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LOC108281123 hESC enhancers GRCh37_chr19:289901-290599 and GRCh37_chr19:290600-291297 [ Homo sapiens (human) ]

Gene ID: 108281123, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281123
Gene description
hESC enhancers GRCh37_chr19:289901-290599 and GRCh37_chr19:290600-291297
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 PLPP2 (phospholipid phosphatase 2) gene. Two subregions were validated as active enhancers by ChIP-STARR-seq in naive human embryonic stem cells, where both are marked by the H3K27ac histone modification and one is additionally marked by H3K4me1. An overlapping subregion was also validated as a functional enhancer by reporter assays in HeLa cells, where it was defined as a low expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
19p13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (289901..291297)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (240946..242342)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (290056..290651)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928344 Neighboring gene uncharacterized LOC107985295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9596 Neighboring gene MPRA-validated peak3201 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:278731-279381 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:281525-282216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:282217-282907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:287125-287626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:287627-288126 Neighboring gene vomeronasal 2 receptor 11 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:293997-294846 Neighboring gene phospholipid phosphatase 2 Neighboring gene uncharacterized LOC124904605 Neighboring gene MPRA-validated peak3203 silencer Neighboring gene MIER family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:327661-328161 Neighboring gene MPRA-validated peak3205 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:341127-341714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:342901-343852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9597 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9599

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. 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

  • H3K27ac hESC enhancer GRCh37_chr19:290600-291297
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:289901-290599
  • PLPP2 intron CAGE-defined low expression enhancer
  • PLPP2 intron low 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_051066.2 

    Range
    101..1497
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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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    289901..291297
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    240946..242342
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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