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LOC122128458 Sharpr-MPRA regulatory region 3396 [ Homo sapiens (human) ]

Gene ID: 122128458, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122128458
Gene description
Sharpr-MPRA regulatory region 3396
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 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 Repressive DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). A subregion was also identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. That subregion was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq MPRAs in K562 cells. [provided by RefSeq, Apr 2023]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160978499..160978793)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (160115561..160115855)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160948289..160948583)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904441 Neighboring gene uncharacterized LOC101928372 Neighboring gene intelectin 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:160931121-160931639 Neighboring gene Sharpr-MPRA regulatory region 578 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:160960931-160961769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:160975781-160976290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:160976291-160976800 Neighboring gene F11 receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:160976801-160977309 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:160985695-160986292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1969 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:160991075-160991672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:161002153-161003089 Neighboring gene GLR5 pseudogene 2

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, Free PMC Article
  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

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

  • MPRA-validated peak434 silencer

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_076478.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    160978499..160978793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    160115561..160115855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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