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LOC122152303 Sharpr-MPRA regulatory region 4850 [ Homo sapiens (human) ]

Gene ID: 122152303, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122152303
Gene description
Sharpr-MPRA regulatory region 4850
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jul 2021]
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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 (221634627..221634921)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (220874439..220874733)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (221807969..221808263)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985462 Neighboring gene solute carrier family 35 member E3 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:221728686-221729186 Neighboring gene uncharacterized LOC105372937 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:221750608-221750764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2560 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:221887070-221888269 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:221888831-221889360 Neighboring gene dual specificity phosphatase 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2563 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:221914501-221915138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1830 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:221915139-221915776 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:221915777-221916414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2567 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2570 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:222009541-222009747 Neighboring gene long intergenic non-protein coding RNA 1655 Neighboring gene RNA, U6 small nuclear 403, pseudogene

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_076577.1 

    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
    221634627..221634921
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    220874439..220874733
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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