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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
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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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