RPL13A ribosomal protein L13a [Homo sapiens (human)] - Gene

Summary

Official Symbol: RPL13Aprovided by HGNC
Official Full Name: ribosomal protein L13aprovided by HGNC
Primary source: HGNC:HGNC:10304
See related: Ensembl:ENSG00000142541 MIM:619225; AllianceGenome:HGNC:10304
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: L13A; uL13; TSTA1
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 member of the L13P family of ribosomal proteins that is a component of the 60S subunit. The encoded protein also plays a role in the repression of inflammatory genes as a component of the IFN-gamma-activated inhibitor of translation (GAIT) complex. This gene is co-transcribed with the small nucleolar RNA genes U32, U33, U34, and U35, which are located in the second, fourth, fifth, and sixth introns, respectively. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed throughout the genome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]
Expression: Ubiquitous expression in ovary (RPKM 1600.3), lymph node (RPKM 1020.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.33

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (49487608..49492308)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (52487574..52492273)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (49990865..49995565)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Moonlight human ribosomal protein L13a downregulation is associated with p53 and HER2/neu expression in breast cancer.
Title: Moonlight human ribosomal protein L13a downregulation is associated with p53 and HER2/neu expression in breast cancer.
show through cellular immunofluorescence experiments that nuclear but not nucleolar localization of L13a is resistant to extensive amino acid alterations, suggesting that multiple complex nuclear import signals are present within this protein
Title: Mutually exclusive amino acid residues of L13a are responsible for its ribosomal incorporation and translational silencing leading to resolution of inflammation.
The expression of RPL13A and EEF1A1 was not affected by differentiation, thus being these genes the most stable candidates as reference genes for RT-PCR.
Title: RPL13A and EEF1A1 Are Suitable Reference Genes for qPCR during Adipocyte Differentiation of Vascular Stromal Cells from Patients with Different BMI and HOMA-IR.
This work identified the arginine residue at position 68 of L13A as being essential for L13A binding to rRNA and incorporation into ribosomes.
Title: Insights into the mechanism of ribosomal incorporation of mammalian L13a protein during ribosome biogenesis.
Ribosomal protein l13a is a reference gene for human bone marrow-derived mesenchymal stromal cells during expansion, adipo-, chondro-, and osteogenesis
Title: Ribosomal protein l13a as a reference gene for human bone marrow-derived mesenchymal stromal cells during expansion, adipo-, chondro-, and osteogenesis.
GAPDH functions as a chaperone, shielding newly released RPL13a from proteasomal degradation.
Title: Protection of extraribosomal RPL13a by GAPDH and dysregulation by S-nitrosylation.
The study found two ribosomal proteins, RPS7 and RPL13A that interact with the HMG (high-mobility group) box domain of SRY.
Title: SRY interacts with ribosomal proteins S7 and L13a in nuclear speckles.
Data show that EF1alpha, RPL13a and YWHAZ are suitable genes for the RT-qPCR analysis and comparison of several sources of human MSC during in vitro characterization and differentiation as well as in an ex vivo animal model of global cerebral ischemia.
Title: EF1alpha and RPL13a represent normalization genes suitable for RT-qPCR analysis of bone marrow derived mesenchymal stem cells.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of hematological and biochemical traits in a Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH27395 (e-PCR)
- UniSTS:89108

D19S1002 (e-PCR)
- UniSTS:154691

D19S1021 (e-PCR)
- UniSTS:49529

RH38886 (e-PCR)
- UniSTS:92099

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
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	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular response to type II interferon	IDA Inferred from Direct Assay 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 homeostatic process	IEA Inferred from Electronic Annotation more info
involved_in lung morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in macrophage chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of formation of translation preinitiation complex	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of translation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of translation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in translation	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of GAIT complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	HDA more info	PubMed
located_in cytoplasm	NAS Non-traceable Author Statement more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
part_of cytosolic large ribosomal subunit	HDA more info	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 focal adhesion	HDA more info	PubMed
part_of large ribosomal subunit	TAS Traceable Author Statement more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nucleolus	HDA more info	PubMed
located_in nucleus	HDA more info	PubMed
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in ribosome	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: large ribosomal subunit protein uL13

Names: 23 kDa highly basic protein; 60S ribosomal protein L13a; epididymis secretory sperm binding protein; highly basic protein 23 kDa; tissue specific transplantation antigen 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)

NM_001270491.2 → NP_001257420.1 large ribosomal subunit protein uL13 isoform 2

See identical proteins and their annotated locations for NP_001257420.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal exon, uses an alternate splice site and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC010619, BC062537, BQ069994

Consensus CDS

CCDS74421.1

UniProtKB/TrEMBL

Q0VGL3, Q8J015

Related

ENSP00000477755.1, ENST00000621674.4

Conserved Domains (1) summary

cl00333
Location:1 → 139

Ribosomal_L13; Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the ...
NM_012423.4 → NP_036555.1 large ribosomal subunit protein uL13 isoform 1

See identical proteins and their annotated locations for NP_036555.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).

Source sequence(s)

AK291120, BC062537

Consensus CDS

CCDS12768.1

UniProtKB/Swiss-Prot

A8K505, P40429

UniProtKB/TrEMBL

A0A384ME37, Q53H34, Q5QTS3

Related

ENSP00000375730.4, ENST00000391857.9

Conserved Domains (1) summary

PTZ00068
Location:6 → 200

PTZ00068; 60S ribosomal protein L13a; Provisional

RNA

NR_073024.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB082924, BC062537, BC105605

Related

ENST00000624069.3