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LOC113788275 Sharpr-MPRA regulatory region 4987 [ Homo sapiens (human) ]

Gene ID: 113788275, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113788275
Gene description
Sharpr-MPRA regulatory region 4987
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 3:PromF, promoter flanking) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (29296452..29296746)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (29574652..29574946)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (29153969..29154263)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene homeobox containing 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:28913988-28915187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27181 Neighboring gene Sharpr-MPRA regulatory region 8281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28924055-28924554 Neighboring gene RNA, 5S ribosomal pseudogene 260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28927814-28928543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28932443-28932946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28932947-28933448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28937642-28938205 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:28945064-28945235 Neighboring gene kinesin family member 13B Neighboring gene MPRA-validated peak6973 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr8:29063474-29063627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27183 Neighboring gene high mobility group box 1 pseudogene 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19069 Neighboring gene uncharacterized LOC124901922 Neighboring gene uncharacterized LOC124901923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27184 Neighboring gene Sharpr-MPRA regulatory region 3532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19070 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:29207199-29207700 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:29207701-29208200 Neighboring gene dual specificity phosphatase 4

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_062568.1 

    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
    29296452..29296746
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    29574652..29574946
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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