NOP2 NOP2 nucleolar protein [Homo sapiens (human)] - Gene

Summary

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 rRNA (cytosine-C5-)-methyltransferase activity. Involved in positive regulation of cell population proliferation; regulation of signal transduction by p53 class mediator; and ribosome biogenesis. Located in nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
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

Location:: 12p13.31

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (6556871..6568291, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (6567230..6578651, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (6666037..6677457, complement)

Chromosome 12 - NC_000012.12 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?

NOP2 facilitates EZH2-mediated epithelial-mesenchymal transition by enhancing EZH2 mRNA stability via m5C methylation in lung cancer progression.
Title: NOP2 facilitates EZH2-mediated epithelial-mesenchymal transition by enhancing EZH2 mRNA stability via m5C methylation in lung cancer progression.
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.
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.
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.
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.
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.
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.
p120 has an rRNA:5-Methylcytosine-Methyltransferase activity.
Title: Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120.
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.

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Phenotypes

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-15438 (e-PCR)
- UniSTS:75552

RH125 (e-PCR)
- UniSTS:82479

D12S1466 (e-PCR)
- UniSTS:24641

RH64827 (e-PCR)
- UniSTS:78038

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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
enables rRNA (cytosine-C5-)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables rRNA (cytosine-C5-)-methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed

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 rRNA processing	IDA Inferred from Direct Assay 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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ribosomal large subunit biogenesis	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in nucleolus	HDA more info	PubMed
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	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: 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; probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase; 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)

NM_001033714.3 → NP_001028886.1 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
NM_001258308.2 → NP_001245237.1 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
NM_001258309.2 → NP_001245238.1 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]
NM_001258310.2 → NP_001245239.1 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
NM_006170.4 → NP_006161.2 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