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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
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Genomic context

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See RPL13 in Genome Data Viewer
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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