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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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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

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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