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LOC121048733 Sharpr-MPRA regulatory regions 5224 and 9858 [ Homo sapiens (human) ]

Gene ID: 121048733, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121048733
Gene description
Sharpr-MPRA regulatory regions 5224 and 9858
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. Two overlapping subregions, #9858 and #5224, were validated as functional enhancers 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 1:Tss, and HepG2 Activating DNase unmatched - State 1:Tss, respectively, active promoter, TSS/CpG island region). The #9858 subregion also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - 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 (194537000..194537314)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (197235598..197235912)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (194257729..194258043)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATPase 13A3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21026 Neighboring gene ATP13A3 divergent transcript Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:194218672-194219871 Neighboring gene Sharpr-MPRA regulatory region 12272 Neighboring gene RNA, U6 small nuclear 1101, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21027 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:194274365-194274563 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:194276967-194277466 Neighboring gene ribosomal protein L23a pseudogene 93 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:194292893-194294092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21029 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:194304263-194304928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21030 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:194309417-194310616 Neighboring gene TMEM44 antisense RNA 1 Neighboring gene transmembrane protein 44

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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 5224
  • Sharpr-MPRA regulatory region 9858

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_074104.2 

    Range
    101..415
    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
    194537000..194537314
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    197235598..197235912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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