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LOC113788258 Sharpr-MPRA regulatory region 13712 [ Homo sapiens (human) ]

Gene ID: 113788258, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113788258
Gene description
Sharpr-MPRA regulatory region 13712
Gene type
biological region
Feature type(s)
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was 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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 24:Quies, heterochromatin/dead zone), with weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 24:Quies). [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (134231446..134231740)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (135349399..135349693)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (135243689..135243983)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene MIA SH3 domain ER export factor 2 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135180517-135181018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135181019-135181518 Neighboring gene uncharacterized LOC124902070 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19567 Neighboring gene MPRA-validated peak7183 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135469463-135469963 Neighboring gene NANOG hESC enhancer GRCh37_chr8:135512751-135513262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:135534207-135534774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28012 Neighboring gene zinc finger and AT-hook domain containing Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:135593335-135594534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28016 Neighboring gene ZFAT antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135697807-135698308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:135698309-135698808 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:135698888-135699054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28019 Neighboring gene NANOG hESC enhancer GRCh37_chr8:135721671-135722354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28021 Neighboring gene uncharacterized LOC124902072

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. 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)

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_062551.1 

    Range
    101..395
    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
    134231446..134231740
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    135349399..135349693
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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