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    ZCCHC9 zinc finger CCHC-type containing 9 [ Homo sapiens (human) ]

    Gene ID: 84240, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ZCCHC9provided by HGNC
    Official Full Name
    zinc finger CCHC-type containing 9provided by HGNC
    Primary source
    HGNC:HGNC:25424
    See related
    Ensembl:ENSG00000131732 MIM:620382; AllianceGenome:HGNC:25424
    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
    PPP1R41
    Summary
    Enables RNA binding activity. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in placenta (RPKM 8.9), appendix (RPKM 8.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZCCHC9 in Genome Data Viewer
    Location:
    5q14.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (81301587..81313297)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (81786162..81797883)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (80597406..80609116)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Ras protein specific guanine nucleotide releasing factor 2 Neighboring gene uncharacterized LOC124901017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22730 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:80564272-80565471 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:80565548-80566100 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:80566101-80566651 Neighboring gene CKMT2 antisense RNA 1 Neighboring gene MPRA-validated peak5313 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:80597135-80597924 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:80597925-80598714 Neighboring gene creatine kinase, mitochondrial 2 Neighboring gene acyl-CoA thioesterase 12 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:80728863-80729548 Neighboring gene NANOG hESC enhancer GRCh37_chr5:80746651-80747152 Neighboring gene single stranded DNA binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16141 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:80983594-80984094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16143 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16146 Neighboring gene CRISPRi-validated cis-regulatory element chr5.2009 Neighboring gene CRISPRi-validated cis-regulatory element chr5.2010 Neighboring gene uncharacterized LOC107986384

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. A nuclear localized protein ZCCHC9 is expressed in cerebral cortex and suppresses the MAPK signal pathway. Zhou A, et al. J Genet Genomics, 2008 Aug. PMID 18721783
    2. ZCCHC9 promotes proliferation and invasion of lung cancer through regulating the JNK pathway. Shi X, et al. J Cell Biochem, 2019 Jun. PMID 30644129
    3. ATRX proximal protein associations boast roles beyond histone deposition. Scott WA, et al. PLoS Genet, 2021 Nov. PMID 34780483, Free PMC Article
    4. Docking motif-guided mapping of the interactome of protein phosphatase-1. Hendrickx A, et al. Chem Biol, 2009 Apr 24. PMID 19389623
    5. A Role for Mitochondrial Translation in Promotion of Viability in K-Ras Mutant Cells. Martin TD, et al. Cell Rep, 2017 Jul 11. PMID 28700943, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Cytoplasmic ZCCHC9 could promote the proliferation and invasion of non-small cell lung cancer through the JNK pathway.
      Title: ZCCHC9 promotes proliferation and invasion of lung cancer through regulating the JNK pathway.
    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

    • DKFZp761J139

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    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
    zinc finger CCHC domain-containing protein 9
    Names
    protein phosphatase 1, regulatory subunit 41
    zinc finger, CCHC domain containing 9

    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_001131035.2 → NP_001124507.1  zinc finger CCHC domain-containing protein 9

      See identical proteins and their annotated locations for NP_001124507.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate splice site, which results in a shorter 5' UTR, as compared to variant 1.
      Source sequence(s)
      AC008411, AI961614, BC032736, BG776648, CB126982
      Consensus CDS
      CCDS4054.1
      UniProtKB/Swiss-Prot
      B2RAE7, Q8N567, Q9H027
      Related
      ENSP00000385047.3, ENST00000407610.8
      Conserved Domains (1) summary
      PTZ00368
      Location:130 → 229
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

    2. NM_001131036.2 → NP_001124508.1  zinc finger CCHC domain-containing protein 9

      See identical proteins and their annotated locations for NP_001124508.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an alternate splice site, which results in a shorter 5' UTR, as compared to variant 1.
      Source sequence(s)
      AC008411, AI961614, BC032736, BG776648, CN261947
      Consensus CDS
      CCDS4054.1
      UniProtKB/Swiss-Prot
      B2RAE7, Q8N567, Q9H027
      Related
      ENSP00000369546.5, ENST00000380199.9
      Conserved Domains (1) summary
      PTZ00368
      Location:130 → 229
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

    3. NM_032280.3 → NP_115656.1  zinc finger CCHC domain-containing protein 9

      See identical proteins and their annotated locations for NP_115656.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is the longest transcript. Variants 1-3 encode the same protein.
      Source sequence(s)
      AC008411, AI961614, AK314160, BC022799, BC032736, BG776648
      Consensus CDS
      CCDS4054.1
      UniProtKB/Swiss-Prot
      B2RAE7, Q8N567, Q9H027
      Related
      ENSP00000412637.2, ENST00000438268.2
      Conserved Domains (1) summary
      PTZ00368
      Location:130 → 229
      PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional

    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
      81301587..81313297
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417827.1 → XP_047273783.1  zinc finger CCHC domain-containing protein 9 isoform X1

      UniProtKB/Swiss-Prot
      B2RAE7, Q8N567, Q9H027

    2. XM_047417828.1 → XP_047273784.1  zinc finger CCHC domain-containing protein 9 isoform X1

      UniProtKB/Swiss-Prot
      B2RAE7, Q8N567, Q9H027
      Related
      ENSP00000254037.2, ENST00000254037.6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      81786162..81797883
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353682.1 → XP_054209657.1  zinc finger CCHC domain-containing protein 9 isoform X1

    2. XM_054353683.1 → XP_054209658.1  zinc finger CCHC domain-containing protein 9 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N567.2 GenPept UniProtKB/Swiss-Prot:Q8N567

    Gene LinkOut

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

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