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LOC124153145 Sharpr-MPRA regulatory region 4493 [ Homo sapiens (human) ]

Gene ID: 124153145, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124153145
Gene description
Sharpr-MPRA regulatory region 4493
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
8p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (38138191..38138485)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38415181..38415475)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (37995709..37996003)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 54 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37892967-37893468 Neighboring gene eukaryotic translation initiation factor 4E binding protein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:37911667-37911880 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:37927359-37928086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37929540-37930265 Neighboring gene Sharpr-MPRA regulatory region 11218 Neighboring gene CRISPRi-validated cis-regulatory element chr8.1253 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:37960345-37960633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19116 Neighboring gene ASH2 like, histone lysine methyltransferase complex subunit Neighboring gene RNA, U6 small nuclear 988, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:37990733-37991476 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:37991477-37992222 Neighboring gene STAR 5' regulatory region Neighboring gene uncharacterized LOC105379382 Neighboring gene steroidogenic acute regulatory protein Neighboring gene LSM1 homolog, mRNA degradation associated

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_078533.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    38138191..38138485
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    38415181..38415475
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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