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    NOP16 NOP16 nucleolar protein [ Homo sapiens (human) ]

    Gene ID: 51491, updated on 2-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
    mouse all
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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 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?
    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)

    Genotypes

    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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