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

Gene ID: 84240, updated on 27-Nov-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, Nov 2024]
Expression
Ubiquitous expression in placenta (RPKM 8.9), appendix (RPKM 8.7) and 25 other tissues See more
Orthologs
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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: 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. 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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