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LOC121530599 Sharpr-MPRA regulatory regions 3481 and 15421 [ Homo sapiens (human) ]

Gene ID: 121530599, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121530599
Gene description
Sharpr-MPRA regulatory regions 3481 and 15421
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121530599 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (81275068..81275382)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (79139131..79139445)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (81567409..81567723)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9948 Neighboring gene cilia and flagella associated protein 161 Neighboring gene acidic nuclear phosphoprotein 32 family member B pseudogene 3 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:81481874-81483073 Neighboring gene interleukin 16 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9951 Neighboring gene NANOG hESC enhancer GRCh37_chr15:81585795-81586313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:81588972-81589538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:81589539-81590103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9956 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:81595578-81596777 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:81600895-81601072 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:81605226-81606425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6743 Neighboring gene StAR related lipid transfer domain containing 5 Neighboring gene TMC3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:81648807-81649306 Neighboring gene transmembrane channel like 3

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 15421
  • Sharpr-MPRA regulatory region 3481

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_074797.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    81275068..81275382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    79139131..79139445
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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