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LOC112163548 Sharpr-MPRA regulatory region 13841 [ Homo sapiens (human) ]

Gene ID: 112163548, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163548
Gene description
Sharpr-MPRA regulatory region 13841
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. A subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss). An overlapping accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 cells. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (22046035..22046471)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (21924091..21924527)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (22198969..22199263)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369689 Neighboring gene ATP binding cassette subfamily C member 9 Neighboring gene VISTA enhancer hs2151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:22052130-22052630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:22052631-22053131 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:22093793-22094770 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_26510 Neighboring gene thioesterase superfamily member 4 pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:22199579-22200284 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:22201245-22201850 Neighboring gene uncharacterized LOC105369690 Neighboring gene cytidine monophosphate N-acetylneuraminic acid synthetase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4287 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:22289754-22290362 Neighboring gene sulfotransferase family 6B member 2, 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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 4286
  • ReSE screen-validated silencer GRCh37_chr12:22199049-22199276

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_056572.3 

    Range
    101..537
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    22046035..22046471
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    21924091..21924527
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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