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    ZSCAN5B zinc finger and SCAN domain containing 5B [ Homo sapiens (human) ]

    Gene ID: 342933, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ZSCAN5Bprovided by HGNC
    Official Full Name
    zinc finger and SCAN domain containing 5Bprovided by HGNC
    Primary source
    HGNC:HGNC:34246
    See related
    Ensembl:ENSG00000197213 MIM:620918; AllianceGenome:HGNC:34246
    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
    ZNF371; ZNF495B
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in testis (RPKM 1.5) and prostate (RPKM 0.1) See more
    Orthologs
    all
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    Genomic context

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    See ZSCAN5B in Genome Data Viewer
    Location:
    19q13.43
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (56189686..56197890, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (59288471..59327080, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (56701055..56709259, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15116 Neighboring gene MPRA-validated peak3570 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56686512-56687062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56687063-56687613 Neighboring gene galanin like peptide Neighboring gene CRISPRi-validated cis-regulatory element chr19.6329 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51953 Neighboring gene zinc finger and SCAN domain containing 5C Neighboring gene ribosomal protein L13 pseudogene 13

    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 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. Using piggyBac transposon gene expression vectors to transfect Zscan5b gene into mouse pluripotent stem cells. Yamada M, et al. STAR Protoc, 2021 Sep 17. PMID 34541557, Free PMC Article
    2. ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression. Sun Y, et al. Oncotarget, 2016 Nov 8. PMID 27732952, Free PMC Article
    3. The DNA sequence and biology of human chromosome 19. Grimwood J, et al. Nature, 2004 Apr 1. PMID 15057824
    4. The sequence of the human genome. Venter JC, et al. Science, 2001 Feb 16. PMID 11181995
    5. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Fasci D, et al. Mol Cell Proteomics, 2018 Oct. PMID 30021884, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Using piggyBac transposon gene expression vectors to transfect Zscan5b gene into mouse pluripotent stem cells.
      Title: Using piggyBac transposon gene expression vectors to transfect Zscan5b gene into mouse pluripotent stem cells.
    2. Data implicate the role of ZSCAN5 genes in regulation of Pol III genes and nearby Pol II loci, ultimately influencing cell cycle progression and differentiation in a variety of tissues.
      Title: ZSCAN5B and primate-specific paralogs bind RNA polymerase III genes and extra-TFIIIC (ETC) sites to modulate mitotic progression.
    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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    Homology

    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 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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 5B

    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_001080456.5 → NP_001073925.2  zinc finger and SCAN domain-containing protein 5B

      See identical proteins and their annotated locations for NP_001073925.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC024580
      Consensus CDS
      CCDS46203.1
      UniProtKB/Swiss-Prot
      A6NJL1
      Related
      ENSP00000466072.2, ENST00000586855.7
      Conserved Domains (4) summary
      cd07936
      Location:40 → 124
      SCAN; SCAN oligomerization domain
      sd00017
      Location:385 → 405
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:355 → 377
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:453 → 478
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001385638.1 → NP_001372567.1  zinc finger and SCAN domain-containing protein 5B

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC024580
      Consensus CDS
      CCDS46203.1
      UniProtKB/Swiss-Prot
      A6NJL1
      Conserved Domains (4) summary
      cd07936
      Location:40 → 124
      SCAN; SCAN oligomerization domain
      sd00017
      Location:385 → 405
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:355 → 377
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:453 → 478
      zf-H2C2_2; Zinc-finger double domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      56189686..56197890 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      59288471..59327080 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320849.1 → XP_054176824.1  zinc finger and SCAN domain-containing protein 5B isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A6NJL1.1 GenPept UniProtKB/Swiss-Prot:A6NJL1

    Gene LinkOut

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

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