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LOC124625834 Sharpr-MPRA regulatory region 13162 [ Homo sapiens (human) ]

Gene ID: 124625834, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625834
Gene description
Sharpr-MPRA regulatory region 13162
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (110200264..110200558)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (110210077..110210371)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene RNA polymerase II, I and III subunit E pseudogene Neighboring gene Sharpr-MPRA regulatory region 12390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5499 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3885 Neighboring gene zinc finger CCCH-type containing 12C Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:109998850-109999372 Neighboring gene VISTA enhancer hs1311 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:110044207-110045122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:110052423-110053111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5500 Neighboring gene MPRA-validated peak1465 silencer Neighboring gene radixin Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:110166436-110167308 Neighboring gene uncharacterized LOC124902752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5502 Neighboring gene Sharpr-MPRA regulatory region 14338 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:110233983-110234504 Neighboring gene long intergenic non-protein coding RNA 2732 Neighboring gene uncharacterized LOC107984385

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

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_079435.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    110200264..110200558
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    110210077..110210371
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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