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LOC113002594 Sharpr-MPRA regulatory region 2428 [ Homo sapiens (human) ]

Gene ID: 113002594, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113002594
Gene description
Sharpr-MPRA regulatory region 2428
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. 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 matched - State 5:Enh, candidate strong enhancer, open chromatin). 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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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (78727786..78728155)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (79209266..79209635)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (78023609..78023903)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77656090-77656686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:77687375-77687953 Neighboring gene MPRA-validated peak5302 silencer Neighboring gene secretory carrier membrane protein 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77753154-77753763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77788199-77788702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22709 Neighboring gene Sharpr-MPRA regulatory region 4849 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77800693-77801201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16121 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77805941-77806562 Neighboring gene Sharpr-MPRA regulatory region 4833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77828783-77829282 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77838469-77839288 Neighboring gene LHFPL tetraspan subfamily member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77839289-77840106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22713 Neighboring gene Sharpr-MPRA regulatory region 10457 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:77911679-77912878 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:77922186-77922385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77928669-77929170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:77929171-77929670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16124 Neighboring gene uncharacterized LOC124900191 Neighboring gene high mobility group box 1 pseudogene 21 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:77995230-77996429 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:78105507-78106007 Neighboring gene Sharpr-MPRA regulatory region 14877 Neighboring gene arylsulfatase B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22720 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:78270456-78270975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:78270976-78271494 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16127 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:78293710-78294909 Neighboring gene IMPACT pseudogene Neighboring gene dimethylglycine dehydrogenase

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 active region 22714

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_061605.2 

    Range
    101..470
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    78727786..78728155
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    79209266..79209635
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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