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ERI1 exoribonuclease 1 [ Homo sapiens (human) ]

Gene ID: 90459, updated on 5-Mar-2024

Summary

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Official Symbol
ERI1provided by HGNC
Official Full Name
exoribonuclease 1provided by HGNC
Primary source
HGNC:HGNC:23994
See related
Ensembl:ENSG00000104626 MIM:608739; AllianceGenome:HGNC:23994
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HEXO; HXAL; THEX1; 3'HEXO; SEMDGC; SEMDGS
Summary
Enables 3'-5' exonuclease activity. Predicted to be involved in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 5.2), appendix (RPKM 4.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
8p23.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (9002897..9100104)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (10644016..10741931, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (8860407..8957614)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901866 Neighboring gene Sharpr-MPRA regulatory region 10847 Neighboring gene uncharacterized LOC105379227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26980 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:8872161-8872870 Neighboring gene NANOG hESC enhancer GRCh37_chr8:8918074-8918619 Neighboring gene microRNA 4660 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:8923326-8923532 Neighboring gene small nucleolar RNA, C/D box 3I Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:8935205-8935705 Neighboring gene RNA, U7 small nuclear 55 pseudogene Neighboring gene uncharacterized LOC112268402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8989159-8989659 Neighboring gene Sharpr-MPRA regulatory region 9732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8997999-8998498 Neighboring gene uncharacterized LOC124901882 Neighboring gene protein phosphatase 1 regulatory subunit 3B

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Null and missense mutations of ERI1 cause a recessive phenotypic dichotomy in humans. Guo L, et al. Am J Hum Genet, 2023 Jul 6. PMID 37352860, Free PMC Article
  2. Homozygous microdeletion of the ERI1 and MFHAS1 genes in a patient with intellectual disability, limb abnormalities, and cardiac malformation. Choucair N, et al. Am J Med Genet A, 2017 Jul. PMID 28488351
  3. Eri1: a conserved enzyme at the crossroads of multiple RNA-processing pathways. Thomas MF, et al. Trends Genet, 2014 Jul. PMID 24929628, Free PMC Article
  4. Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP. Cheng Y, et al. J Mol Biol, 2004 Oct 15. PMID 15451662, Free PMC Article
  5. Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription. Declercq M, et al. Nucleic Acids Res, 2020 Oct 9. PMID 32960265, Free PMC Article

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Null and missense mutations of ERI1 cause a recessive phenotypic dichotomy in humans.
    Title: Null and missense mutations of ERI1 cause a recessive phenotypic dichotomy in humans.
  2. Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription.
    Title: Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription.
  3. the crystal structure of a ternary complex of human SLBP RNA binding domain, human 3'hExo, and a 26-nucleotide stem-loop RNA is reported.
    Title: Structure of histone mRNA stem-loop, human stem-loop binding protein, and 3'hExo ternary complex.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. 3'hExo is a 3' exonuclease specifically interacting with the 3' end of histone mRNA
    Title: Characterization of 3'hExo, a 3' exonuclease specifically interacting with the 3' end of histone mRNA.
  6. 3'hExo is a primary candidate for the exonuclease that initiates rapid decay of histone mRNA upon completion and/or inhibition of DNA replication
    Title: A 3' exonuclease that specifically interacts with the 3' end of histone mRNA.
  7. Data describe the structure of the nuclease domain of 3'-5'-exoribonuclease (3'hExo) complexed with rAMP in the presence of magnesium at 1.6 A resolution.
    Title: Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP.
  8. molecular cloning; degrades siRNAs in vitro[ERI-1]
    Title: A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans.
Submit: New GeneRIF Correction

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
Hoxha-Aliu syndrome
MedGen: CN375878 OMIM: 620662 GeneReviews: Not available
not available
Spondyloepimetaphyseal dysplasia, Guo-Campeau type
MedGen: CN375879 OMIM: 620663 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
EBI GWAS Catalog
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC35395

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5' exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 3'-5'-RNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone pre-mRNA stem-loop binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables rRNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables ribosome binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
  
