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LOC108281168 HLCS intron CAGE-defined mid-level expression enhancer [ Homo sapiens (human) ]

Gene ID: 108281168, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281168
Gene description
HLCS intron CAGE-defined mid-level 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 an intron of the HLCS (holocarboxylase synthetase) gene. It was defined as a mid-level 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 HeLa cells. A sub-region was also validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh). [provided by RefSeq, Jul 2018]
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Genomic context

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Location:
21q22.13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (36860045..36860633)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (35242255..35242843)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (38232345..38232933)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene holocarboxylase synthetase Neighboring gene uncharacterized LOC105369305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38158985-38159520 Neighboring gene Sharpr-MPRA regulatory region 9348 Neighboring gene RNA, 5S ribosomal pseudogene 491 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:38281839-38283038 Neighboring gene Sharpr-MPRA regulatory region 2954 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:38300053-38300245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38312167-38312666 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:38319174-38319727 Neighboring gene divergent-paired related homeobox pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18441 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:38338431-38338761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13291 Neighboring gene HLCS antisense RNA 1

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
  2. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

  • HLCS intron mid CAGE FANTOM5 enhancer
  • Sharpr-MPRA regulatory region 4242

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_051128.1 

    Range
    101..689
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    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    36860045..36860633
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    35242255..35242843
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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