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

Gene ID: 55596, updated on 27-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
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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
  • 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

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