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LOC121725152 Sharpr-MPRA regulatory region 11159 [ Homo sapiens (human) ]

Gene ID: 121725152, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725152
Gene description
Sharpr-MPRA regulatory region 11159
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (100186365..100186659)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (102891702..102891996)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (99905209..99905503)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene cms1 ribosomal small subunit homolog Neighboring gene filamin A interacting protein 1 like Neighboring gene uncharacterized LOC124909400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14568 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:99792322-99792856 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:99792857-99793391 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:99809017-99809517 Neighboring gene uncharacterized LOC105374009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20151 Neighboring gene transmembrane protein 30C, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14569 Neighboring gene dual specificity phosphatase 12 pseudogene 1 Neighboring gene vesicle transport through interaction with t-SNAREs 1B pseudogene 1

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_075622.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    100186365..100186659
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    102891702..102891996
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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