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    RPL3 ribosomal protein L3 [ Homo sapiens (human) ]

    Gene ID: 6122, updated on 9-Dec-2024

    Summary

    Official Symbol
    RPL3provided by HGNC
    Official Full Name
    ribosomal protein L3provided by HGNC
    Primary source
    HGNC:HGNC:10332
    See related
    Ensembl:ENSG00000100316 MIM:604163; AllianceGenome:HGNC:10332
    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
    L3; uL3; ASC-1; TARBP-B
    Summary
    Ribosomes, the complexes 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 L3P family of ribosomal proteins and it is located in the cytoplasm. The protein can bind to the HIV-1 TAR mRNA, and it has been suggested that the protein contributes to tat-mediated transactivation. This gene is co-transcribed with several small nucleolar RNA genes, which are located in several of this gene's introns. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in ovary (RPKM 2560.0), skin (RPKM 1107.2) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See RPL3 in Genome Data Viewer
    Location:
    22q13.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39312882..39319623, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39783532..39790275, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39708887..39715628, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39632330-39633224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39633225-39634119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13747 Neighboring gene platelet derived growth factor subunit B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13748 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr22:39650154-39650932 and GRCh37_chr22:39650933-39651711 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39658425-39658924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39664844-39665376 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39673716-39673890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39673875-39674634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39677709-39678208 Neighboring gene uncharacterized LOC124905119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39690515-39691375 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39692677-39693342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39693343-39694006 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:39704579-39705778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13749 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39706697-39707237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39712838-39713726 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39714617-39715506 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39715507-39716396 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39716397-39717285 Neighboring gene small nucleolar RNA, C/D box 83B Neighboring gene small nucleolar RNA, C/D box 83A Neighboring gene Sharpr-MPRA regulatory region 3662 Neighboring gene small nucleolar RNA, C/D box 139 Neighboring gene small nucleolar RNA, C/D box 43 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39753396-39753924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39755840-39756638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39757867-39758453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39758454-39759039 Neighboring gene synaptogyrin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39769919-39770434 Neighboring gene Sharpr-MPRA regulatory region 1576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811177-39811678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811679-39812178 Neighboring gene TGF-beta activated kinase 1 (MAP3K7) binding protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39824885-39825527 Neighboring gene uncharacterized LOC100506472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39829518-39830236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39830237-39830954

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of ribosomal protein L3 (RPL3) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify ribosomal protein L3 (RPL3; HIV-1 TAR RNA-binding protein B), 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 L3 (RPL3; HIV-1 TAR RNA-binding protein B), 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 L3 (RPL3; HIV-1 TAR RNA-binding protein B), 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 L3 (RPL3; HIV-1 TAR RNA-binding protein B), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Rev rev HIV-1 Rev interacting protein, ribosomal protein L3 (RPL3), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed
    Tat tat TARBP-b binds to HIV-1 TAR RNA and data suggests that TARBP-b interacts with HIV-1 Tat to mediate transactivation of the HIV-1 LTR promoter PubMed
    retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human 60S ribosomal protein L3 (RPL3) at amino acid residues 331-332 and 381-382 by the HIV-1 protease PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC104284

    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 NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to interleukin-4 IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cytoplasmic translation IC
    Inferred by Curator
    more info
    PubMed 
    involved_in translation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in translation NAS
    Non-traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    large ribosomal subunit protein uL3
    Names
    60S ribosomal protein L3
    HIV-1 TAR RNA-binding protein B
    NP_000958.1
    NP_001029025.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_000967.4NP_000958.1  large ribosomal subunit protein uL3 isoform a

      See identical proteins and their annotated locations for NP_000958.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AK130450, BC012146, BC071666
      Consensus CDS
      CCDS13988.1
      UniProtKB/Swiss-Prot
      B2RDV9, P39023, Q15548, Q5I0G0
      UniProtKB/TrEMBL
      Q96QL0
      Related
      ENSP00000346001.3, ENST00000216146.9
      Conserved Domains (1) summary
      PTZ00103
      Location:1400
      PTZ00103; 60S ribosomal protein L3; Provisional
    2. NM_001033853.2NP_001029025.1  large ribosomal subunit protein uL3 isoform b

      See identical proteins and their annotated locations for NP_001029025.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses alternate in-frame splice sites in two exons, compared to variant 1, resulting in a shorter protein (isoform b).
      Source sequence(s)
      AK092695, BC008492, BC071666
      UniProtKB/TrEMBL
      B3KS36
      Conserved Domains (1) summary
      cl00324
      Location:1351
      Ribosomal_L3; Ribosomal protein L3

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      39312882..39319623 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      39783532..39790275 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)