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LOC113146424 Sharpr-MPRA regulatory region 12068 [ Homo sapiens (human) ]

Gene ID: 113146424, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113146424
Gene description
Sharpr-MPRA regulatory region 12068
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin), with weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Sep 2018]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (15908178..15908472)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (15780450..15780744)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (15908409..15908703)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724520 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:15745025-15745698 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:15745699-15746372 Neighboring gene MPRA-validated peak5688 silencer Neighboring gene MPRA-validated peak5689 silencer Neighboring gene uncharacterized LOC105374948 Neighboring gene MPRA-validated peak5691 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:15855489-15856036 Neighboring gene MPRA-validated peak5692 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24088 Neighboring gene Sharpr-MPRA regulatory region 4250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24094 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:15912456-15913115 Neighboring gene actin related protein 2/3 complex subunit 3 pseudogene 5 Neighboring gene uncharacterized LOC105374949 Neighboring gene Sharpr-MPRA regulatory region 8871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24095

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_061649.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    15908178..15908472
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    15780450..15780744
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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