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YPEL3 yippee like 3 [ Homo sapiens (human) ]

Gene ID: 83719, updated on 2-Nov-2024

Summary

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Official Symbol
YPEL3provided by HGNC
Official Full Name
yippee like 3provided by HGNC
Primary source
HGNC:HGNC:18327
See related
Ensembl:ENSG00000090238 MIM:609724; AllianceGenome:HGNC:18327
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
Summary
Predicted to enable metal ion binding activity. Involved in positive regulation of cellular senescence. Predicted to be located in nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in spleen (RPKM 26.2), brain (RPKM 22.3) and 25 other tissues See more
Orthologs
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Genomic context

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See YPEL3 in Genome Data Viewer
Location:
16p11.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30092314..30096213, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30374954..30378853, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30103635..30107534, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10689 Neighboring gene protein phosphatase 4 catalytic subunit Neighboring gene ReSE screen-validated silencer GRCh37_chr16:30096821-30096985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30101709-30102582 Neighboring gene T-box transcription factor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30107354-30107960 Neighboring gene YPEL3 divergent transcript Neighboring gene glycerophosphodiester phosphodiesterase domain containing 3 Neighboring gene Sharpr-MPRA regulatory region 9068 Neighboring gene mitogen-activated protein kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7356

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Steroid sulfatase deficiency causes cellular senescence and abnormal differentiation by inducing Yippee-like 3 expression in human keratinocytes.
    Title: Steroid sulfatase deficiency causes cellular senescence and abnormal differentiation by inducing Yippee-like 3 expression in human keratinocytes.
  2. yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development.
    Title: yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development.
  3. Expression of the YPEL3 gene was upregulated in human colonic adenocarcinoma tissue.
    Title: Increased Expression of the YPEL3 Gene in Human Colonic Adenocarcinoma Tissue and the Effects on Proliferation, Migration, and Invasion of Colonic Adenocarcinoma Cells In Vitro via the Wnt/b-Catenin Signaling Pathway.
  4. Data show that YPEL3 is downregulated in nasopharyngeal carcinoma (NPC) cell lines and tissue samples and it suppresses NPC EMT and metastasis by suppressing the Wnt/beta-catenin signaling pathway.
    Title: YPEL3 suppresses epithelial-mesenchymal transition and metastasis of nasopharyngeal carcinoma cells through the Wnt/β-catenin signaling pathway.
  5. YPEL3 expression, which is induced by the removal of estrogen or treatment with tamoxifen triggers cellular senescence in MCF-7 cells while loss of YPEL3 increases the growth rate of MCF-7 cells.
    Title: Novel senescence associated gene, YPEL3, is repressed by estrogen in ER+ mammary tumor cells and required for tamoxifen-induced cellular senescence.
  6. YPEL3 is downregulated in colon tumors.
    Title: Senescence-associated gene YPEL3 is downregulated in human colon tumors.
  7. In this review we show that transcriptionally active forms of p73 and p63, family members of p53, can transactivate the human YPEL3 gene[review]
    Title: Why YPEL3 represents a novel tumor suppressor.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Centrosome-related genes, genetic variation, and risk of breast cancer.
  9. Findings point to YPEL3 being a novel tumor suppressor, which upon induction triggers a permanent growth arrest in human tumor and normal cells.
    Title: YPEL3, a p53-regulated gene that induces cellular senescence.
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

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

  • MGC10500

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in positive regulation of cellular senescence IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein yippee-like 3

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_001145524.2 → NP_001138996.1  protein yippee-like 3 isoform 2

    See identical proteins and their annotated locations for NP_001138996.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) represents alternate splicing in the first exon (of variant 1) resulting in predicted use of a downstream translation start site and a shorter protein (isoform 2).
    Source sequence(s)
    AB098737, AC012645
    Consensus CDS
    CCDS45459.1
    UniProtKB/Swiss-Prot
    P61236, Q65Z99, Q86VK6, Q9BSJ4, Q9CQB6
    UniProtKB/TrEMBL
    H3BME7
    Related
    ENSP00000381818.4, ENST00000398838.8
    Conserved Domains (1) summary
    cl13152
    Location:21 → 110
    RLR_C_like; C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and similar protein domains

  2. NM_031477.5 → NP_113665.3  protein yippee-like 3 isoform 1

    See identical proteins and their annotated locations for NP_113665.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents a longer transcript and longer protein isoform (1).
    Source sequence(s)
    AC012645, BC050664
    Consensus CDS
    CCDS42147.1
    UniProtKB/TrEMBL
    A0A0B4J290
    Related
    ENSP00000381821.1, ENST00000398841.6
    Conserved Domains (1) summary
    cl13152
    Location:59 → 148
    RLR_C_like; C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and similar protein domains

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    30092314..30096213 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    30374954..30378853 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P61236.1 GenPept UniProtKB/Swiss-Prot:P61236

Gene LinkOut

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