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    RPL13 ribosomal protein L13 [ Homo sapiens (human) ]

    Gene ID: 6137, updated on 7-Apr-2024

    Summary

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    Official Symbol
    RPL13provided by HGNC
    Official Full Name
    ribosomal protein L13provided by HGNC
    Primary source
    HGNC:HGNC:10303
    See related
    Ensembl:ENSG00000167526 MIM:113703; AllianceGenome:HGNC:10303
    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
    L13; BBC1; eL13; D16S44E; SEMDIST; D16S444E
    Summary
    Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L13E family of ribosomal proteins. It is located in the cytoplasm. This gene is expressed at significantly higher levels in benign breast lesions than in breast carcinomas. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2011]
    Expression
    Ubiquitous expression in ovary (RPKM 234.6), spleen (RPKM 109.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    16q24.3; 17p11.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (89560657..89566829)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95641207..95647429)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (89627065..89633237)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101930112 Neighboring gene uncharacterized LOC101927863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7909 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7911 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89585576-89586076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89586077-89586577 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:89588494-89589051 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89589052-89589608 Neighboring gene SPG7 matrix AAA peptidase subunit, paraplegin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89601956-89602646 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:89625532-89625751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11417 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89630776-89631518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89631519-89632262 Neighboring gene small nucleolar RNA, C/D box 68 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:89640372-89640629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7916 Neighboring gene copine 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89665942-89666855 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:89679650-89679808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89681214-89681918 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89681919-89682621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89689900-89690772 Neighboring gene dipeptidase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89698470-89699324

    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. Activation of the ribosomal protein L13 gene in human gastrointestinal cancer. Kobayashi T, et al. Int J Mol Med, 2006 Jul. PMID 16786168
    2. Isolation and characterization of a novel gene with differential expression in benign and malignant human breast tumours. Adams SM, et al. Hum Mol Genet, 1992 May. PMID 1301162
    3. Novel RPL13 Variants and Variable Clinical Expressivity in a Human Ribosomopathy With Spondyloepimetaphyseal Dysplasia. Costantini A, et al. J Bone Miner Res, 2021 Feb. PMID 32916022, Free PMC Article
    4. RPL13 Variants Cause Spondyloepimetaphyseal Dysplasia with Severe Short Stature. Le Caignec C, et al. Am J Hum Genet, 2019 Nov 7. PMID 31630789, Free PMC Article
    5. Cloning and characterization of human karyopherin beta3. Yaseen NR, et al. Proc Natl Acad Sci U S A, 1997 Apr 29. PMID 9114010, Free PMC Article

    See all (219) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel RPL13 Variants and Variable Clinical Expressivity in a Human Ribosomopathy With Spondyloepimetaphyseal Dysplasia.
      Title: Novel RPL13 Variants and Variable Clinical Expressivity in a Human Ribosomopathy With Spondyloepimetaphyseal Dysplasia.
    2. Using a combination of human genetics and cardiac model systems, RPL13 gene was identified as a new candidate for congenital heart pathogenesis.
      Title: Model system identification of novel congenital heart disease gene candidates: focus on RPL13.
    3. The identified RPL13 variants cause a human ribosomopathy defined by a rare skeletal dysplasia.
      Title: RPL13 Variants Cause Spondyloepimetaphyseal Dysplasia with Severe Short Stature.
    4. This protein has been found differentially expressed in the temporal lobe from patients with schizophrenia.
      Title: Alterations in oligodendrocyte proteins, calcium homeostasis and new potential markers in schizophrenia anterior temporal lobe are revealed by shotgun proteome analysis.
    5. Ribosomal protein L13 plays an essential role in the progression of some gastrointestinal malignancies.
      Title: Activation of the ribosomal protein L13 gene in human gastrointestinal cancer.
    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
    Spondyloepimetaphyseal dysplasia, Isidor-Toutain type
    MedGen: C5231478 OMIM: 618728 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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify ribosomal protein L13 (RPL13), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify ribosomal protein L13 (RPL13), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify ribosomal protein L13 (RPL13), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify ribosomal protein L13 (RPL13), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Tat tat Expression of HIV-1 Tat upregulates the abundance of ribosomal protein L13 (RPL13) in the nucleoli of Jurkat T-cells PubMed
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of ribosomal protein L13 (RPL13) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ27453, FLJ27454, FLJ38635, MGC71373, MGC117342

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables structural constituent of ribosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables structural constituent of ribosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables structural constituent of ribosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables structural constituent of ribosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in blastocyst development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in bone development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cytoplasmic translation IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in cytoplasmic translation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in translation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of cytosolic large ribosomal subunit HDA PubMed 
    part_of cytosolic large ribosomal subunit IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of cytosolic large ribosomal subunit IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of cytosolic large ribosomal subunit IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytosolic ribosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus HDA PubMed 
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    large ribosomal subunit protein eL13
    Names
    60S ribosomal protein L13
    breast basic conserved 1
    breast basic conserved protein 1
    NP_000968.2
    NP_001230060.1
    NP_150254.1

    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_000977.4 → NP_000968.2  large ribosomal subunit protein eL13 isoform 1

      See identical proteins and their annotated locations for NP_000968.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the predominant transcript. It encodes the longest isoform (1).
      Source sequence(s)
      AC092123, BC106058
      Consensus CDS
      CCDS10979.1
      UniProtKB/Swiss-Prot
      B4DLX3, F5H1S2, P26373, Q3KQT8, Q567Q8, Q9BPX0
      UniProtKB/TrEMBL
      A8K4C8, Q6NZ55
      Related
      ENSP00000307889.5, ENST00000311528.10
      Conserved Domains (1) summary
      pfam01294
      Location:8 → 187
      Ribosomal_L13e; Ribosomal protein L13e

    2. NM_001243131.1 → NP_001230060.1  large ribosomal subunit protein eL13 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an additional splice junction in the CDS, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AC092123, AK297198, BC106058
      Consensus CDS
      CCDS58492.1
      UniProtKB/Swiss-Prot
      P26373
      Related
      ENSP00000438959.2, ENST00000452368.7
      Conserved Domains (1) summary
      cl01799
      Location:13 → 137
      Ribosomal_L13e; Ribosomal protein L13e

    3. NM_033251.2 → NP_150254.1  large ribosomal subunit protein eL13 isoform 1

      See identical proteins and their annotated locations for NP_150254.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has a different 5' UTR, compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AC092123, BC020804
      Consensus CDS
      CCDS10979.1
      UniProtKB/Swiss-Prot
      B4DLX3, F5H1S2, P26373, Q3KQT8, Q567Q8, Q9BPX0
      UniProtKB/TrEMBL
      A8K4C8, Q6NZ55
      Related
      ENSP00000376811.3, ENST00000393099.3
      Conserved Domains (1) summary
      pfam01294
      Location:8 → 187
      Ribosomal_L13e; Ribosomal protein L13e

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      89560657..89566829
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      95641207..95647429
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001243130.1: Suppressed sequence

      Description
      NM_001243130.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P26373.4 GenPept UniProtKB/Swiss-Prot:P26373

    Gene LinkOut

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

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