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LOC124174305 Sharpr-MPRA regulatory region 4694 [ Homo sapiens (human) ]

Gene ID: 124174305, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124174305
Gene description
Sharpr-MPRA regulatory region 4694
Gene type
biological region
Feature type(s)
regulatory: silencer
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 repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 19:H4K20, transcription, primarily H4K20me1, more intronic). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124174305 in Genome Data Viewer
Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (102392701..102392995)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (103518613..103518907)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (103404929..103405223)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27748 Neighboring gene SUMO2 pseudogene 19 Neighboring gene UBR5 divergent transcript Neighboring gene ubiquitin protein ligase E3 component n-recognin 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27750 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:103329370-103329870 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:103335870-103336617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27751 Neighboring gene uncharacterized LOC124902086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27753 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:103423320-103424098 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:103424099-103424877 Neighboring gene uncharacterized LOC105375683 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27757 Neighboring gene RNA, U6atac small nuclear 8, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:103446806-103447531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:103447532-103448256 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:103449587-103450136 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:103450137-103450684 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 14

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_078599.1 

    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
    102392701..102392995
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    103518613..103518907
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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