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LOC112695090 Sharpr-MPRA regulatory region 8034 [ Homo sapiens (human) ]

Gene ID: 112695090, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112695090
Gene description
Sharpr-MPRA regulatory region 8034
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer, transcriptional_cis_regulatory_region
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 weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss). In addition, this genomic region was validated as a cis-regulatory element for the GCAT (glycine C-acetyltransferase) gene on chromosome 22 based on multiplex CRISPR/Cas9-mediated perturbation 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, May 2023]
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Genomic context

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See LOC112695090 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (37802074..37803970)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (38263714..38265610)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (38198081..38199977)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene TRIO and F-actin binding protein Neighboring gene uncharacterized LOC124905115 Neighboring gene uncharacterized LOC102724378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13697 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:38147547-38148746 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:38150829-38152028 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:38153498-38153662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38158448-38158948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:38177743-38178242 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13699 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:38201632-38202327 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13700 Neighboring gene H1.0 linker histone Neighboring gene glycine C-acetyltransferase

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. 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
  5. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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 13698
  • CRISPRi-validated cis-regulatory element chr22.1789

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_060869.2 

    Range
    101..1997
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    37802074..37803970
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    38263714..38265610
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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