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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
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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)

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

  • 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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