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LOC123987609 Sharpr-MPRA regulatory region 9194 [ Homo sapiens (human) ]

Gene ID: 123987609, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123987609
Gene description
Sharpr-MPRA regulatory region 9194
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 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 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies). [provided by RefSeq, Jan 2022]
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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 (2914627..2914921)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (2668540..2668834)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (2772149..2772443)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377784 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:2362643-2363842 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:2383723-2384449 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:2382994-2383722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:2419495-2420034 Neighboring gene long intergenic non-protein coding RNA 3021 Neighboring gene uncharacterized LOC107986865 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:2547000-2547500 Neighboring gene uncharacterized LOC105377785 Neighboring gene Sharpr-MPRA regulatory region 12422 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_102978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:2670718-2671218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:2671219-2671719 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:2734767-2735966 Neighboring gene Sharpr-MPRA regulatory region 746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:2743811-2744593 Neighboring gene uncharacterized LOC124901871 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:2842983-2843550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:2883555-2884056 Neighboring gene NANOG hESC enhancer GRCh37_chr8:2916031-2916747 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:2928398-2928606 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:2964721-2965920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:2990813-2991505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:3020562-3021062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:3021063-3021563 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:3025942-3027141 Neighboring gene CUB and Sushi multiple domains 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:3068799-3069337 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:3101495-3102167 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:3102168-3102840 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:3102841-3103512 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:3203901-3204560 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103217 Neighboring gene uncharacterized LOC105377791 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:3350221-3351420 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:3396011-3396511 Neighboring gene RNA, 5S ribosomal pseudogene 251

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_078482.1 

    Range
    101..395
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    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
    2914627..2914921
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    2668540..2668834
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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