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LOC114004391 Sharpr-MPRA regulatory region 11151 [ Homo sapiens (human) ]

Gene ID: 114004391, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114004391
Gene description
Sharpr-MPRA regulatory region 11151
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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2019]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (176611388..176611682)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177157971..177158265)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176038389..176038683)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175976615-175977548 Neighboring gene RNA, 7SL, cytoplasmic 684, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175979197-175979830 Neighboring gene cadherin related family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175993117-175994082 Neighboring gene Sharpr-MPRA regulatory region 7457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16659 Neighboring gene G protein regulated inducer of neurite outgrowth 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16663 Neighboring gene synuclein beta Neighboring gene microRNA 4281 Neighboring gene eukaryotic translation initiation factor 4E family member 1B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176070445-176071086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176071087-176071726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176072308-176072818 Neighboring gene Sharpr-MPRA regulatory region 4950

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_063811.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    176611388..176611682
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177157971..177158265
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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