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    MRPL39 mitochondrial ribosomal protein L39 [ Homo sapiens (human) ]

    Gene ID: 54148, updated on 2-Nov-2024

    Summary

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    Official Symbol
    MRPL39provided by HGNC
    Official Full Name
    mitochondrial ribosomal protein L39provided by HGNC
    Primary source
    HGNC:HGNC:14027
    See related
    Ensembl:ENSG00000154719 MIM:611845; AllianceGenome:HGNC:14027
    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
    L5mt; mL39; L39mt; MRPL5; RPML5; MRP-L5; PRED22; PRED66; COXPD59; MSTP003; C21orf92
    Summary
    Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. Two transcript variants encoding distinct isoforms have been described. A pseudogene corresponding to this gene is found on chromosome 5q. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 23.0), adrenal (RPKM 13.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MRPL39 in Genome Data Viewer
    Location:
    21q21.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (25585656..25607859, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (23943220..23965426, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (26957968..26979793, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene MIR155 host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18313 Neighboring gene microRNA 155 Neighboring gene long intergenic non-protein coding RNA 515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:27012080-27012580 Neighboring gene uncharacterized LOC124905001 Neighboring gene RNA guanylyltransferase and 5'-phosphatase pseudogene 1 Neighboring gene junctional adhesion molecule 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:27054065-27054224 Neighboring gene ferredoxin 1 pseudogene 2

    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. Multi-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease. Amarasekera SSC, et al. Hum Mol Genet, 2023 Jul 20. PMID 37133451, Free PMC Article
    2. Heart-specific splice-variant of a human mitochondrial ribosomal protein (mRNA processing; tissue specific splicing). Spirina O, et al. Gene, 2000 Dec 31. PMID 11167009
    3. Long Noncoding RNA MRPL39 Inhibits Gastric Cancer Proliferation and Progression by Directly Targeting miR-130. Yu MJ, et al. Genet Test Mol Biomarkers, 2018 Nov. PMID 30452299
    4. Evolution of a protein-rich mitochondrial ribosome: implications for human genetic disease. O'Brien TW. Gene, 2002 Mar 6. PMID 11943462
    5. Mammalian mitochondrial ribosomal proteins (2). Amino acid sequencing, characterization, and identification of corresponding gene sequences. O'Brien TW, et al. J Biol Chem, 1999 Dec 17. PMID 10593885

    See all (83) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Multi-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease.
      Title: Multi-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease.
    2. We found that MRPL39 was significantly downregulated in Gastric Cancer tissues and cell lines and that its expression level was negatively associated with carcinoma size, tumor, lymph node, metastasis (TNM) stage, and lymphatic metastasis. Patients with low MRPL39 expression levels revealed a short overall and disease-free survival period.
      Title: Long Noncoding RNA MRPL39 Inhibits Gastric Cancer Proliferation and Progression by Directly Targeting miR-130.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    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
    Combined oxidative phosphorylation deficiency 59
    MedGen: C5882730 OMIM: 620646 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)

    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

    • MGC3400, FLJ20451, MGC104174

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mitochondrial translation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrial inner membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of mitochondrial large ribosomal subunit IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of mitochondrial large ribosomal subunit NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrial ribosome NAS
    Non-traceable Author Statement
    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 

    General protein information

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    Preferred Names
    large ribosomal subunit protein mL39
    Names
    39S ribosomal protein L39, mitochondrial
    39S ribosomal protein L5, mitochondrial
    mitochondrial large ribosomal subunit protein mL39

    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_017446.4 → NP_059142.3  large ribosomal subunit protein mL39 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the predominant isoform (a).
      Source sequence(s)
      AP000223
      Consensus CDS
      CCDS13573.1
      UniProtKB/Swiss-Prot
      C9JYA5, Q32Q74, Q5QTR3, Q96Q65, Q9BSQ7, Q9BZV6, Q9NX44, Q9NYK5
      UniProtKB/TrEMBL
      C9JG87
      Related
      ENSP00000284967.7, ENST00000352957.9
      Conserved Domains (1) summary
      PLN02908
      Location:44 → 303
      PLN02908; threonyl-tRNA synthetase

    2. NM_080794.4 → NP_542984.3  large ribosomal subunit protein mL39 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as MRP-L5V1 or the heart-specific transcript variant, includes an alternate segment, when compared to variant 1, that causes a frameshift. The encoded isoform (b) has a distinct and longer C-terminus, compared to isoform a.
      Source sequence(s)
      AP000223
      Consensus CDS
      CCDS33522.1
      UniProtKB/TrEMBL
      C9JG87
      Related
      ENSP00000305682.7, ENST00000307301.11
      Conserved Domains (1) summary
      PLN02908
      Location:44 → 303
      PLN02908; threonyl-tRNA synthetase

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      25585656..25607859 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529651.3 → XP_011527953.1  large ribosomal subunit protein mL39 isoform X1

      UniProtKB/TrEMBL
      C9JG87
      Conserved Domains (1) summary
      cd01667
      Location:34 → 88
      TGS_ThrRS_N; TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and ...

    2. XM_006724026.5 → XP_006724089.1  large ribosomal subunit protein mL39 isoform X2

      UniProtKB/TrEMBL
      C9JG87
      Conserved Domains (1) summary
      PLN02908
      Location:44 → 303
      PLN02908; threonyl-tRNA synthetase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      23943220..23965426 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324690.1 → XP_054180665.1  large ribosomal subunit protein mL39 isoform X1

    2. XM_054324691.1 → XP_054180666.1  large ribosomal subunit protein mL39 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NYK5.3 GenPept UniProtKB/Swiss-Prot:Q9NYK5

    Gene LinkOut

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