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    KHNYN KH and NYN domain containing [ Homo sapiens (human) ]

    Gene ID: 23351, updated on 3-Apr-2024

    Summary

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    Official Symbol
    KHNYNprovided by HGNC
    Official Full Name
    KH and NYN domain containingprovided by HGNC
    Primary source
    HGNC:HGNC:20166
    See related
    Ensembl:ENSG00000100441 MIM:619579; AllianceGenome:HGNC:20166
    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
    KIAA0323
    Summary
    The protein encoded by this gene contains a ribonuclease NYN domain and belongs to the N4BP1 family. The protein is a cofactor for the zinc finger antiviral protein (ZAP protein) which targets viral RNA for degradation and restricts SARS-CoV-2 infection. [provided by RefSeq, Sep 2021]
    Expression
    Ubiquitous expression in stomach (RPKM 18.8), small intestine (RPKM 18.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KHNYN in Genome Data Viewer
    Location:
    14q12
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (24423165..24441843)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (18621854..18640575)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (24898492..24911049)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5642 Neighboring gene NYN domain and retroviral integrase containing Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:24899891-24900454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:24900455-24901016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:24901017-24901578 Neighboring gene cerebellin 3 precursor Neighboring gene uncharacterized LOC101927045 Neighboring gene short chain dehydrogenase/reductase family 39U member 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:24949129-24949670 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:24976080-24977279 Neighboring gene chymase 1

    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. SARS-CoV-2 Is Restricted by Zinc Finger Antiviral Protein despite Preadaptation to the Low-CpG Environment in Humans. Nchioua R, et al. mBio, 2020 Oct 16. PMID 33067384, Free PMC Article
    2. KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides. Ficarelli M, et al. Elife, 2019 Jul 9. PMID 31284899, Free PMC Article
    3. CGIN1: a retroviral contribution to mammalian genomes. Marco A, et al. Mol Biol Evol, 2009 Oct. PMID 19561090
    4. CUBAN, a Case Study of Selective Binding: Structural Details of the Discrimination between Ubiquitin and NEDD8. Santonico E, et al. Int J Mol Sci, 2019 Mar 8. PMID 30857167, Free PMC Article
    5. Selectivity of the CUBAN domain in the recognition of ubiquitin and NEDD8. Castagnoli L, et al. FEBS J, 2019 Feb. PMID 30659753

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Crystallization and biochemical studies of the NYN domain of human KHNYN.
      Title: Crystallization and biochemical studies of the NYN domain of human KHNYN.
    2. KHNYN as a novel cofactor for ZAP to target CpG-containing retroviral RNA for degradation.
      Title: KHNYN is essential for the zinc finger antiviral protein (ZAP) to restrict HIV-1 containing clustered CpG dinucleotides.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
    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

    EBI GWAS Catalog

    Description
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0323

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    is_active_in cytoplasmic ribonucleoprotein granule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein KHNYN

    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_034018.2 RefSeqGene

      Range
      11791..23680
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001290256.2 → NP_001277185.1  protein KHNYN isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded protein (isoform 2) has a longer N-terminus, compared to isoform 1.
      Source sequence(s)
      AA493312, AB002321, AL132800, BX161465
      UniProtKB/TrEMBL
      A8K6L5
      Conserved Domains (1) summary
      pfam11977
      Location:477 → 630
      RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

    2. NM_001290257.2 → NP_001277186.1  protein KHNYN isoform 1

      See identical proteins and their annotated locations for NP_001277186.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same protein (isoform 1).
      Source sequence(s)
      AA493312, AB002321, AK291680, AL132800, BX161465
      Consensus CDS
      CCDS32058.1
      UniProtKB/Swiss-Prot
      O15037, Q86TZ6, Q8IUQ2, Q96BA9
      UniProtKB/TrEMBL
      A8K6L5
      Related
      ENSP00000451106.1, ENST00000556842.5
      Conserved Domains (1) summary
      pfam11977
      Location:436 → 589
      RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

    3. NM_015299.3 → NP_056114.1  protein KHNYN isoform 1

      See identical proteins and their annotated locations for NP_056114.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1. Variants 1 and 3 encode the same protein.
      Source sequence(s)
      AL132800, BC015780, BX161465, CB115247, DA674601
      Consensus CDS
      CCDS32058.1
      UniProtKB/Swiss-Prot
      O15037, Q86TZ6, Q8IUQ2, Q96BA9
      UniProtKB/TrEMBL
      A8K6L5
      Related
      ENSP00000450799.1, ENST00000553935.6
      Conserved Domains (1) summary
      pfam11977
      Location:436 → 589
      RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      24423165..24441843
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536590.3 → XP_011534892.1  protein KHNYN isoform X1

      UniProtKB/TrEMBL
      A8K6L5
      Conserved Domains (1) summary
      pfam11977
      Location:479 → 632
      RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

    2. XM_047431169.1 → XP_047287125.1  protein KHNYN isoform X4

    3. XM_047431168.1 → XP_047287124.1  protein KHNYN isoform X3

    4. XM_047431167.1 → XP_047287123.1  protein KHNYN isoform X3

    5. XM_005267474.6 → XP_005267531.1  protein KHNYN isoform X2

      See identical proteins and their annotated locations for XP_005267531.1

      UniProtKB/Swiss-Prot
      O15037, Q86TZ6, Q8IUQ2, Q96BA9
      UniProtKB/TrEMBL
      A8K6L5
      Conserved Domains (1) summary
      pfam11977
      Location:436 → 589
      RNase_Zc3h12a; Zc3h12a-like Ribonuclease NYN domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      18621854..18640575
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375713.1 → XP_054231688.1  protein KHNYN isoform X1

    2. XM_054375716.1 → XP_054231691.1  protein KHNYN isoform X3

    3. XM_054375715.1 → XP_054231690.1  protein KHNYN isoform X3

    4. XM_054375717.1 → XP_054231692.1  protein KHNYN isoform X4

    5. XM_054375714.1 → XP_054231689.1  protein KHNYN isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15037.3 GenPept UniProtKB/Swiss-Prot:O15037

    Gene LinkOut

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