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LOC123956285 Sharpr-MPRA regulatory region 8832 [ Homo sapiens (human) ]

Gene ID: 123956285, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956285
Gene description
Sharpr-MPRA regulatory region 8832
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956285 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (159037078..159037372)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (160263433..160263727)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (158829769..158830063)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158768653-158769393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158806403-158807032 Neighboring gene LINC00689 intron CAGE-defined high expression enhancer Neighboring gene long intergenic non-protein coding RNA 689 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158820859-158821787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158823906-158824558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158832214-158832714 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158850668-158851867 Neighboring gene vasoactive intestinal peptide receptor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158876624-158877154 Neighboring gene VISTA enhancer hs1753 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158905439-158906114 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:158939357-158940556 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158961997-158963196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158984505-158985004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18875 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:159035435-159035650 Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 pseudogene 2 Neighboring gene Sharpr-MPRA regulatory region 2850

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_078476.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    159037078..159037372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    160263433..160263727
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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