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    ERI1 exoribonuclease 1 [ Homo sapiens (human) ]

    Gene ID: 90459, updated on 2-Nov-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. Involved in maturation of 5.8S rRNA. Located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 5.2), appendix (RPKM 4.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ERI1 in Genome Data Viewer
    Location:
    8p23.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (9002897..9100104)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (10644016..10741931, complement)
    RS_2024_09 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 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. 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
    2. 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
    3. 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
    4. 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
    5. Structure of histone mRNA stem-loop, human stem-loop binding protein, and 3'hExo ternary complex. Tan D, et al. Science, 2013 Jan 18. PMID 23329046, Free PMC Article

    See all (45) 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: C5882736 OMIM: 620662 GeneReviews: Not available
    		not available
    Spondyloepimetaphyseal dysplasia, Guo-Campeau type
    MedGen: C5882737 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 maturation of 5.8S rRNA 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
      UniProtKB/TrEMBL
      A0AAG2UWX2
      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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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