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LOC108254663 LINC00689 intron CAGE-defined high expression enhancer [ Homo sapiens (human) ]

Gene ID: 108254663, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108254663
Gene description
LINC00689 intron 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 region is located in an intron of the LINC00689 (long intergenic non-protein coding RNA 689) gene. A subregion 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), and was validated as an enhancer by reporter assays in both HeLa and HepG2 cells. Another subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
7q36.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (159015310..159016228)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (160241022..160241929)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (158808001..158808606)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901794 Neighboring gene uncharacterized LOC124901795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158768653-158769393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158806403-158807032 Neighboring gene long intergenic non-protein coding RNA 689 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158820859-158821787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158823906-158824558 Neighboring gene Sharpr-MPRA regulatory region 8832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158832214-158832714 Neighboring gene vasoactive intestinal peptide receptor 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158850668-158851867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158876624-158877154 Neighboring gene VISTA enhancer hs1753 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158905439-158906114 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:158939357-158940556 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158961997-158963196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158984505-158985004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18875 Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 pseudogene 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
  2. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K4me1 hESC enhancer GRCh37_chr7:158808291-158808919
  • LINC00689 intron 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_051009.2 

    Range
    101..1019
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    159015310..159016228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    160241022..160241929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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