1. The encoded isoform (e) has a distinct and shorter N-terminus, compared to isoform a. Both variants 5 and 6 encode isoform e.

Source sequence(s)

AF151866, BI550688, BM692452

UniProtKB/Swiss-Prot

Q9Y3B2

Conserved Domains (1) summary

cl09927
Location:29 → 68

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_016046.5 → NP_057130.1 exosome complex component CSL4 isoform a

See identical proteins and their annotated locations for NP_057130.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AF151866, BC022067, BI550688

Consensus CDS

CCDS7459.1

UniProtKB/Swiss-Prot

B2R9B3, Q5JTH3, Q9Y3B2

UniProtKB/TrEMBL

B1AMU4

Related

ENSP00000359939.3, ENST00000370902.8

Conserved Domains (2) summary

cd05791
Location:62 → 154

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 ...

pfam14382
Location:8 → 39

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

RNA

NR_134586.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF151866, BU569997
NR_134587.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (8) lacks two alternate internal exons and uses an alternate splice site in the 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF151866, AK307229, BI550688

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

97435909..97446006 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011539847.3 → XP_011538149.1 exosome complex component CSL4 isoform X1

Conserved Domains (1) summary

cd05791
Location:27 → 119

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 ...