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    ZCCHC8 zinc finger CCHC-type containing 8 [ Homo sapiens (human) ]

    Gene ID: 55596, updated on 14-Nov-2024

    Summary

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    Official Symbol
    ZCCHC8provided by HGNC
    Official Full Name
    zinc finger CCHC-type containing 8provided by HGNC
    Primary source
    HGNC:HGNC:25265
    See related
    Ensembl:ENSG00000033030 MIM:616381; AllianceGenome:HGNC:25265
    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
    PFBMFT5
    Summary
    This gene encodes a scaffold protein which serves as an assessory factor to the nuclear RNA exosome complex. The encoded protein forms a trimeric human nuclear exosome targeting (NEXT) complex, together with hMTR4 and the RNA-binding factor RBM7 which promotes the exosomal degradation of non-coding promoter-upstream transcripts, enhancer RNAs and 3'-extended products of histone- and small nuclear RNA transcription. This complex is also thought to recruit the exosome to degrade intronic RNAs via its interaction with both the exosome and the spliceosome. It contains both an N-terminal zinc-knuckle domain and a C-terminal proline-rich domain. [provided by RefSeq, Apr 2017]
    Expression
    Ubiquitous expression in bone marrow (RPKM 13.2), testis (RPKM 5.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZCCHC8 in Genome Data Viewer
    Location:
    12q24.31
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (122471600..122500932, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (122467426..122496741, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (122956147..122985479, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene CAP-Gly domain containing linker protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122869287-122869920 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:122870555-122871186 Neighboring gene ribosomal protein L21 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122885121-122885806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122885807-122886492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7219 Neighboring gene CLIP1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7221 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122916171-122916672 Neighboring gene Sharpr-MPRA regulatory region 9757 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122927953-122928453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7226 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122984447-122985138 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122985139-122985832 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122985833-122986524 Neighboring gene MPRA-validated peak2019 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7231 Neighboring gene arginine and serine rich coiled-coil 2 Neighboring gene kinetochore associated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7232

    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. The regulation and functions of the nuclear RNA exosome complex. Kilchert C, et al. Nat Rev Mol Cell Biol, 2016 Apr. PMID 26726035
    2. Expanding the understanding of telomere biology disorder with reports from two families harboring variants in ZCCHC8 and TERC. Nitschke NJ, et al. Clin Genet, 2024 Aug. PMID 38606545
    3. Identification of ZCCHC8 as fusion partner of ROS1 in a case of congenital glioblastoma multiforme with a t(6;12)(q21;q24.3). Coccé MC, et al. Genes Chromosomes Cancer, 2016 Sep. PMID 27121553
    4. ZCCHC8, the nuclear exosome targeting component, is mutated in familial pulmonary fibrosis and is required for telomerase RNA maturation. Gable DL, et al. Genes Dev, 2019 Oct 1. PMID 31488579, Free PMC Article
    5. p38MAPK/MK2-mediated phosphorylation of RBM7 regulates the human nuclear exosome targeting complex. Tiedje C, et al. RNA, 2015 Feb. PMID 25525152, Free PMC Article

    See all (104) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expanding the understanding of telomere biology disorder with reports from two families harboring variants in ZCCHC8 and TERC.
      Title: Expanding the understanding of telomere biology disorder with reports from two families harboring variants in ZCCHC8 and TERC.
    2. Data show that the nuclear exosome adaptors nuclear valosin-containing protein-like (NVL) and zinc finger, CCHC domain containing 8 protein (ZCCHC8) bind the Mtr4 exosome RNA helicase (MTR4) KOW domain on a surface.
      Title: The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs.
    3. ZCCHC8 associated with telomerase RNA and was required for telomerase function
      Title: ZCCHC8, the nuclear exosome targeting component, is mutated in familial pulmonary fibrosis and is required for telomerase RNA maturation.
    4. a proline-rich segment of ZCCHC8 as the interaction site for the RNA-recognition motif (RRM) of RBM7 and present the crystal structure of the corresponding complex at 2.0 A resolution.
      Title: Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors.
    5. ZCCHC8-ROS1 fusion is associated with congenital glioblastoma multiforme.
      Title: Identification of ZCCHC8 as fusion partner of ROS1 in a case of congenital glioblastoma multiforme with a t(6;12)(q21;q24.3).
    6. Zcchc8 is a glycogen synthase kinase-3 substrate with a role in RNA metabolism
      Title: Zcchc8 is a glycogen synthase kinase-3 substrate that interacts with RNA-binding proteins.
    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

