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CASC15 cancer susceptibility 15 [ Homo sapiens (human) ]

Gene ID: 401237, updated on 20-Nov-2023

Summary

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Official Symbol
CASC15provided by HGNC
Official Full Name
cancer susceptibility 15provided by HGNC
Primary source
HGNC:HGNC:28245
See related
MIM:616610; AllianceGenome:HGNC:28245
Gene type
ncRNA
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CANT; LINC00340; lnc-SOX4-1
Summary
This gene produces a long non-coding RNA that may regulate cell proliferation. This RNA is upregulated in hepatocellular carcinoma, where it is thought to function as an oncogene. However, some splice variants of this gene may function as a tumor suppressor in neuroblastoma and other tumor types. Circular RNA variants were observed at this gene. [provided by RefSeq, Dec 2017]
Expression
Broad expression in ovary (RPKM 2.9), endometrium (RPKM 1.9) and 14 other tissues See more
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Genomic context

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Location:
6p22.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (21666413..22195820)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (21539084..22068639)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (21666644..22196049)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24142 Neighboring gene bolA family member 2 pseudogene 3 Neighboring gene MPRA-validated peak5729 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:21649156-21649656 Neighboring gene uncharacterized LOC124901483 Neighboring gene Sharpr-MPRA regulatory region 7931 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:21721085-21721584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21739035-21739957 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:21740882-21741804 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:21741805-21742728 Neighboring gene uncharacterized LOC124901274 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:21769680-21770293 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:21770817-21771316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21773448-21774170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21798093-21798690 Neighboring gene uncharacterized LOC105374970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24144 Neighboring gene Sharpr-MPRA regulatory region 6328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16987 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:21873881-21875080 Neighboring gene Sharpr-MPRA regulatory region 8833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24146 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:22027355-22028066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24148 Neighboring gene RN7SK pseudogene 240 Neighboring gene NANOG hESC enhancer GRCh37_chr6:22145447-22145948 Neighboring gene VISTA enhancer hs1335 Neighboring gene neuroblastoma associated transcript 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:22198729-22199928 Neighboring gene uncharacterized LOC124901275 Neighboring gene NGRN pseudogene 4

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. LncRNA-CASC15 knockdown inhibits the progression of esophageal squamous cell carcinoma through targeting miR-33a-5p/PTGS2 axis. Zhou WZ, et al. Histol Histopathol, 2023 Feb. PMID 36111503
  2. CASC15 Gene Polymorphisms and Glioma Susceptibility in Chinese Children. Lin HR, et al. Curr Med Sci, 2022 Aug. PMID 35819658
  3. LncRNA CASC15 regulates breast cancer cell stemness via the miR-654-5p/MEF2D axis. Shen P, et al. J Biochem Mol Toxicol, 2022 May. PMID 35235236
  4. A study of the prognostic value of long non-coding RNA CASC15 in human solid tumors utilizing The Cancer Genome Atlas (TCGA) datasets and a meta-analysis. Chen W, et al. Clin Exp Med, 2023 Feb. PMID 35103883
  5. lncRNA‑CASC15 promotes osteosarcoma proliferation and metastasis by regulating epithelial‑mesenchymal transition via the Wnt/β‑catenin signaling pathway. Wang H, et al. Oncol Rep, 2021 May. PMID 33760218, Free PMC Article

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Prognostic value of CASC15 and LINC01600 as competitive endogenous RNAs in lung adenocarcinoma: An observational study.
    Title: Prognostic value of CASC15 and LINC01600 as competitive endogenous RNAs in lung adenocarcinoma: An observational study.
  2. A study of the prognostic value of long non-coding RNA CASC15 in human solid tumors utilizing The Cancer Genome Atlas (TCGA) datasets and a meta-analysis.
    Title: A study of the prognostic value of long non-coding RNA CASC15 in human solid tumors utilizing The Cancer Genome Atlas (TCGA) datasets and a meta-analysis.
  3. LncRNA-CASC15 knockdown inhibits the progression of esophageal squamous cell carcinoma through targeting miR-33a-5p/PTGS2 axis.
    Title: LncRNA-CASC15 knockdown inhibits the progression of esophageal squamous cell carcinoma through targeting miR-33a-5p/PTGS2 axis.
  4. CASC15 Gene Polymorphisms and Glioma Susceptibility in Chinese Children.
    Title: CASC15 Gene Polymorphisms and Glioma Susceptibility in Chinese Children.
  5. [Clinical Significance of Low Expression of LncRNA CASC15 in Acute Myeloid Leukemia with NPM1 Mutations].
    Title: [Clinical Significance of Low Expression of LncRNA CASC15 in Acute Myeloid Leukemia with NPM1 Mutations].
  6. LncRNA CASC15 regulates breast cancer cell stemness via the miR-654-5p/MEF2D axis.
    Title: LncRNA CASC15 regulates breast cancer cell stemness via the miR-654-5p/MEF2D axis.
  7. LncRNA CASC15, MiR-23b Cluster and SMAD3 form a Novel Positive Feedback Loop to promote Epithelial-Mesenchymal Transition and Metastasis in Ovarian Cancer.
    Title: LncRNA CASC15, MiR-23b Cluster and SMAD3 form a Novel Positive Feedback Loop to promote Epithelial-Mesenchymal Transition and Metastasis in Ovarian Cancer.
  8. lncRNACASC15 promotes osteosarcoma proliferation and metastasis by regulating epithelialmesenchymal transition via the Wnt/betacatenin signaling pathway.
    Title: lncRNA‑CASC15 promotes osteosarcoma proliferation and metastasis by regulating epithelial‑mesenchymal transition via the Wnt/β‑catenin signaling pathway.
  9. Long noncoding RNA CASC15 facilitates esophageal squamous cell carcinoma tumorigenesis via decreasing SIM2 stability via FTOmediated demethylation.
    Title: Long non‑coding RNA CASC15 facilitates esophageal squamous cell carcinoma tumorigenesis via decreasing SIM2 stability via FTO‑mediated demethylation.
  10. The long non-coding RNA <i>Cancer Susceptibility 15</i> (<i>CASC15</i>) is induced by isocitrate dehydrogenase (IDH) mutations and maintains an immature phenotype in adult acute myeloid leukemia.
    Title: The long non-coding RNA Cancer Susceptibility 15 (CASC15) is induced by isocitrate dehydrogenase (IDH) mutations and maintains an immature phenotype in adult acute myeloid leukemia.
Submit: New GeneRIF Correction See all GeneRIFs (26)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Chromosome 6p22 locus associated with clinically aggressive neuroblastoma.
EBI GWAS Catalog
Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma.
EBI GWAS Catalog
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
EBI GWAS Catalog
Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium.
EBI GWAS Catalog
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
EBI GWAS Catalog
Integrative genomics identifies LMO1 as a neuroblastoma oncogene.
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)

Genotypes

General gene information

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Markers

Other Names

  • cancer susceptibility 15 (non-protein coding)
  • cancer susceptibility candidate 15 (non-protein coding)
  • long intergenic non-protein coding RNA 340

Clone Names

  • FLJ12803, FLJ17254, FLJ22536, FLJ51318

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.

RNA

  1. NR_015410.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AK026189, AL161436, AL359694, HY067675

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    21666413..22195820
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    21539084..22068639
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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