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NOP16 NOP16 nucleolar protein [ Homo sapiens (human) ]

Gene ID: 51491, updated on 27-Nov-2024

Summary

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Official Symbol
NOP16provided by HGNC
Official Full Name
NOP16 nucleolar proteinprovided by HGNC
Primary source
HGNC:HGNC:26934
See related
Ensembl:ENSG00000048162 MIM:612861; AllianceGenome:HGNC:26934
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
HSPC111; HSPC185
Summary
This gene encodes a protein that is localized to the nucleolus. Expression of this gene is induced by estrogens and Myc protein and is a marker of poor patient survival in breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
Expression
Ubiquitous expression in colon (RPKM 17.7), appendix (RPKM 14.8) and 25 other tissues See more
Orthologs
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Genomic context

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See NOP16 in Genome Data Viewer
Location:
5q35.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (176383946..176388598, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (176928308..176932956, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (175810949..175815599, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene KIAA1191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16649 Neighboring gene ARF like GTPase 10 Neighboring gene microRNA 1271 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:175805661-175805825 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:175815238-175816437 Neighboring gene HIG1 hypoxia inducible domain family member 2A Neighboring gene clathrin light chain B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16652

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. Cancer-derived exosomal HSPC111 promotes colorectal cancer liver metastasis by reprogramming lipid metabolism in cancer-associated fibroblasts. Zhang C, et al. Cell Death Dis, 2022 Jan 13. PMID 35027547, Free PMC Article
  2. HSPC111 governs breast cancer growth by regulating ribosomal biogenesis. Zhang C, et al. Mol Cancer Res, 2014 Apr. PMID 24425784
  3. Elevated Expression of NOP16 as a Novel Prognostic Biomarker of Prostate Cancer. Yang T, et al. Ann Clin Lab Sci, 2023 Jul. PMID 37625836
  4. The estrogen and c-Myc target gene HSPC111 is over-expressed in breast cancer and associated with poor patient outcome. Butt AJ, et al. Breast Cancer Res, 2008. PMID 18373870, Free PMC Article
  5. NOP16 promotes hepatocellular carcinoma progression and triggers EMT through the Keap1-Nrf2 signaling pathway. Mu S, et al. Technol Health Care, 2024. PMID 38251077, Free PMC Article

See all (93) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NOP16 promotes hepatocellular carcinoma progression and triggers EMT through the Keap1-Nrf2 signaling pathway.
    Title: NOP16 promotes hepatocellular carcinoma progression and triggers EMT through the Keap1-Nrf2 signaling pathway.
  2. Elevated Expression of NOP16 as a Novel Prognostic Biomarker of Prostate Cancer.
    Title: Elevated Expression of NOP16 as a Novel Prognostic Biomarker of Prostate Cancer.
  3. Cancer-derived exosomal HSPC111 promotes colorectal cancer liver metastasis by reprogramming lipid metabolism in cancer-associated fibroblasts.
    Title: Cancer-derived exosomal HSPC111 promotes colorectal cancer liver metastasis by reprogramming lipid metabolism in cancer-associated fibroblasts.
  4. RNA 3'-phosphate cyclase (RTCD1/RTCA) interacted with HSPC111, and RTCD1 was involved in the HSPC111 multiprotein complex in regulating rRNA production and ribosomal biogenesis.
    Title: HSPC111 governs breast cancer growth by regulating ribosomal biogenesis.
  5. HSPC111 is an estrogen and c-Myc target gene that is over-expressed in breast cancer and is associated with an adverse patient outcome.
    Title: The estrogen and c-Myc target gene HSPC111 is over-expressed in breast cancer and associated with poor patient outcome.
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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
Process Evidence Code Pubs
involved_in ribosomal large subunit biogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
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
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
nucleolar protein 16
Names
HBV pre-S2 trans-regulated protein 3
NOP16 nucleolar protein homolog
hypothetical protein HSPC111
nucleolar protein 16 homolog

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_001256539.4 → NP_001243468.2  nucleolar protein 16 isoform 1

