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LOC108228207 CASC19-CCAT1 intergenic CAGE-defined high expression enhancer [ Homo sapiens (human) ]

Gene ID: 108228207, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108228207
Gene description
CASC19-CCAT1 intergenic CAGE-defined high expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic element is located in the intergenic region between the CASC19 (cancer susceptibility candidate 19) and CCAT1 (colon cancer associated transcript 1) non-coding genes. It was defined as a high expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). It was validated as a functional enhancer by reporter assays in both HeLa and HepG2 cells. [provided by RefSeq, Jul 2016]
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Genomic context

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Location:
8q24.21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (127205854..127206690)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (128333055..128333891)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (128218099..128218935)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene prostate cancer associated non-coding RNA 1 Neighboring gene serine/arginine repetitive matrix 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27933 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19526 Neighboring gene CCAT1 intron CAGE-defined B cell enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27934 Neighboring gene Sharpr-MPRA regulatory region 9947 Neighboring gene cancer susceptibility 19 Neighboring gene colon cancer associated transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27936 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128264283-128264878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27938 Neighboring gene cancer susceptibility 21 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:128295539-128296172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128304713-128305280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27940 Neighboring gene cancer susceptibility 8 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:128352096-128353295 Neighboring gene NANOG hESC enhancer GRCh37_chr8:128383298-128383801

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • CASC19-CCAT1 interval high CAGE FANTOM5 enhancer

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.

Genomic

  1. NG_050985.1 

    Range
    101..937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    127205854..127206690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    128333055..128333891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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