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LOC122094848 Sharpr-MPRA regulatory region 15496 [ Homo sapiens (human) ]

Gene ID: 122094848, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122094848
Gene description
Sharpr-MPRA regulatory region 15496
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122094848 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (67689626..67689920)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (67567145..67567439)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (68155309..68155603)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12613 Neighboring gene heterogeneous nuclear ribonucleoprotein C pseudogene 9 Neighboring gene RNA, 7SL, cytoplasmic 392, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr1.6815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 983 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:68151855-68153054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:68174006-68174506 Neighboring gene Sharpr-MPRA regulatory region 6234 Neighboring gene growth arrest and DNA damage inducible alpha Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1183 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:68211594-68212415 Neighboring gene uncharacterized LOC105378781 Neighboring gene G protein subunit gamma 12 Neighboring gene Sharpr-MPRA regulatory region 6160 Neighboring gene RNA, U7 small nuclear 80 pseudogene Neighboring gene Sharpr-MPRA regulatory region 9183 Neighboring gene GNG12, DIRAS3 and WLS antisense RNA 1 Neighboring gene uncharacterized LOC124900403

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_076362.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    67689626..67689920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    67567145..67567439
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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