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NOP2 NOP2 nucleolar protein [ Homo sapiens (human) ]

Gene ID: 4839, updated on 7-Apr-2024

Summary

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Official Symbol
NOP2provided by HGNC
Official Full Name
NOP2 nucleolar proteinprovided by HGNC
Primary source
HGNC:HGNC:7867
See related
Ensembl:ENSG00000111641 MIM:164031; AllianceGenome:HGNC:7867
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
NOL1; p120; NSUN1; NOP120
Summary
Enables RNA binding activity. Involved in positive regulation of cell population proliferation; regulation of signal transduction by p53 class mediator; and ribosomal large subunit assembly. Located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 12.9), bone marrow (RPKM 12.9) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
12p13.31
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6556871..6568291, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6567230..6578651, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6666037..6677457, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6643463-6644236 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6645785-6646558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5866 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase Neighboring gene intermediate filament family orphan 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6658582-6659082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6659083-6659583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6660263-6660762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6661035-6661552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6663184-6663684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6663685-6664185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4171 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:6677307-6677928 Neighboring gene Sharpr-MPRA regulatory region 3501 Neighboring gene chromodomain helicase DNA binding protein 4 Neighboring gene small Cajal body-specific RNA 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6705357-6705858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6705859-6706358 Neighboring gene uncharacterized LOC124902867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5869

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. Human NOP2/NSUN1 regulates ribosome biogenesis through non-catalytic complex formation with box C/D snoRNPs. Liao H, et al. Nucleic Acids Res, 2022 Oct 14. PMID 36161484, Free PMC Article
  2. Upregulated expression of NOP2 predicts worse prognosis of gastric adenocarcinoma by promoting tumor growth. Feng J, et al. Saudi J Gastroenterol, 2022 Sep-Oct. PMID 35381832, Free PMC Article
  3. Telomerase activates transcription of cyclin D1 gene through an interaction with NOL1. Hong J, et al. J Cell Sci, 2016 Apr 15. PMID 26906424
  4. Identification and characterization of a human proliferation-associated nucleolar antigen with a molecular weight of 120,000 expressed in early G1 phase. Freeman JW, et al. Cancer Res, 1988 Mar 1. PMID 3422591
  5. Cloning of the cDNA and sequence of the human proliferating-cell nucleolar protein P120. Fonagy A, et al. Cancer Commun, 1989. PMID 2576976

See all (188) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NOP2-mediated m5C methylation of XPD is associated with hepatocellular carcinoma progression.
    Title: NOP2-mediated m5C methylation of XPD is associated with hepatocellular carcinoma progression.
  2. Human NOP2/NSUN1 regulates ribosome biogenesis through non-catalytic complex formation with box C/D snoRNPs.
    Title: Human NOP2/NSUN1 regulates ribosome biogenesis through non-catalytic complex formation with box C/D snoRNPs.
  3. Upregulated expression of NOP2 predicts worse prognosis of gastric adenocarcinoma by promoting tumor growth.
    Title: Upregulated expression of NOP2 predicts worse prognosis of gastric adenocarcinoma by promoting tumor growth.
  4. Long noncoding RNA LINC00963 induces NOP2 expression by sponging tumor suppressor miR-542-3p to promote metastasis in prostate cancer.
    Title: Long noncoding RNA LINC00963 induces NOP2 expression by sponging tumor suppressor miR-542-3p to promote metastasis in prostate cancer.
  5. Mechanistically, NOP2 associates with HIV-1 5' LTR, interacts with HIV-1 TAR RNA by competing with HIV-1 Tat protein, as well as contributes to TAR m5C methylation. RNA MTase catalytic domain (MTD) of NOP2 mediates its competition with Tat and binding with TAR. Overall, these findings verified that NOP2 suppresses HIV-1 transcription and promotes viral latency.
    Title: Nucleolar protein NOP2/NSUN1 suppresses HIV-1 transcription and promotes viral latency by competing with Tat for TAR binding and methylation.
  6. NOL1 represents a new route by which telomerase activates transcription of cyclin D1 gene, thus maintaining cell proliferation capacity
    Title: Telomerase activates transcription of cyclin D1 gene through an interaction with NOL1.
  7. p120 has an rRNA:5-Methylcytosine-Methyltransferase activity.
    Title: Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120.
  8. Findings suggest a newly discovered role of Nop2 in both mature neurons and in cells possibly involved in the regeneration of nervous tissue
    Title: Nop2 is expressed during proliferation of neural stem cells and in adult mouse and human brain.
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

