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ZSCAN4 zinc finger and SCAN domain containing 4 [ Homo sapiens (human) ]

Gene ID: 201516, updated on 5-Mar-2024

Summary

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Official Symbol
ZSCAN4provided by HGNC
Official Full Name
zinc finger and SCAN domain containing 4provided by HGNC
Primary source
HGNC:HGNC:23709
See related
Ensembl:ENSG00000180532 MIM:613419; AllianceGenome:HGNC:23709
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
ZNF494
Summary
The ZSCAN4 gene encodes a protein involved in telomere maintenance and with a key role in the critical feature of mouse embryonic stem (ES) cells, namely, defying cellular senescence and maintaining normal karyotype for many cell divisions in culture (Zalzman et al., 2010 [PubMed 20336070]).[supplied by OMIM, May 2010]
Expression
Low expression observed in reference dataset See more
Orthologs
all
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Genomic context

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Location:
19q13.43
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (57651476..57679152)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (60748405..60776081)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (58162844..58190520)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11077 Neighboring gene zinc finger protein 134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15152 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11078 Neighboring gene zinc finger protein 211 Neighboring gene MPRA-validated peak3574 silencer Neighboring gene tumor protein p63 regulated 1 like pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:58193037-58193660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11079 Neighboring gene zinc finger protein 551 Neighboring gene zinc finger protein 154 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:58220160-58220799

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. Low expression of ZSCAN4 predicts unfavorable outcome in urothelial carcinoma of upper urinary tract and urinary bladder. He HL, et al. World J Surg Oncol, 2023 Feb 25. PMID 36841776, Free PMC Article
  2. ZSCAN4 facilitates chromatin remodeling and promotes the cancer stem cell phenotype. Portney BA, et al. Oncogene, 2020 Jun. PMID 32507861, Free PMC Article
  3. Zscan4 is expressed specifically during late meiotic prophase in both spermatogenesis and oogenesis. Ishiguro KI, et al. In Vitro Cell Dev Biol Anim, 2017 Feb. PMID 27699653, Free PMC Article
  4. The senescence-associated secretory phenotype is potentiated by feedforward regulatory mechanisms involving Zscan4 and TAK1. Zhang B, et al. Nat Commun, 2018 Apr 30. PMID 29712904, Free PMC Article
  5. ZSCAN4 is negatively regulated by the ubiquitin-proteasome system and the E3 ubiquitin ligase RNF20. Portney BA, et al. Biochem Biophys Res Commun, 2018 Mar 25. PMID 29477841, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ZSCAN4-binding motif-TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes.
    Title: ZSCAN4-binding motif-TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes.
  2. Low expression of ZSCAN4 predicts unfavorable outcome in urothelial carcinoma of upper urinary tract and urinary bladder.
    Title: Low expression of ZSCAN4 predicts unfavorable outcome in urothelial carcinoma of upper urinary tract and urinary bladder.
  3. The Zscan4-Tet2 Transcription Nexus Regulates Metabolic Rewiring and Enhances Proteostasis to Promote Reprogramming.
    Title: The Zscan4-Tet2 Transcription Nexus Regulates Metabolic Rewiring and Enhances Proteostasis to Promote Reprogramming.
  4. ZSCAN4 facilitates chromatin remodeling and promotes the cancer stem cell phenotype.
    Title: ZSCAN4 facilitates chromatin remodeling and promotes the cancer stem cell phenotype.
  5. The senescence-associated secretory phenotype is potentiated by feedforward regulatory mechanisms involving Zscan4 and TAK1.
    Title: The senescence-associated secretory phenotype is potentiated by feedforward regulatory mechanisms involving Zscan4 and TAK1.
  6. RNF20 depletion stabilizes the ZSCAN4 protein half-life, suggesting that RNF20 negatively regulates ZSCAN4 stability.
    Title: ZSCAN4 is negatively regulated by the ubiquitin-proteasome system and the E3 ubiquitin ligase RNF20.
  7. Zscan4 may play critical roles during late meiotic prophase in both males and females.
    Title: Zscan4 is expressed specifically during late meiotic prophase in both spermatogenesis and oogenesis.
  8. the expression and function of each gene copy of Zscan4 locus in a physiological context, is reported.
    Title: Expression analysis of the endogenous Zscan4 locus and its coding proteins in mouse ES cells and preimplantation embryos.
  9. ZSCAN4 indirectly interacts with TRF1 in cancer cells. We show that ZSCAN4 plays an important role independent of telomere maintenance pathways (telomerase positive and alternative pathway) or cell lineage.
    Title: ZSCAN4 and TRF1: A functionally indirect interaction in cancer cells independent of telomerase activity.
  10. The direct interaction between Zscan4 and Rap1 may explain how Zscan4 rapidly increases telomere length, yielding important information about the role of these proteins in telomere biology.
    Title: Zscan4 interacts directly with human Rap1 in cancer cells regardless of telomerase status.
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

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

  • FLJ35105, MGC126787, MGC126789

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of mitotic recombination ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in telomere maintenance via telomere lengthening ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Component Evidence Code Pubs
located_in chromosome, telomeric region ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger and SCAN domain-containing protein 4
Names
zinc finger protein 494

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_001384833.1 → NP_001371762.1  zinc finger and SCAN domain-containing protein 4

    Status: VALIDATED

    Source sequence(s)
    AC003682, AC004017
    Consensus CDS
    CCDS12958.1
    UniProtKB/Swiss-Prot
    Q3MIQ2, Q8NAM6
    Conserved Domains (4) summary
    cd07936
    Location:40 → 124
    SCAN; SCAN oligomerization domain
    sd00017
    Location:342 → 362
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:368 → 390
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:382 → 407
    zf-H2C2_2; Zinc-finger double domain

  2. NM_152677.4 → NP_689890.1  zinc finger and SCAN domain-containing protein 4

    See identical proteins and their annotated locations for NP_689890.1

    Status: VALIDATED

    Source sequence(s)
    AC004017
    Consensus CDS
    CCDS12958.1
    UniProtKB/Swiss-Prot
    Q3MIQ2, Q8NAM6
    Related
    ENSP00000321963.4, ENST00000318203.9
    Conserved Domains (4) summary
    cd07936
    Location:40 → 124
    SCAN; SCAN oligomerization domain
    sd00017
    Location:342 → 362
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:368 → 390
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:382 → 407
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    57651476..57679152
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017026458.1 → XP_016881947.1  zinc finger and SCAN domain-containing protein 4 isoform X1

    UniProtKB/Swiss-Prot
    Q3MIQ2, Q8NAM6
    Conserved Domains (4) summary
    cd07936
    Location:40 → 124
    SCAN; SCAN oligomerization domain
    sd00017
    Location:342 → 362
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:368 → 390
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:382 → 407
    zf-H2C2_2; Zinc-finger double domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    60748405..60776081
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320180.1 → XP_054176155.1  zinc finger and SCAN domain-containing protein 4 isoform X1

    UniProtKB/Swiss-Prot
    Q3MIQ2, Q8NAM6
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NAM6.1 GenPept UniProtKB/Swiss-Prot:Q8NAM6

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