    See identical proteins and their annotated locations for NP_001243468.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF151875, BC019331, CB122385
    Consensus CDS
    CCDS78091.1
    UniProtKB/Swiss-Prot
    Q9Y3C1
    Related
    ENSP00000483001.1, ENST00000618911.4
    Conserved Domains (1) summary
    pfam09420
    Location:16 → 131
    Nop16; Ribosome biogenesis protein Nop16

  2. NM_001256540.4 → NP_001243469.2  nucleolar protein 16 isoform 2

    See identical proteins and their annotated locations for NP_001243469.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The resulting isoform (2) is shorter than isoform 1.
    Source sequence(s)
    BC019331
    Consensus CDS
    CCDS58991.2
    UniProtKB/TrEMBL
    A0A0C4DGU5
    Related
    ENSP00000479445.1, ENST00000621444.4
    Conserved Domains (1) summary
    pfam09420
    Location:9 → 132
    Nop16; Ribosome biogenesis protein Nop16

  3. NM_001291305.3 → NP_001278234.1  nucleolar protein 16 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses alternate splice sites at two exons and initiates translation at an alternate start codon, compared to variant 1. The resulting isoform (4) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC019331, BU741840
    UniProtKB/TrEMBL
    Q9P0T8
    Conserved Domains (1) summary
    pfam09420
    Location:60 → 119
    Nop16; Ribosome biogenesis protein Nop16

  4. NM_001291307.3 → NP_001278236.1  nucleolar protein 16 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting isoform (6) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC019331, BU594763
    UniProtKB/TrEMBL
    D6RIC3
    Related
    ENSP00000427489.1, ENST00000509257.1
    Conserved Domains (1) summary
    pfam09420
    Location:9 → 132
    Nop16; Ribosome biogenesis protein Nop16

  5. NM_001291308.3 → NP_001278237.1  nucleolar protein 16 isoform 7

    See identical proteins and their annotated locations for NP_001278237.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an internal coding exon, which results in a frameshift, and uses an alternate splice site in the 3' terminal exon, compared to variant 1. The resulting isoform (7) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AF151875, BC019331, BM826387
    UniProtKB/Swiss-Prot
    Q9Y3C1
    Conserved Domains (1) summary
    pfam09420
    Location:16 → 63
    Nop16; Ribosome biogenesis protein Nop16

  6. NM_001317975.2 → NP_001304904.1  nucleolar protein 16 isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) contains an additional segment in the 5' region and uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It initiates translation at an alternate start codon. The resulting isoform (8) has distinct N- and C-termini and is shorter than isoform 1.
    Source sequence(s)
    AF161460, BP234677
    UniProtKB/Swiss-Prot
    Q9Y3C1
    Conserved Domains (1) summary
    pfam09420
    Location:34 → 148
    Nop16; Ribosome biogenesis protein Nop16

  7. NM_016391.8 → NP_057475.2  nucleolar protein 16 isoform 3

    See identical proteins and their annotated locations for NP_057475.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AF161460, BC019331
    Consensus CDS
    CCDS43403.1
    UniProtKB/Swiss-Prot
    B4DV13, D6RGD3, Q05D05, Q6IAI6, Q6PIM0, Q8IXL5, Q9Y3C1
    Related
    ENSP00000480832.2, ENST00000614830.5
    Conserved Domains (1) summary
    pfam09420
    Location:20 → 153
    Nop16; Ribosome biogenesis protein Nop16

RNA

  1. NR_134316.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) contains an alternate segment in the 5' region and uses two alternate splice sites compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 8, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF151875, AF161460, AW837047

  2. NR_134318.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) contains an alternate internal exon and uses an alternate splice site in the 3' terminal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC138956, BC019331, HY064071

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    176383946..176388598 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    176928308..176932956 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001291306.1: Suppressed sequence

    Description
    NM_001291306.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y3C1.2 GenPept UniProtKB/Swiss-Prot:Q9Y3C1

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