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

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

  • MGC117384, MGC149287, MGC149288

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables rRNA (cytosine-C5-)-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in maturation of LSU-rRNA IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cell population proliferation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in rRNA base methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of signal transduction by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ribosomal large subunit assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleolus HDA PubMed 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase
Names
NOL1/NOP2/Sun domain family, member 1
NOP2 nucleolar protein homolog
nucleolar protein 1, 120kDa
nucleolar protein 2 homolog
proliferating-cell nucleolar antigen p120
proliferation-associated nucleolar protein p120
putative ribosomal RNA methyltransferase NOP2

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_001033714.3 → NP_001028886.1  probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase isoform 1

    See identical proteins and their annotated locations for NP_001028886.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    BC065257, DC316656
    Consensus CDS
    CCDS44811.1
    UniProtKB/Swiss-Prot
    P46087
    Related
    ENSP00000382392.2, ENST00000399466.6
    Conserved Domains (3) summary
    COG0144
    Location:253 → 582
    RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]
    pfam01189
    Location:373 → 581
    Nol1_Nop2_Fmu; 16S rRNA methyltransferase RsmF
    pfam17125
    Location:295 → 369
    Methyltr_RsmF_N; N-terminal domain of 16S rRNA methyltransferase RsmF

  2. NM_001258308.2 → NP_001245237.1  probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase isoform 2

    See identical proteins and their annotated locations for NP_001245237.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is longer than isoform 1.
    Source sequence(s)
    BC128183, CX868076
    Consensus CDS
    CCDS58203.1
    UniProtKB/Swiss-Prot
    A1A4Z3, B3KPD6, P46087, Q05BA7, Q0P5S5, Q3KQS4, Q58F30
    Related
    ENSP00000313272.6, ENST00000322166.10
    Conserved Domains (3) summary
    COG0144
    Location:257 → 586
    RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]
    pfam01189
    Location:377 → 585
    Nol1_Nop2_Fmu; 16S rRNA methyltransferase RsmF
    pfam17125
    Location:299 → 373
    Methyltr_RsmF_N; N-terminal domain of 16S rRNA methyltransferase RsmF

  3. NM_001258309.2 → NP_001245238.1  probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase isoform 3

    See identical proteins and their annotated locations for NP_001245238.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate exon and uses an alternate splice site in the coding region, but maintians the reading frame, compared to variant 1. The encoded isoform (3) is longer than isoform 1.
    Source sequence(s)
    BC106072, DC316656
    Consensus CDS
    CCDS58204.1
    UniProtKB/Swiss-Prot
    P46087
    Related
    ENSP00000371858.3, ENST00000382421.7
    Conserved Domains (1) summary
    COG0144
    Location:290 → 619
    RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

  4. NM_001258310.2 → NP_001245239.1  probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase isoform 4

    See identical proteins and their annotated locations for NP_001245239.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate internal exon in the 3' region, which results in a frameshift, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC082985, DC316656
    Consensus CDS
    CCDS58202.1
    UniProtKB/Swiss-Prot
    P46087
    Related
    ENSP00000439422.1, ENST00000545200.5
    Conserved Domains (3) summary
    TIGR00446
    Location:308 → 582
    nop2p; NOL1/NOP2/sun family putative RNA methylase
    pfam01189
    Location:373 → 581
    Nol1_Nop2_Fmu; 16S rRNA methyltransferase RsmF
    pfam17125
    Location:295 → 369
    Methyltr_RsmF_N; N-terminal domain of 16S rRNA methyltransferase RsmF

  5. NM_006170.4 → NP_006161.2  probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase isoform 1

    See identical proteins and their annotated locations for NP_006161.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AK056208
    Consensus CDS
    CCDS44811.1
    UniProtKB/Swiss-Prot
    P46087
    Related
    ENSP00000443150.1, ENST00000541778.5
    Conserved Domains (3) summary
    COG0144
    Location:253 → 582
    RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]
    pfam01189
    Location:373 → 581
    Nol1_Nop2_Fmu; 16S rRNA methyltransferase RsmF
    pfam17125
    Location:295 → 369
    Methyltr_RsmF_N; N-terminal domain of 16S rRNA methyltransferase RsmF

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6556871..6568291 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6567230..6578651 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P46087.2 GenPept UniProtKB/Swiss-Prot:P46087

Gene LinkOut

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