    Clone Names

    • DKFZp434E2220

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in snRNA catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of TRAMP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    NOT located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc finger CCHC domain-containing protein 8
    Names
    TRAMP-like complex RNA-binding factor ZCCHC8
    zinc finger, CCHC domain containing 8

    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.

    Genomic

    1. NG_053194.1 RefSeqGene

      Range
      5142..34474
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001350935.2 → NP_001337864.1  zinc finger CCHC domain-containing protein 8 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks three alternate exons in the 5' coding region, compared to variant (1). The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC127002
      Conserved Domains (1) summary
      smart00581
      Location:206 → 258
      PSP; proline-rich domain in spliceosome associated proteins

    2. NM_001350936.2 → NP_001337865.1  zinc finger CCHC domain-containing protein 8 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC127002
      Conserved Domains (2) summary
      smart00581
      Location:184 → 236
      PSP; proline-rich domain in spliceosome associated proteins
      pfam00098
      Location:128 → 145
      zf-CCHC; Zinc knuckle

    3. NM_001350937.2 → NP_001337866.1  zinc finger CCHC domain-containing protein 8 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1. Both variants 4 and 5 encode the same isoform (4).
      Source sequence(s)
      AC127002
      Consensus CDS
      CCDS86340.1
      UniProtKB/TrEMBL
      A8K559
      Related
      ENSP00000438993.1, ENST00000543897.5
      Conserved Domains (1) summary
      smart00581
      Location:45 → 97
      PSP; proline-rich domain in spliceosome associated proteins

    4. NM_001350938.2 → NP_001337867.1  zinc finger CCHC domain-containing protein 8 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1. Both variants 4 and 5 encode the same isoform (4).
      Source sequence(s)
      AC127002
      Consensus CDS
      CCDS86340.1
      UniProtKB/TrEMBL
      A8K559
      Conserved Domains (1) summary
      smart00581
      Location:45 → 97
      PSP; proline-rich domain in spliceosome associated proteins

    5. NM_017612.5 → NP_060082.2  zinc finger CCHC domain-containing protein 8 isoform 1

      See identical proteins and their annotated locations for NP_060082.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC127002, AK074638, BE048845
      Consensus CDS
      CCDS91763.1
      UniProtKB/Swiss-Prot
      Q6NZY4, Q7L2P6, Q8N2K5, Q96SK7, Q9NSS2, Q9NSS3
      Related
      ENSP00000488055.1, ENST00000633063.3
      Conserved Domains (2) summary
      smart00581
      Location:283 → 335
      PSP; proline-rich domain in spliceosome associated proteins
      pfam00098
      Location:227 → 244
      zf-CCHC; Zinc knuckle

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      122471600..122500932 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429117.1 → XP_047285073.1  zinc finger CCHC domain-containing protein 8 isoform X1

    2. XM_047429118.1 → XP_047285074.1  zinc finger CCHC domain-containing protein 8 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      122467426..122496741 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372493.1 → XP_054228468.1  zinc finger CCHC domain-containing protein 8 isoform X1

    2. XM_054372494.1 → XP_054228469.1  zinc finger CCHC domain-containing protein 8 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NZY4.2 GenPept UniProtKB/Swiss-Prot:Q6NZY4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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