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    ELAC2 elaC ribonuclease Z 2 [ Homo sapiens (human) ]

    Gene ID: 60528, updated on 3-Nov-2024

    Summary

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    Official Symbol
    ELAC2provided by HGNC
    Official Full Name
    elaC ribonuclease Z 2provided by HGNC
    Primary source
    HGNC:HGNC:14198
    See related
    Ensembl:ENSG00000006744 MIM:605367; AllianceGenome:HGNC:14198
    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
    ELC2; HPC2; COXPD17
    Summary
    The protein encoded by this gene has a C-terminal domain with tRNA 3′ processing endoribonuclease activity, which catalyzes the removal of the 3' trailer from precursor tRNAs. The protein also interacts with activated Smad family member 2 (Smad2) and its nuclear partner forkhead box H1 (also known as FAST-1), and reduced expression can suppress transforming growth factor-beta induced growth arrest. Mutations in this gene result in an increased risk of prostate cancer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
    Expression
    Ubiquitous expression in colon (RPKM 15.0), testis (RPKM 14.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ELAC2 in Genome Data Viewer
    Location:
    17p12
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (12991612..13018027, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (12899079..12925488, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (12894929..12921344, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene myocardin Neighboring gene ARHGAP44 and MYOCD antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11737 Neighboring gene Rho GTPase activating protein 44 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11739 Neighboring gene microRNA 1269b Neighboring gene Sharpr-MPRA regulatory region 8598 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:12920660-12921160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8207 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:12999283-13000482 Neighboring gene VISTA enhancer hs1497 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:13044042-13044662 Neighboring gene uncharacterized LOC124904097 Neighboring gene long intergenic non-protein coding RNA 2093

    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. HPC2/ELAC2 gene variants associated with incident prostate cancer. Adler D, et al. J Hum Genet, 2003. PMID 14625808
    2. A Study of Ser217Leu and Ala541Thr Polymorphism in the Men Afflicted with Prostate Cancer and in the Men being Suspicious of Prostate Cancer. Zahiri Z, et al. Asian Pac J Cancer Prev, 2020 Jun 1. PMID 32592348, Free PMC Article
    3. Mutations in ELAC2 associated with hypertrophic cardiomyopathy impair mitochondrial tRNA 3'-end processing. Saoura M, et al. Hum Mutat, 2019 Oct. PMID 31045291, Free PMC Article
    4. The Phenotype and Outcome of Infantile Cardiomyopathy Caused by a Homozygous ELAC2 Mutation. Shinwari ZMA, et al. Cardiology, 2017. PMID 28441660
    5. A homozygous splicing mutation in ELAC2 suggests phenotypic variability including intellectual disability with minimal cardiac involvement. Akawi NA, et al. Orphanet J Rare Dis, 2016 Oct 21. PMID 27769300, Free PMC Article

    See all (119) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ELAC2 is a functional prostate cancer risk allele.
      Title: ELAC2 is a functional prostate cancer risk allele.
    2. A Study of Ser217Leu and Ala541Thr Polymorphism in the Men Afflicted with Prostate Cancer and in the Men being Suspicious of Prostate Cancer.
      Title: A Study of Ser217Leu and Ala541Thr Polymorphism in the Men Afflicted with Prostate Cancer and in the Men being Suspicious of Prostate Cancer.
    3. Our study thus broadly confirms the correlation of ELAC2 variants with severe infantile-onset forms of HCM and mitochondrial respiratory chain dysfunction.
      Title: Mutations in ELAC2 associated with hypertrophic cardiomyopathy impair mitochondrial tRNA 3'-end processing.
    4. This study describes the cardiac phenotype and outcome of ELAC2 mutation in Infantile Cardiomyopathy
      Title: The Phenotype and Outcome of Infantile Cardiomyopathy Caused by a Homozygous ELAC2 Mutation.
    5. ELAC2 rs11545302 polymorphism was associated with PSA > 20 and rs4792311 was associated with TNM > 2.
      Title: Association between RNASEL, MSR1, and ELAC2 single nucleotide polymorphisms and gene expression in prostate cancer risk.
    6. A homozygous splicing mutation in ELAC2 suggests phenotypic variability including intellectual disability with minimal cardiac involvement
      Title: A homozygous splicing mutation in ELAC2 suggests phenotypic variability including intellectual disability with minimal cardiac involvement.
    7. ELAC2 mutations cause a mitochondrial RNA processing defect associated with hypertrophic cardiomyopathy.
      Title: ELAC2 mutations cause a mitochondrial RNA processing defect associated with hypertrophic cardiomyopathy.
    8. results indicate that ELAC2 functions as a tRNase Z in human mitochondria and suggest that mt-tRNase Z preferentially cleaves molecules already processed by the proteinaceous mtRNase P
      Title: Involvement of human ELAC2 gene product in 3' end processing of mitochondrial tRNAs.
    9. ELAC2 and PTCD1 affect the 3' end processing of tRNAs.
      Title: RNA processing in human mitochondria.
    10. analysis of dual nuclear/mitochondrial targeting of the ELAC2 gene product by alternative translation initiation
      Title: Localization of human RNase Z isoforms: dual nuclear/mitochondrial targeting of the ELAC2 gene product by alternative translation initiation.
    Submit: New GeneRIF Correction See all GeneRIFs (40)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Combined oxidative phosphorylation defect type 17
    MedGen: C3809526 OMIM: 615440 GeneReviews: Not available
    		not available
    Prostate cancer, hereditary, 2
    MedGen: C3539120 OMIM: 614731 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)

