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LOC113146422 Sharpr-MPRA regulatory region 5218 [ Homo sapiens (human) ]

Gene ID: 113146422, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113146422
Gene description
Sharpr-MPRA regulatory region 5218
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 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 9:DNaseU, primarily UW DNase, weaker open chromatin sites). It also displayed weak repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Sep 2018]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (144202712..144203006)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (145395335..145395629)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (144523849..144524143)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144507610-144508110 Neighboring gene syntaxin 11 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144537315-144537779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25213 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144550475-144550694 Neighboring gene tRNA-Leu (anticodon TAA) 1-1 Neighboring gene TPT1 pseudogene 4 Neighboring gene MPRA-validated peak6183 silencer Neighboring gene MPRA-validated peak6184 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144586575-144587308 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:144587309-144588042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17641 Neighboring gene uncharacterized LOC124901418 Neighboring gene utrophin

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_061647.1 

    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
    144202712..144203006
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    145395335..145395629
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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