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    ZZZ3 zinc finger ZZ-type containing 3 [ Homo sapiens (human) ]

    Gene ID: 26009, updated on 10-Dec-2024

    Summary

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    Official Symbol
    ZZZ3provided by HGNC
    Official Full Name
    zinc finger ZZ-type containing 3provided by HGNC
    Primary source
    HGNC:HGNC:24523
    See related
    Ensembl:ENSG00000036549 MIM:619892; AllianceGenome:HGNC:24523
    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
    ATAC1
    Summary
    Enables histone reader activity; lysine-acetylated histone binding activity; and methylated histone binding activity. Involved in several processes, including regulation of cell division; regulation of transcription by RNA polymerase II; and regulation of tubulin deacetylation. Located in nucleolus and nucleoplasm. Part of ATAC complex. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 9.6), ovary (RPKM 6.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZZZ3 in Genome Data Viewer
    Location:
    1p31.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (77562416..77683398, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (77401275..77522228, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (78028101..78149083, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene adenylate kinase 5 Neighboring gene uncharacterized LOC124904202 Neighboring gene RNA, U7 small nuclear 8 pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:77962170-77963369 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:77980030-77980998 Neighboring gene Sharpr-MPRA regulatory region 12904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1215 Neighboring gene RNA, 5S ribosomal pseudogene 20 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:78127789-78128288 Neighboring gene RNA, 7SL, cytoplasmic 370, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1002 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:78149296-78150069 Neighboring gene ubiquitin specific peptidase 33 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1220 Neighboring gene actin gamma 1 pseudogene 21

    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. Unraveling the impact of ZZZ3 on the mTOR/ribosome pathway in human embryonic stem cells homeostasis. Lo Conte M, et al. Stem Cell Reports, 2024 May 14. PMID 38701777, Free PMC Article
    2. The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation. Mi W, et al. Nat Commun, 2018 Sep 14. PMID 30217978, Free PMC Article
    3. NF-Y affects histone acetylation and H2A.Z deposition in cell cycle promoters. Gatta R, et al. Epigenetics, 2011 Apr. PMID 21304275
    4. Host cell factor and an uncharacterized SANT domain protein are stable components of ATAC, a novel dAda2A/dGcn5-containing histone acetyltransferase complex in Drosophila. Guelman S, et al. Mol Cell Biol, 2006 Feb. PMID 16428443, Free PMC Article
    5. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Krebs AR, et al. Mol Cell, 2011 Nov 4. PMID 22055187, Free PMC Article

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Unraveling the impact of ZZZ3 on the mTOR/ribosome pathway in human embryonic stem cells homeostasis.
      Title: Unraveling the impact of ZZZ3 on the mTOR/ribosome pathway in human embryonic stem cells homeostasis.
    2. Study identifies the ZZ domain of ZZZ3 as a histone H3 reader that is required for the ATAC complex-mediated maintenance of histone acetylation and gene activation.
      Title: The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation.
    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
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10362, DKFZp564I052, DKFZp313N0119

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone reader activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables lysine-acetylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cell division IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cell division ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of embryonic development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of embryonic development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of tubulin deacetylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of tubulin deacetylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of ATAC complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of ATAC complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitotic spindle NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    ZZ-type zinc finger-containing protein 3
    Names
    ATAC component 1 homolog
    zinc finger, ZZ domain containing 3

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001308237.2 → NP_001295166.1  ZZ-type zinc finger-containing protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001295166.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon, lacks an alternate exon in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC093575, BC035079, BC035818, BX640658, CA448091
      Consensus CDS
      CCDS76172.1
      UniProtKB/Swiss-Prot
      Q8IYH5
      Related
      ENSP00000359834.1, ENST00000370798.5
      Conserved Domains (2) summary
      cd00167
      Location:161 → 209
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
      cd02341
      Location:327 → 378
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.

    2. NM_001376146.1 → NP_001363075.1  ZZ-type zinc finger-containing protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549
      Consensus CDS
      CCDS677.1
      UniProtKB/Swiss-Prot
      B7WPC6, Q6N004, Q6N070, Q8IYH5, Q8IYP0, Q8IYR1, Q8TEK4, Q9Y4U0
      Conserved Domains (2) summary
      cd02341
      Location:821 → 872
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
      pfam00249
      Location:655 → 703
      Myb_DNA-binding; Myb-like DNA-binding domain

    3. NM_001376147.1 → NP_001363076.1  ZZ-type zinc finger-containing protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549
      Consensus CDS
      CCDS677.1
      UniProtKB/Swiss-Prot
      B7WPC6, Q6N004, Q6N070, Q8IYH5, Q8IYP0, Q8IYR1, Q8TEK4, Q9Y4U0
      Conserved Domains (2) summary
      cd02341
      Location:821 → 872
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
      pfam00249
      Location:655 → 703
      Myb_DNA-binding; Myb-like DNA-binding domain

