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LOC113939937 Sharpr-MPRA regulatory region 2123 [ Homo sapiens (human) ]

Gene ID: 113939937, updated on 17-Sep-2024

Summary

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Gene symbol
LOC113939937
Gene description
Sharpr-MPRA regulatory region 2123
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 repressive element by Sharpr-MPRA (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 4:PromP, inactive/poised promoter, highly conserved). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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 LOC113939937 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (96489431..96489825)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (96463592..96463986)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (96883209..96883603)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96709352-96709984 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96709985-96710615 Neighboring gene RNA, U4 small nuclear 24, pseudogene Neighboring gene cyclin dependent kinase 17 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6830 Neighboring gene RN7SK pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6832 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:96878154-96878351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6831 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:96894427-96895626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4746 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:96915910-96916410 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:96916411-96916911 Neighboring gene cilia and flagella associated protein 54 Neighboring gene MPRA-validated peak1903 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6835 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:97122708-97123302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6837 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 33 Neighboring gene NEDD1 gamma-tubulin ring complex targeting factor

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
  2. 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 active region 6833

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_063722.2 

    Range
    101..495
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    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    96489431..96489825
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    96463592..96463986
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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