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LOC112997540 Sharpr-MPRA regulatory region 13773 [ Homo sapiens (human) ]

Gene ID: 112997540, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997540
Gene description
Sharpr-MPRA regulatory region 13773
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). 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 LOC112997540 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (83284501..83284930)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (86614597..86615026)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (84205789..84206083)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10366 Neighboring gene uncharacterized LOC124900167 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:84091705-84092904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21680 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:84102258-84102833 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:84115858-84116088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21685 Neighboring gene aminomethyltransferase pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:84210168-84210668 Neighboring gene coenzyme Q2, polyprenyltransferase Neighboring gene uncharacterized LOC105377313 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:84237230-84238429 Neighboring gene heparanase Neighboring gene ReSE screen-validated silencer GRCh37_chr4:84242552-84242745 Neighboring gene Sharpr-MPRA regulatory region 10996 Neighboring gene chromosome 18 open reading frame 21 pseudogene

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 15541

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_061533.2 

    Range
    101..530
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    83284501..83284930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    86614597..86615026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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