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LOC114004412 Sharpr-MPRA regulatory region 1869 [ Homo sapiens (human) ]

Gene ID: 114004412, updated on 17-Sep-2024

Summary

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Gene symbol
LOC114004412
Gene description
Sharpr-MPRA regulatory region 1869
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 non-DNase unmatched - State 19:H4K20, transcription, primarily H4K20me1, more intronic) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched). 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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See LOC114004412 in Genome Data Viewer
Location:
8q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (141516649..141516943)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (142645494..142645788)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (142526749..142527043)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142517660-142518180 Neighboring gene uncharacterized LOC124902031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19593 Neighboring gene uncharacterized LOC105375791 Neighboring gene Sharpr-MPRA regulatory region 1454 Neighboring gene chromosome 8 open reading frame 90 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142545064-142545649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142558100-142558604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142558605-142559109 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142561559-142562060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142562061-142562560 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:142566739-142567001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142569505-142570496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142570497-142571488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142585360-142585860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142587423-142588412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142591081-142591580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142592469-142593282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142599778-142600296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142608084-142608974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142623529-142624078 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:142653536-142653719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142655873-142656419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142659443-142660272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142689993-142690836 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:142692286-142692461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142710650-142711224 Neighboring gene MPRA-validated peak7195 silencer Neighboring gene uncharacterized LOC124902074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:142740701-142741201 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:142745139-142746338 Neighboring gene microRNA 1302-7

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 peak7193 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_063912.1 

    Range
    101..395
    Download
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    141516649..141516943
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791786.1 Reference GRCh38.p14 PATCHES

    Range
    183203..183497
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    142645494..142645788
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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