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LOC122128426 Sharpr-MPRA regulatory region 4547 [ Homo sapiens (human) ]

Gene ID: 122128426, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122128426
Gene description
Sharpr-MPRA regulatory region 4547
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122128426 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151921793..151922087)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (151045297..151045591)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151894269..151894563)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene C2CD4D and THEM5 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151820400-151821167 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151832751-151833558 Neighboring gene thioesterase superfamily member 5 Neighboring gene thioesterase superfamily member 4 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:151870195-151871394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151878733-151879272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1727 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:151882372-151882959 Neighboring gene uncharacterized LOC124904421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1331 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:151909054-151909699 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:151918150-151918685 Neighboring gene keratin 8 pseudogene 28 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151941289-151941789 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:151964375-151965574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1332 Neighboring gene S100 calcium binding protein A10

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_076446.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    151921793..151922087
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    151045297..151045591
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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