    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

    • FLJ10530, FLJ36693, FLJ42848

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-tRNA processing endoribonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding HDA PubMed 
    enables RNA endonuclease activity TAS
    Traceable Author Statement
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables tRNA-specific ribonuclease activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mitochondrial tRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial tRNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondrial tRNA processing TAS
    Traceable Author Statement
    more info
    		  
    involved_in tRNA 3'-end processing TAS
    Traceable Author Statement
    more info
    		  
    involved_in tRNA decay TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrial nucleoid IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    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
    zinc phosphodiesterase ELAC protein 2
    Names
    RNase Z 2
    elaC homolog 2
    elaC homolog protein 2
    elaC-like protein 2
    heredity prostate cancer protein 2
    putative prostate cancer susceptibility protein HPC2/ELAC2
    ribonuclease Z 2
    tRNA 3 endonuclease 2
    tRNase Z (long form)
    tRNase Z 2
    NP_001159434.1
    NP_060597.4
    NP_776065.1
    XP_024306628.1
    XP_024306629.1
    XP_054172839.1
    XP_054172840.1

    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.

    Genomic

    1. NG_015808.1 RefSeqGene

      Range
      5038..31453
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001165962.2 → NP_001159434.1  zinc phosphodiesterase ELAC protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001159434.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AA706335, AC005277, AK298397, DC394013
      Consensus CDS
      CCDS54093.1
      UniProtKB/TrEMBL
      B4DT15
      Related
      ENSP00000405223.3, ENST00000426905.7
      Conserved Domains (4) summary
      COG1234
      Location:442 → 712
      ElaC; Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis]
      cd07718
      Location:443 → 648
      RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
      cd16296
      Location:60 → 271
      RNaseZ_ELAC2-N-term-like_MBL-fold; Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase domain
      cl23716
      Location:616 → 690
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

    2. NM_018127.7 → NP_060597.4  zinc phosphodiesterase ELAC protein 2 isoform 1

      See identical proteins and their annotated locations for NP_060597.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA706335, AC005277, AF304370, DC394013
      Consensus CDS
      CCDS11164.1
      UniProtKB/Swiss-Prot
      B4DPL9, Q6IA94, Q9BQ52, Q9HAS8, Q9HAS9, Q9NVT1
      UniProtKB/TrEMBL
      A0A0S2Z5M8, B4DT15
      Related
      ENSP00000337445.4, ENST00000338034.9
      Conserved Domains (4) summary
      COG1234
      Location:482 → 752
      ElaC; Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis]
      cd07718
      Location:483 → 688
      RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
      cd16296
      Location:60 → 311
      RNaseZ_ELAC2-N-term-like_MBL-fold; Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase domain
      cl23716
      Location:656 → 730
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

    3. NM_173717.2 → NP_776065.1  zinc phosphodiesterase ELAC protein 2 isoform 2

      See identical proteins and their annotated locations for NP_776065.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region. The resulting isoform (2) lacks one amino acid, compared to isoform 1.
      Source sequence(s)
      AA706335, AC005277, AK001392, BC001939, DC394013
      UniProtKB/TrEMBL
      B4DT15
      Conserved Domains (4) summary
      COG1234
      Location:481 → 751
      ElaC; Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis]
      cd07718
      Location:482 → 687
      RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
      cd16296
      Location:60 → 311
      RNaseZ_ELAC2-N-term-like_MBL-fold; Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase domain
      cl23716
      Location:655 → 729
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase 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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      12991612..13018027 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450861.2 → XP_024306629.1  zinc phosphodiesterase ELAC protein 2 isoform X1

      UniProtKB/TrEMBL
      G5E9D5
      Related
      ENSP00000463740.2, ENST00000584650.5
      Conserved Domains (2) summary
      cd07718
      Location:389 → 594
      RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
      cl23716
      Location:1 → 217
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

    2. XM_024450860.2 → XP_024306628.1  zinc phosphodiesterase ELAC protein 2 isoform X1

      UniProtKB/TrEMBL
      G5E9D5
      Conserved Domains (2) summary
      cd07718
      Location:389 → 594
      RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
      cl23716
      Location:1 → 217
      metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      12899079..12925488 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316864.1 → XP_054172839.1  zinc phosphodiesterase ELAC protein 2 isoform X1

    2. XM_054316865.1 → XP_054172840.1  zinc phosphodiesterase ELAC protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BQ52.2 GenPept UniProtKB/Swiss-Prot:Q9BQ52

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