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    ZC3H18 zinc finger CCCH-type containing 18 [ Homo sapiens (human) ]

    Gene ID: 124245, updated on 3-Nov-2024

    Summary

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    Official Symbol
    ZC3H18provided by HGNC
    Official Full Name
    zinc finger CCCH-type containing 18provided by HGNC
    Primary source
    HGNC:HGNC:25091
    See related
    Ensembl:ENSG00000158545 AllianceGenome:HGNC:25091
    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
    NHN1
    Summary
    Enables mRNA cap binding complex binding activity and protein-macromolecule adaptor activity. Involved in RNA destabilization. Located in nuclear speck. Part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 13.0), spleen (RPKM 10.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZC3H18 in Genome Data Viewer
    Location:
    16q24.2
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (88570403..88631964)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (94638009..94699796)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (88636811..88698372)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein, FOG family member 1 Neighboring gene ZFPM1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88591868-88592455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88592456-88593042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88593270-88594010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88594011-88594750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88599832-88600392 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:88600393-88600954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88606102-88606704 Neighboring gene ZC3H18 antisense RNA 1 (head to head) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11355 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11356 Neighboring gene Sharpr-MPRA regulatory region 13594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11357 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:88673559-88674059 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88676553-88677498 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88694002-88694718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88694719-88695433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88701182-88702111 Neighboring gene uncharacterized LOC124903755 Neighboring gene interleukin 17C

    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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    Related articles in PubMed

    1. ZC3H18 specifically binds and activates the BRCA1 promoter to facilitate homologous recombination in ovarian cancer. Kanakkanthara A, et al. Nat Commun, 2019 Oct 11. PMID 31604914, Free PMC Article
    2. Control of pre-mRNA splicing by the general splicing factors PUF60 and U2AF(65). Hastings ML, et al. PLoS One, 2007 Jun 20. PMID 17579712, Free PMC Article
    3. NCBP3 positively impacts mRNA biogenesis. Dou Y, et al. Nucleic Acids Res, 2020 Oct 9. PMID 32960271, Free PMC Article
    4. Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate. Giacometti S, et al. Cell Rep, 2017 Mar 14. PMID 28297668, Free PMC Article
    5. Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts. Meola N, et al. Mol Cell, 2016 Nov 3. PMID 27871484

    See all (104) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NCBP3 positively impacts mRNA biogenesis.
      Title: NCBP3 positively impacts mRNA biogenesis.
    2. ZC3H18 copy number losses could contribute to homologous recombination defects in high-grade serous ovarian cancers.
      Title: ZC3H18 specifically binds and activates the BRCA1 promoter to facilitate homologous recombination in ovarian cancer.
    3. examination of ZC3H18 function, by genome-wide analyses, demonstrated its impact on transcription of a subset of protein-coding genes. This activity requires the CBC-interacting domain of the protein, with some genes being also dependent on the NEXT- and/or histone-interacting domains.
      Title: Characterizing ZC3H18, a Multi-domain Protein at the Interface of RNA Production and Destruction Decisions.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    Clone Names

    • FLJ22664, FLJ34530, FLJ36075

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA cap binding complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-macromolecule adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA destabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc finger CCCH domain-containing protein 18
    Names
    conserved nuclear protein NHN1
    nuclear protein NHN1

    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_001294340.2 → NP_001281269.1  zinc finger CCCH domain-containing protein 18 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK026317, AK300254, BC001584, CN299707, DA313229, DB007291
      Consensus CDS
      CCDS73924.1
      UniProtKB/TrEMBL
      B4DTK7, E7ERS3
      Related
      ENSP00000416951.2, ENST00000452588.6
      Conserved Domains (1) summary
      COG5271
      Location:17 → 187
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

    2. NM_144604.4 → NP_653205.3  zinc finger CCCH domain-containing protein 18 isoform 2

      See identical proteins and their annotated locations for NP_653205.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AK026317, BC001584, CN299704, DA313229
      Consensus CDS
      CCDS10967.1
      UniProtKB/Swiss-Prot
      Q86VM9, Q96DG4, Q96MP7
      UniProtKB/TrEMBL
      B4DTK7
      Related
      ENSP00000301011.5, ENST00000301011.10
      Conserved Domains (1) summary
      smart00356
      Location:215 → 243
      ZnF_C3H1; zinc finger

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      88570403..88631964
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011522863.2 → XP_011521165.1  zinc finger CCCH domain-containing protein 18 isoform X2

      UniProtKB/TrEMBL
      B4DTK7
      Conserved Domains (1) summary
      COG5271
      Location:17 → 187
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

    2. XM_047433612.1 → XP_047289568.1  zinc finger CCCH domain-containing protein 18 isoform X4

    3. XM_047433609.1 → XP_047289565.1  zinc finger CCCH domain-containing protein 18 isoform X1

    4. XM_047433613.1 → XP_047289569.1  zinc finger CCCH domain-containing protein 18 isoform X5

    5. XM_047433611.1 → XP_047289567.1  zinc finger CCCH domain-containing protein 18 isoform X3

    6. XM_047433614.1 → XP_047289570.1  zinc finger CCCH domain-containing protein 18 isoform X6

    7. XM_017022934.2 → XP_016878423.1  zinc finger CCCH domain-containing protein 18 isoform X8

    8. XM_047433615.1 → XP_047289571.1  zinc finger CCCH domain-containing protein 18 isoform X7

    9. XM_047433616.1 → XP_047289572.1  zinc finger CCCH domain-containing protein 18 isoform X9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      94638009..94699796
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379588.1 → XP_054235563.1  zinc finger CCCH domain-containing protein 18 isoform X2

    2. XM_054379590.1 → XP_054235565.1  zinc finger CCCH domain-containing protein 18 isoform X4

    3. XM_054379587.1 → XP_054235562.1  zinc finger CCCH domain-containing protein 18 isoform X1

    4. XM_054379591.1 → XP_054235566.1  zinc finger CCCH domain-containing protein 18 isoform X5

    5. XM_054379589.1 → XP_054235564.1  zinc finger CCCH domain-containing protein 18 isoform X3

    6. XM_054379592.1 → XP_054235567.1  zinc finger CCCH domain-containing protein 18 isoform X6

    7. XM_054379594.1 → XP_054235569.1  zinc finger CCCH domain-containing protein 18 isoform X8

    8. XM_054379593.1 → XP_054235568.1  zinc finger CCCH domain-containing protein 18 isoform X7

    9. XM_054379595.1 → XP_054235570.1  zinc finger CCCH domain-containing protein 18 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86VM9.2 GenPept UniProtKB/Swiss-Prot:Q86VM9

    Gene LinkOut

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