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NOP53 NOP53 ribosome biogenesis factor [ Homo sapiens (human) ]

Gene ID: 29997, updated on 3-Mar-2024

Summary

Official Symbol
NOP53provided by HGNC
Official Full Name
NOP53 ribosome biogenesis factorprovided by HGNC
Primary source
HGNC:HGNC:4333
See related
Ensembl:ENSG00000105373 MIM:605691; AllianceGenome:HGNC:4333
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PICT1; PICT-1; GLTSCR2
Summary
Enables 5S rRNA binding activity; identical protein binding activity; and p53 binding activity. Involved in several processes, including negative regulation of transcription, DNA-templated; regulation of cellular protein metabolic process; and regulation of intracellular signal transduction. Located in cytosol; fibrillar center; and nucleoplasm. Colocalizes with rDNA heterochromatin. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 175.8), spleen (RPKM 136.0) and 25 other tissues See more
Orthologs
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Genomic context

See NOP53 in Genome Data Viewer
Location:
19q13.33
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (47745546..47757058)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (50576356..50587868)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48248803..48260315)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10861 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10865 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48115860-48116691 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48118354-48119183 Neighboring gene BICRA antisense RNA 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48123829-48124389 Neighboring gene BRD4 interacting chromatin remodeling complex associated protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48130149-48130723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48135834-48136477 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48148954-48149534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48153858-48154564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48164109-48164610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48164611-48165110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48196325-48196884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48196885-48197442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48201812-48202354 Neighboring gene Sharpr-MPRA regulatory region 9389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48228755-48229521 Neighboring gene uncharacterized LOC124904733 Neighboring gene EH domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48238171-48238671 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48249496-48249996 Neighboring gene NOP53 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 15394 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:48270445-48270705 Neighboring gene small nucleolar RNA, C/D box 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48284325-48284910 Neighboring gene selenoprotein W Neighboring gene ribosomal protein L23a pseudogene 80

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5S rRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables 5S rRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA binding HDA PubMed 
enables identical protein binding IDA
Inferred from Direct Assay
more info
PubMed 
enables p53 binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in DNA repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cellular response to hypoxia IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mitotic G2 DNA damage checkpoint signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of protein-containing complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of signal transduction by p53 class mediator IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription of nucleolar large rRNA by RNA polymerase I IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of proteasomal ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of protein K63-linked deubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in protein localization to nucleolus IEA
Inferred from Electronic Annotation
more info
 
involved_in protein localization to nucleoplasm IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in protein stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in rRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of RIG-I signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of aerobic respiration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of protein phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of signal transduction by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in ribosomal large subunit assembly IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in ribosomal large subunit assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in fibrillar center IDA
Inferred from Direct Assay
more info
PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
part_of rDNA heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
ribosome biogenesis protein NOP53
Names
glioma tumor suppressor candidate region gene 2 protein
p60
protein interacting with carboxyl terminus 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_015710.5NP_056525.2  ribosome biogenesis protein NOP53

    See identical proteins and their annotated locations for NP_056525.2

    Status: VALIDATED

    Source sequence(s)
    BC004229, BC006311, CX866974
    Consensus CDS
    CCDS12705.1
    UniProtKB/Swiss-Prot
    Q9BTC6, Q9HAX6, Q9NPP1, Q9NPR4, Q9NZM5, Q9UFI2
    UniProtKB/TrEMBL
    Q53YP0
    Related
    ENSP00000246802.4, ENST00000246802.10
    Conserved Domains (1) summary
    pfam07767
    Location:59445
    Nop53; Nop53 (60S ribosomal biogenesis)

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    47745546..47757058
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    50576356..50587868
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)