NOT involved_in histone mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in rRNA 3'-end processing ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulatory ncRNA-mediated gene silencing 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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of histone pre-mRNA 3'end processing complex ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
3'-5' exoribonuclease 1
Names
3' exoribonuclease
3'-5' exonuclease ERI1
enhanced RNAi three prime mRNA exonuclease homolog 1
histone mRNA 3' end-specific exonuclease
histone mRNA 3'-end-specific exoribonuclease
histone mRNA 3'-exonuclease 1
three prime histone mRNA exonuclease 1
three prime mRNA exonuclease 1

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_001354635.2 → NP_001341564.1  3'-5' exoribonuclease 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC087579, AC087763
    Conserved Domains (2) summary
    cd06133
    Location:52 → 232
    ERI-1_3'hExo_like; DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins
    pfam02037
    Location:1 → 32
    SAP; SAP domain

  2. NM_001354636.2 → NP_001341565.1  3'-5' exoribonuclease 1 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC087579, AC087763
    Conserved Domains (1) summary
    cd06133
    Location:15 → 195
    ERI-1_3'hExo_like; DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins

  3. NM_001354638.2 → NP_001341567.1  3'-5' exoribonuclease 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC087579, AC087763
    Conserved Domains (2) summary
    cd06133
    Location:130 → 273
    ERI-1_3'hExo_like; DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins
    pfam02037
    Location:76 → 110
    SAP; SAP domain

  4. NM_153332.4 → NP_699163.2  3'-5' exoribonuclease 1 isoform 1

    See identical proteins and their annotated locations for NP_699163.2

    Status: VALIDATED

    Source sequence(s)
    AC087579, AV709794, BC035279
    Consensus CDS
    CCDS5972.1
    UniProtKB/Swiss-Prot
    A8K4U7, Q8IV48, Q9NSX3
    Related
    ENSP00000250263.7, ENST00000250263.8
    Conserved Domains (2) summary
    cd06133
    Location:130 → 310
    ERI-1_3'hExo_like; DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins
    pfam02037
    Location:76 → 110
    SAP; SAP domain

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

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    9002897..9100104
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422402.1 → XP_047278358.1  3'-5' exoribonuclease 1 isoform X1

  2. XM_005272401.4 → XP_005272458.1  3'-5' exoribonuclease 1 isoform X3

    See identical proteins and their annotated locations for XP_005272458.1

    Conserved Domains (2) summary
    cd06133
    Location:52 → 232
    ERI-1_3'hExo_like; DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins
    pfam02037
    Location:1 → 32
    SAP; SAP domain

  3. XM_011543849.3 → XP_011542151.1  3'-5' exoribonuclease 1 isoform X2

    Conserved Domains (2) summary
    cd06133
    Location:130 → 269
    ERI-1_3'hExo_like; DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins
    pfam02037
    Location:76 → 110
    SAP; SAP domain

  4. XM_011543850.4 → XP_011542152.1  3'-5' exoribonuclease 1 isoform X3

    See identical proteins and their annotated locations for XP_011542152.1

    Conserved Domains (2) summary
    cd06133
    Location:52 → 232
    ERI-1_3'hExo_like; DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins
    pfam02037
    Location:1 → 32
    SAP; SAP domain

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    4251550..4349758 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332274.1 → XP_054188249.1  3'-5' exoribonuclease 1 isoform X4

  2. XM_054332275.1 → XP_054188250.1  3'-5' exoribonuclease 1 isoform X2

  3. XM_054332277.1 → XP_054188252.1  3'-5' exoribonuclease 1 isoform X3

  4. XM_054332276.1 → XP_054188251.1  3'-5' exoribonuclease 1 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    10644016..10741931 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054361466.1 → XP_054217441.1  3'-5' exoribonuclease 1 isoform X1

  2. XM_054361465.1 → XP_054217440.1  3'-5' exoribonuclease 1 isoform X1

  3. XM_054361467.1 → XP_054217442.1  3'-5' exoribonuclease 1 isoform X2

  4. XM_054361464.1 → XP_054217439.1  3'-5' exoribonuclease 1 isoform X5

  5. XM_054361468.1 → XP_054217443.1  3'-5' exoribonuclease 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IV48.3 GenPept UniProtKB/Swiss-Prot:Q8IV48

Gene LinkOut

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