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LOC122128454 Sharpr-MPRA regulatory regions 3039 and 8536 [ Homo sapiens (human) ]

Gene ID: 122128454, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122128454
Gene description
Sharpr-MPRA regulatory regions 3039 and 8536
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. Two overlapping subregions were validated as functional repressive elements 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 Repressive DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). One subregion also displayed repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122128454 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (159910419..159910753)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159047487..159047821)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (159880209..159880543)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 45 Neighboring gene uncharacterized LOC124904435 Neighboring gene microRNA 4259 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159882219-159882720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:159887707-159888596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1911 Neighboring gene uncharacterized LOC124904437 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:159893727-159894926 Neighboring gene transgelin 2 Neighboring gene immunoglobulin superfamily member 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:159904768-159905268 Neighboring gene uncharacterized LOC124904438 Neighboring gene Sharpr-MPRA regulatory region 11999

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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 3039
  • Sharpr-MPRA regulatory region 8536

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_076474.1 

    Range
    101..435
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    159910419..159910753
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    159047487..159047821
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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