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LOC108251797 HCCAT5-C16orf47 intergenic CAGE-defined high expression enhancer [ Homo sapiens (human) ]

Gene ID: 108251797, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108251797
Gene description
HCCAT5-C16orf47 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 HCCAT5 (hepatocellular carcinoma associated transcript 5, non-protein coding) and C16orf47 (chromosome 16 open reading frame 47) 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:
16q22.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (73124102..73124601)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (78941804..78942303)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (73158001..73158500)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene zinc finger homeobox 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73081321-73081856 Neighboring gene uncharacterized LOC124903719 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73082393-73082928 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73087036-73087536 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73087537-73088037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73089102-73089614 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73091454-73092186 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7694 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73098351-73098972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73126852-73127352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73127353-73127853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11103 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:73186584-73187107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73190308-73190808 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73190809-73191309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73204295-73204796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73204797-73205296 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73205367-73206216 Neighboring gene hepatocellular carcinoma associated transcript 5 Neighboring gene NANOG hESC enhancer GRCh37_chr16:73230564-73231065 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:73266082-73267281 Neighboring gene uncharacterized LOC124903716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11105 Neighboring gene VISTA enhancer hs1724 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:73368016-73368182 Neighboring gene lncRNA oncogene in head and neck cancer 2

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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • HCCAT5-C16orf47 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_050998.1 

    Range
    101..600
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    73124102..73124601
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    78941804..78942303
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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