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    ZNF589 zinc finger protein 589 [ Homo sapiens (human) ]

    Gene ID: 51385, updated on 5-Mar-2024

    Summary

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    Official Symbol
    ZNF589provided by HGNC
    Official Full Name
    zinc finger protein 589provided by HGNC
    Primary source
    HGNC:HGNC:16747
    See related
    Ensembl:ENSG00000164048 MIM:616702; AllianceGenome:HGNC:16747
    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
    SZF1
    Summary
    Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 4.8), prostate (RPKM 4.7) and 24 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ZNF589 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (48241104..48270990)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (48268885..48298764)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (48282594..48312480)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48237715-48238244 Neighboring gene microRNA 4443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19825 Neighboring gene Sharpr-MPRA regulatory region 12857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48270677-48271176 Neighboring gene cathelicidin antimicrobial peptide Neighboring gene Sharpr-MPRA regulatory region 8193 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48282361-48283278 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48297790-48298360 Neighboring gene mitochondrial ribosomal protein S18A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14325 Neighboring gene FCF1 pseudogene 2 Neighboring gene NME/NM23 nucleoside diphosphate kinase 6 Neighboring gene serine peptidase inhibitor Kazal type 8 (putative) Neighboring gene microRNA 2115

    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 heterochromatin inducing protein differentially recognizes self versus foreign genomes. Burton EM, et al. PLoS Pathog, 2021 Mar. PMID 33730092, Free PMC Article
    2. The stem cell zinc finger 1 (SZF1)/ZNF589 protein has a human-specific evolutionary nucleotide DNA change and acts as a regulator of cell viability in the hematopoietic system. Venturini L, et al. Exp Hematol, 2016 Apr. PMID 26738774
    3. A common DNA-binding site for SZF1 and the BRCA1-associated zinc finger protein, ZBRK1. Peng H, et al. Cancer Res, 2002 Jul 1. PMID 12097288
    4. SZF1: a novel KRAB-zinc finger gene expressed in CD34+ stem/progenitor cells. Liu C, et al. Exp Hematol, 1999 Feb. PMID 10029171
    5. IFI16 Partners with KAP1 to Maintain Epstein-Barr Virus Latency. Xu H, et al. J Virol, 2022 Sep 14. PMID 35969079, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A heterochromatin inducing protein differentially recognizes self versus foreign genomes.
      Title: A heterochromatin inducing protein differentially recognizes self versus foreign genomes.
    2. The stem cell zinc finger 1 (SZF1)/ZNF589 protein has a human-specific evolutionary nucleotide DNA change and acts as a regulator of cell viability in the hematopoietic system
      Title: The stem cell zinc finger 1 (SZF1)/ZNF589 protein has a human-specific evolutionary nucleotide DNA change and acts as a regulator of cell viability in the hematopoietic system.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc finger protein 589
    Names
    KRAB-zinc finger protein SZF1-1
    stem cell zinc finger protein 1

    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_016089.3 → NP_057173.2  zinc finger protein 589

      See identical proteins and their annotated locations for NP_057173.2

      Status: VALIDATED

      Source sequence(s)
      AC104190, AY258146
      Consensus CDS
      CCDS43085.1
      UniProtKB/Swiss-Prot
      Q86UC9, Q86UQ0, Q9BRI6, Q9BRY3, Q9Y611, Q9Y612
      Related
      ENSP00000346729.3, ENST00000354698.8
      Conserved Domains (6) summary
      smart00349
      Location:35 → 84
      KRAB; krueppel associated box
      COG5048
      Location:302 → 364
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:250 → 270
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:249 → 270
      zf-C2H2; Zinc finger, C2H2 type
      pfam01352
      Location:35 → 74
      KRAB; KRAB box
      pfam13465
      Location:291 → 315
      zf-H2C2_2; Zinc-finger double 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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      48241104..48270990
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      48268885..48298764
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86UQ0.1 GenPept UniProtKB/Swiss-Prot:Q86UQ0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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