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LOC113839536 Sharpr-MPRA regulatory region 7884 [ Homo sapiens (human) ]

Gene ID: 113839536, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839536
Gene description
Sharpr-MPRA regulatory region 7884
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region), with weaker activation in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands). 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 LOC113839536 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (132770142..132770601)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (144981376..144981835)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (135645529..135645823)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135486212-135486944 Neighboring gene DEAD-box helicase 31 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135545227-135546094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29221 Neighboring gene general transcription factor IIIC subunit 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135597764-135598270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135599285-135599790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135608498-135608998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135608999-135609499 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:135620695-135621194 Neighboring gene adenylate kinase 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:135683689-135684190 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:135711155-135711317 Neighboring gene U6 spliceosomal RNA Neighboring gene ReSE screen-validated silencer GRCh37_chr9:135729901-135730092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135731149-135731650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135731651-135732150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135732573-135733346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135738096-135738827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29223 Neighboring gene sperm acrosome associated 9

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 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 20437

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_063147.2 

    Range
    101..560
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    132770142..132770601
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    144981376..144981835
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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