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

    Gene ID: 55596, updated on 5-May-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See ZCCHC8 in Genome Data Viewer
    Location:
    12q24.31
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (122471600..122500932, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (122467426..122496741, complement)
    105.20220307 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 RNA processing 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

    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)

    NEW Try the new Transcript table

    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_001350935.2NP_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:206258
      PSP; proline-rich domain in spliceosome associated proteins
    2. NM_001350936.2NP_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:184236
      PSP; proline-rich domain in spliceosome associated proteins
      pfam00098
      Location:128145
      zf-CCHC; Zinc knuckle
    3. NM_001350937.2NP_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:4597
      PSP; proline-rich domain in spliceosome associated proteins
    4. NM_001350938.2NP_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:4597
      PSP; proline-rich domain in spliceosome associated proteins
    5. NM_017612.5NP_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:283335
      PSP; proline-rich domain in spliceosome associated proteins
      pfam00098
      Location:227244
      zf-CCHC; Zinc knuckle

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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_047429117.1XP_047285073.1  zinc finger CCHC domain-containing protein 8 isoform X1

    2. XM_047429118.1XP_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_054372493.1XP_054228468.1  zinc finger CCHC domain-containing protein 8 isoform X1

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