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    CASC15 cancer susceptibility 15 [ Homo sapiens (human) ]

    Gene ID: 401237, updated on 17-Sep-2024

    Summary

    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

    See CASC15 in Genome Data Viewer
    Location:
    6p22.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (21666413..22195820)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (21539084..22068639)
    RS_2024_09 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    General gene information

    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_2024_08

    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)