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LOC122757952 Sharpr-MPRA regulatory region 11227 [ Homo sapiens (human) ]

Gene ID: 122757952, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122757952
Gene description
Sharpr-MPRA regulatory region 11227
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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122757952 in Genome Data Viewer
Location:
2p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (62287874..62288168)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (62294103..62294397)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (62515009..62515303)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374761 Neighboring gene small nucleolar RNA U13 Neighboring gene RNA, 7SL, cytoplasmic 51, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:62523719-62524218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:62532419-62532946 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:62532947-62533472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15859 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:62552835-62554034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:62589276-62589776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:62589777-62590277 Neighboring gene NANOG hESC enhancer GRCh37_chr2:62601400-62601986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15863 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:62638109-62638868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15864 Neighboring gene uncharacterized LOC105374764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11537 Neighboring gene transmembrane protein 17 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:62702751-62703483 Neighboring gene RNA, 7SL, cytoplasmic 18, pseudogene

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_076944.1 

    Range
    101..395
    Download
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    62287874..62288168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    62294103..62294397
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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