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LOC113687182 Sharpr-MPRA regulatory region 8680 [ Homo sapiens (human) ]

Gene ID: 113687182, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113687182
Gene description
Sharpr-MPRA regulatory region 8680
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. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: HepG2 Activating DNase unmatched - State 1:Tss). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (104944959..104945356)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (106259787..106260183)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (104585509..104585803)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene LHFPL tetraspan subfamily member 3 Neighboring gene LHFPL3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26446 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:104550626-104550782 Neighboring gene LHFPL3 antisense RNA 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:104575494-104575658 Neighboring gene uncharacterized LOC101927902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26450 Neighboring gene RNA, 7SL, cytoplasmic 8, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:104627453-104627954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:104627955-104628454 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:104652040-104652580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26454 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:104653661-104654200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26456 Neighboring gene long intergenic non-protein coding RNA 1004 Neighboring gene KMT2E antisense RNA 1

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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  2. 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
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 26449

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_062462.2 

    Range
    101..498
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    104944959..104945356
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    106259787..106260183
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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