    4. NM_001376148.1 → NP_001363077.1  ZZ-type zinc finger-containing protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549
      Conserved Domains (2) summary
      cd02341
      Location:820 → 871
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
      pfam00249
      Location:654 → 702
      Myb_DNA-binding; Myb-like DNA-binding domain

    5. NM_001376149.1 → NP_001363078.1  ZZ-type zinc finger-containing protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549
      Conserved Domains (2) summary
      cd02341
      Location:820 → 871
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
      pfam00249
      Location:654 → 702
      Myb_DNA-binding; Myb-like DNA-binding domain

    6. NM_001376151.1 → NP_001363080.1  ZZ-type zinc finger-containing protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549
      Conserved Domains (2) summary
      cd02341
      Location:820 → 871
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
      pfam00249
      Location:654 → 702
      Myb_DNA-binding; Myb-like DNA-binding domain

    7. NM_001376153.1 → NP_001363082.1  ZZ-type zinc finger-containing protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549
      Conserved Domains (2) summary
      cd02341
      Location:820 → 871
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
      pfam00249
      Location:654 → 702
      Myb_DNA-binding; Myb-like DNA-binding domain

    8. NM_001376154.1 → NP_001363083.1  ZZ-type zinc finger-containing protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549
      Conserved Domains (2) summary
      cd02341
      Location:820 → 871
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
      pfam00249
      Location:654 → 702
      Myb_DNA-binding; Myb-like DNA-binding domain

    9. NM_001376155.1 → NP_001363084.1  ZZ-type zinc finger-containing protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549
      Consensus CDS
      CCDS76172.1
      Conserved Domains (2) summary
      cd00167
      Location:161 → 209
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
      cd02341
      Location:327 → 378
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.

    10. NM_001376156.1 → NP_001363085.1  ZZ-type zinc finger-containing protein 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549
      Conserved Domains (2) summary
      cd00167
      Location:160 → 208
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
      cd02341
      Location:326 → 377
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.

    11. NM_015534.6 → NP_056349.1  ZZ-type zinc finger-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_056349.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC093575, BX640658, BX641001, CA448091
      Consensus CDS
      CCDS677.1
      UniProtKB/Swiss-Prot
      B7WPC6, Q6N004, Q6N070, Q8IYH5, Q8IYP0, Q8IYR1, Q8TEK4, Q9Y4U0
      Related
      ENSP00000359837.3, ENST00000370801.8
      Conserved Domains (2) summary
      cd02341
      Location:821 → 872
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
      pfam00249
      Location:655 → 703
      Myb_DNA-binding; Myb-like DNA-binding domain

    RNA

    1. NR_164775.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549

    2. NR_164776.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549

    3. NR_164777.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC093575, AC114487, AC118549

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      77562416..77683398 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417341.1 → XP_047273297.1  ZZ-type zinc finger-containing protein 3 isoform X3

    2. XM_005270729.5 → XP_005270786.1  ZZ-type zinc finger-containing protein 3 isoform X2

      See identical proteins and their annotated locations for XP_005270786.1

      UniProtKB/Swiss-Prot
      Q8IYH5
      Conserved Domains (2) summary
      cd00167
      Location:161 → 209
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
      cd02341
      Location:327 → 378
      ZZ_ZZZ3; Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.

    3. XM_047417342.1 → XP_047273298.1  ZZ-type zinc finger-containing protein 3 isoform X3

      Related
      ENST00000481346.5

    4. XM_047417333.1 → XP_047273289.1  ZZ-type zinc finger-containing protein 3 isoform X2

    5. XM_047417337.1 → XP_047273293.1  ZZ-type zinc finger-containing protein 3 isoform X3

    6. XM_047417326.1 → XP_047273282.1  ZZ-type zinc finger-containing protein 3 isoform X2

    7. XM_047417329.1 → XP_047273285.1  ZZ-type zinc finger-containing protein 3 isoform X2

    8. XM_047417325.1 → XP_047273281.1  ZZ-type zinc finger-containing protein 3 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      77401275..77522228 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335873.1 → XP_054191848.1  ZZ-type zinc finger-containing protein 3 isoform X3

    2. XM_054335868.1 → XP_054191843.1  ZZ-type zinc finger-containing protein 3 isoform X2

    3. XM_054335874.1 → XP_054191849.1  ZZ-type zinc finger-containing protein 3 isoform X3

    4. XM_054335871.1 → XP_054191846.1  ZZ-type zinc finger-containing protein 3 isoform X2

    5. XM_054335872.1 → XP_054191847.1  ZZ-type zinc finger-containing protein 3 isoform X3

    6. XM_054335869.1 → XP_054191844.1  ZZ-type zinc finger-containing protein 3 isoform X2

    7. XM_054335870.1 → XP_054191845.1  ZZ-type zinc finger-containing protein 3 isoform X2

    8. XM_054335867.1 → XP_054191842.1  ZZ-type zinc finger-containing protein 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IYH5.1 GenPept UniProtKB/Swiss-Prot:Q8IYH5

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