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LOC123575616 Sharpr-MPRA regulatory region 9260 [ Homo sapiens (human) ]

Gene ID: 123575616, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575616
Gene description
Sharpr-MPRA regulatory region 9260
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 21:Repr, strong Polycomb repression). [provided by RefSeq, Dec 2021]
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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 (171835105..171835399)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (172375418..172375712)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (171262109..171262403)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377724 Neighboring gene uncharacterized LOC105377723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171177581-171178080 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:171207801-171209000 Neighboring gene uncharacterized LOC105377725 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:171221789-171222988 Neighboring gene small integral membrane protein 23 Neighboring gene uncharacterized LOC107986476 Neighboring gene F-box and WD repeat domain containing 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171349530-171350030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171350031-171350531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:171370553-171371052 Neighboring gene Sharpr-MPRA regulatory region 1765 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:171407408-171407976 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171410187-171410959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16614 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:171433526-171434153

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_077875.1 

    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
    171835105..171835399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    172375418..172375712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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