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LOC113788295 Sharpr-MPRA regulatory region 4298 [ Homo sapiens (human) ]

Gene ID: 113788295, updated on 17-Sep-2024

Summary

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Gene symbol
LOC113788295
Gene description
Sharpr-MPRA regulatory region 4298
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2018]
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Genomic context

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See LOC113788295 in Genome Data Viewer
Location:
8q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (79853874..79854168)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (80285262..80285556)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (80766109..80766403)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19311 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19313 Neighboring gene uncharacterized LOC101927040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:80695841-80696641 Neighboring gene long intergenic non-protein coding RNA 1607 Neighboring gene U7 small nuclear RNA Neighboring gene hes related family bHLH transcription factor with YRPW motif 1 Neighboring gene RNA, U7 small nuclear 85 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27551 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19315 Neighboring gene uncharacterized LOC124901966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19316 Neighboring gene TPD52-MRPS28 readthrough Neighboring gene mitochondrial ribosomal protein S28 Neighboring gene VISTA enhancer hs1305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:80894241-80894806 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:80909347-80909896 Neighboring gene Sharpr-MPRA regulatory region 4480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19317 Neighboring gene Sharpr-MPRA regulatory region 3052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27553 Neighboring gene tumor protein D52 Neighboring gene uncharacterized LOC105375919

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_062588.1 

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    79853874..79854168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    80285262..80285556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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