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LOC123924900 Sharpr-MPRA regulatory region 4649 [ Homo sapiens (human) ]

Gene ID: 123924900, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123924900
Gene description
Sharpr-MPRA regulatory region 4649
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 non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (8751999..8752293)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (8872847..8873141)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (8791629..8791923)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene islet cell autoantigen 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:8342998-8343560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:8343561-8344122 Neighboring gene ICA1 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:8391097-8391728 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:8391729-8392358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:8473803-8474350 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:8474351-8474898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:8474899-8475446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:8480847-8481347 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:8482526-8482705 Neighboring gene uncharacterized LOC105375144 Neighboring gene neurexophilin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:8783491-8783991 Neighboring gene MPRA-validated peak6368 silencer Neighboring gene ribosomal protein L9 pseudogene 19 Neighboring gene VISTA enhancer hs799 Neighboring gene Sharpr-MPRA regulatory region 911 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:9393157-9393764 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:9394915-9395416 Neighboring gene NANOG hESC enhancer GRCh37_chr7:9497177-9497869 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 68

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_078292.1 

    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
    8751999..8752293
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    8872847..8873141
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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