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    ZNHIT6 zinc finger HIT-type containing 6 [ Homo sapiens (human) ]

    Gene ID: 54680, updated on 5-Mar-2024

    Summary

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    Official Symbol
    ZNHIT6provided by HGNC
    Official Full Name
    zinc finger HIT-type containing 6provided by HGNC
    Primary source
    HGNC:HGNC:26089
    See related
    Ensembl:ENSG00000117174 MIM:620473; AllianceGenome:HGNC:26089
    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
    BCD1; C1orf181; NY-BR-75
    Summary
    Enables ATPase binding activity; TFIID-class transcription factor complex binding activity; and identical protein binding activity. Involved in box C/D snoRNP assembly; protein complex oligomerization; and snoRNA localization. Located in extracellular exosome. Part of pre-snoRNP complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in lymph node (RPKM 2.7), endometrium (RPKM 2.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p22.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (85649417..85708433, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (85490231..85549278, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (86115100..86174116, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD81 Neighboring gene Sharpr-MPRA regulatory region 8792 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:86072656-86073855 Neighboring gene uncharacterized LOC112268231 Neighboring gene Sharpr-MPRA regulatory region 3870 Neighboring gene uncharacterized LOC107985057 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_9316 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:86157154-86157654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:86157655-86158155 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:86173373-86174206 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:86174207-86175039 Neighboring gene uncharacterized LOC105378823 Neighboring gene collagen type XXIV alpha 1 chain Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_9389 Neighboring gene RNA, 5S ribosomal pseudogene 51

    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. Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control. Bizarro J, et al. J Cell Biol, 2014 Nov 24. PMID 25404746, Free PMC Article
    2. Humoral immunity to human breast cancer: antigen definition and quantitative analysis of mRNA expression. Scanlan MJ, et al. Cancer Immun, 2001 Mar 30. PMID 12747765
    3. A dynamic scaffold of pre-snoRNP factors facilitates human box C/D snoRNP assembly. McKeegan KS, et al. Mol Cell Biol, 2007 Oct. PMID 17636026, Free PMC Article
    4. Proximity Mapping of CCP6 Reveals Its Association with Centrosome Organization and Cilium Assembly. Rodriguez-Calado S, et al. Int J Mol Sci, 2023 Jan 9. PMID 36674791, Free PMC Article
    5. A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex. Armour SM, et al. Mol Cell Biol, 2013 Apr. PMID 23382074, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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)

    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

    • FLJ12602, FLJ20729, FLJ20760, MGC131963

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables TFIID-class transcription factor complex binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in box C/D snoRNP assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in box C/D snoRNP assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein complex oligomerization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in snoRNA localization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in snoRNA localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of pre-snoRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of pre-snoRNP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    box C/D snoRNA protein 1
    Names
    box C/D snoRNA essential 1 homolog
    serologically defined breast cancer antigen NY-BR-75
    zinc finger HIT domain-containing protein 6
    zinc finger, HIT type 6

    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_001170670.2 → NP_001164141.1  box C/D snoRNA protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001164141.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment of the 5' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AC092807, AK298149, BQ777734
      Consensus CDS
      CCDS53338.1
      UniProtKB/Swiss-Prot
      Q9NWK9
      Related
      ENSP00000414344.2, ENST00000431532.6
      Conserved Domains (1) summary
      pfam04438
      Location:178 → 207
      zf-HIT; HIT zinc finger

    2. NM_017953.4 → NP_060423.3  box C/D snoRNA protein 1 isoform 1

      See identical proteins and their annotated locations for NP_060423.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC092807, BC026236, BQ777734, DB169943
      Consensus CDS
      CCDS707.1
      UniProtKB/Swiss-Prot
      B2RBA1, B4DP13, D3DT20, Q9H278, Q9H3X3, Q9NWK9, Q9NWN0
      Related
      ENSP00000359606.3, ENST00000370574.4
      Conserved Domains (1) summary
      pfam04438
      Location:217 → 246
      zf-HIT; HIT zinc finger

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      85649417..85708433 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024447736.2 → XP_024303504.1  box C/D snoRNA protein 1 isoform X2

      Conserved Domains (1) summary
      pfam04438
      Location:217 → 246
      zf-HIT; HIT zinc finger

    2. XM_011541614.4 → XP_011539916.1  box C/D snoRNA protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011539916.1

      Conserved Domains (1) summary
      pfam04438
      Location:217 → 246
      zf-HIT; HIT zinc finger

    RNA

    1. XR_007061268.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      85490231..85549278 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337164.1 → XP_054193139.1  box C/D snoRNA protein 1 isoform X2

    2. XM_054337163.1 → XP_054193138.1  box C/D snoRNA protein 1 isoform X1

    RNA

    1. XR_008486069.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NWK9.1 GenPept UniProtKB/Swiss-Prot:Q9NWK9

    Gene LinkOut

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