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

Gene ID: 342933, updated on 11-Apr-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 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, Apr 2022]
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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Location:
19q13.43
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (56189686..56197890, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (59288471..59327080, complement)
105.20220307 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
  • 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
  

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_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
    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

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